AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation ScienceHealth CareGeographicals
MetagenomePlanctomycetalesGenome, BacterialBacteriaPhylogenySequence Analysis, DNASeawaterEnvironmental MicrobiologyBiodiversityGenome, ArchaealGastrointestinal TractMicrobial ConsortiaRhodospirillalesPhotobioreactorsProchloronOceans and SeasSoil MicrobiologyArchaeaRNA, Ribosomal, 16SBiotaMarine BiologyGenomicsHigh-Throughput Nucleotide SequencingSewageHaliclonaTheonellaGenomic LibraryMolecular Sequence DataMicrobiotaDNA, BacterialAquatic OrganismsDatabases, GeneticActinobacteriaVirusesBacteroidetesCluster AnalysisWaste Disposal, FluidWater MicrobiologyPacific OceanEndo-1,4-beta XylanasesEukaryotaHot SpringsBacterial Physiological PhenomenaPlanktonSymbiosisComputational BiologyBiotechnologyMolecular Sequence AnnotationGenome, ViralGeologic SedimentsOpen Reading FramesSoftwareEcosystemSequence AlignmentGene LibraryEsterasesSoilCloning, MolecularAlgorithmsMetabolic Networks and PathwaysDatabase Management SystemsLipaseRumenBacteriophagesTemperatureBacterial ProteinsGene Transfer, HorizontalGenomeInternetBase CompositionGenetic VariationBase SequenceFecesUser-Computer InterfaceAmino Acid Sequence
Metagenome
A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
Planctomycetales
A order of gram-negative bacteria whose members are found in a variety of aquatic habitats as well as animal hosts.
Genome, Bacterial
The genetic complement of a BACTERIA as represented in its DNA.
Bacteria
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
Phylogeny
The relationships of groups of organisms as reflected by their genetic makeup.
Sequence Analysis, DNA
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Seawater
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
Environmental Microbiology
The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.
Biodiversity
The variety of all native living organisms and their various forms and interrelationships.
Genome, Archaeal
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
Gastrointestinal Tract
Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).
Microbial Consortia
A group of different species of microorganisms that act together as a community.
Rhodospirillales
An order of photosynthetic bacteria representing a physiological community of predominantly aquatic bacteria.
Photobioreactors
Devices for generating biological products that use light as the energy source. They are used for controlled BIOMASS production such as growing cyanobacteria, mosses, or algae.
Prochloron
A genus of PROCHLOROPHYTES containing unicellular, spherical bacteria without a mucilaginous sheath. They are found almost exclusively as extracellular symbionts of colonial ASCIDIANS on subtropical or tropical marine shores.
Oceans and Seas
A great expanse of continuous bodies of salt water which together cover more than 70 percent of the earth's surface. Seas may be partially or entirely enclosed by land, and are smaller than the five oceans (Atlantic, Pacific, Indian, Arctic, and Antarctic).
Soil Microbiology
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
Archaea
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
RNA, Ribosomal, 16S
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
Biota
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
Marine Biology
The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.
Genomics
The systematic study of the complete DNA sequences (GENOME) of organisms.
High-Throughput Nucleotide Sequencing
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Sewage
Refuse liquid or waste matter carried off by sewers.
Haliclona
A genus of SPONGES in the family Chalinidae characterized by unispicular secondary lines in the choanosomal skeleton.
Theonella
A genus of shallow-cupped SPONGES with a broad base in the family Theonellidae. They are characterized by ectosomal spicules dominated by phyllotriaenes.
Genomic Library
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Microbiota
The full collection of microbes (bacteria, fungi, virus, etc.) that naturally exist within a particular biological niche such as an organism, soil, a body of water, etc.
DNA, Bacterial
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Aquatic Organisms
Organisms that live in water.
Databases, Genetic
Databases devoted to knowledge about specific genes and gene products.
Actinobacteria
Class of BACTERIA with diverse morphological properties. Strains of Actinobacteria show greater than 80% 16S rDNA/rRNA sequence similarity among each other and also the presence of certain signature nucleotides. (Stackebrandt E. et al, Int. J. Syst. Bacteriol. (1997) 47:479-491)
Viruses
Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
Bacteroidetes
A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.
Cluster Analysis
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Waste Disposal, Fluid
The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.
Water Microbiology
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
Pacific Ocean
Endo-1,4-beta Xylanases
Enzymes which catalyze the endohydrolysis of 1,4-beta-D-xylosidic linkages in XYLANS.
Eukaryota
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
Hot Springs
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
Bacterial Physiological Phenomena
Physiological processes and properties of BACTERIA.
Plankton
Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.
Symbiosis
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Biotechnology
Body of knowledge related to the use of organisms, cells or cell-derived constituents for the purpose of developing products which are technically, scientifically and clinically useful. Alteration of biologic function at the molecular level (i.e., GENETIC ENGINEERING) is a central focus; laboratory methods used include TRANSFECTION and CLONING technologies, sequence and structure analysis algorithms, computer databases, and gene and protein structure function analysis and prediction.
Molecular Sequence Annotation
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Genome, Viral
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Geologic Sediments
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
Open Reading Frames
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Software
Sequential operating programs and data which instruct the functioning of a digital computer.
Ecosystem
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Gene Library
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Esterases
Soil
The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.
Cloning, Molecular
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Algorithms
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Metabolic Networks and Pathways
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
Database Management Systems
Software designed to store, manipulate, manage, and control data for specific uses.
Lipase
An enzyme of the hydrolase class that catalyzes the reaction of triacylglycerol and water to yield diacylglycerol and a fatty acid anion. It is produced by glands on the tongue and by the pancreas and initiates the digestion of dietary fats. (From Dorland, 27th ed) EC 3.1.1.3.
Rumen
The first stomach of ruminants. It lies on the left side of the body, occupying the whole of the left side of the abdomen and even stretching across the median plane of the body to the right side. It is capacious, divided into an upper and a lower sac, each of which has a blind sac at its posterior extremity. The rumen is lined by mucous membrane containing no digestive glands, but mucus-secreting glands are present in large numbers. Coarse, partially chewed food is stored and churned in the rumen until the animal finds circumstances convenient for rumination. When this occurs, little balls of food are regurgitated through the esophagus into the mouth, and are subjected to a second more thorough mastication, swallowed, and passed on into other parts of the compound stomach. (From Black's Veterinary Dictionary, 17th ed)
Bacteriophages
Viruses whose hosts are bacterial cells.
Temperature
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Bacterial Proteins
Proteins found in any species of bacterium.
Gene Transfer, Horizontal
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
Genome
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Internet
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
Base Composition
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Genetic Variation
Genotypic differences observed among individuals in a population.
Base Sequence
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Feces
Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
User-Computer Interface
The portion of an interactive computer program that issues messages to and receives commands from a user.
Amino Acid Sequence
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.

Multilocus sequence typing breathes life into a microbial metagenome. (1/1707)

Shot-gun sequencing of DNA isolated from the environment and the assembly of metagenomes from the resulting data has considerably advanced the study of microbial diversity. However, the subsequent matching of these hypothetical metagenomes to cultivable microorganisms is a limitation of such cultivation-independent methods of population analysis. Using a nucleotide sequence-based genetic typing method, multilocus sequence typing, we were able for the first time to match clonal cultivable isolates to a published and controversial bacterial metagenome, Burkholderia SAR-1, which derived from analysis of the Sargasso Sea. The matching cultivable isolates were all associated with infection and geographically widely distributed; taxonomic analysis demonstrated they were members of Burkholderia cepacia complex Group K. Comparison of the Burkholderia SAR-1 metagenome to closely related B. cepacia complex genomes indicated that it was greater than 98% intact in terms of conserved genes, and it also shared complete sequence identity with the cultivable isolates at random loci beyond the genes sampled by the multilocus sequence typing. Two features of the extant cultivable clones support the argument that the Burkholderia SAR-1 sequence may have been a contaminant in the original metagenomic survey: (i) their growth in conditions reflective of sea water was poor, suggesting the ocean was not their preferred habitat, and (ii) several of the matching isolates were epidemiologically linked to outbreaks of infection that resulted from contaminated medical devices or products, indicating an adaptive fitness of this bacterial strain towards contamination-associated environments. The ability to match identical cultivable strains of bacteria to a hypothetical metagenome is a unique feature of nucleotide sequence-based microbial typing methods; such matching would not have been possible with more traditional methods of genetic typing, such as those based on pattern matching of genomic restriction fragments or amplified DNA fragments. Overall, we have taken the first steps in moving the status of the Burkholderia SAR-1 metagenome from a hypothetical entity towards the basis for life of cultivable strains that may now be analysed in conjunction with the assembled metagenomic sequence data by the wider scientific community.  (+info)

Development of the human infant intestinal microbiota. (2/1707)

Almost immediately after a human being is born, so too is a new microbial ecosystem, one that resides in that person's gastrointestinal tract. Although it is a universal and integral part of human biology, the temporal progression of this process, the sources of the microbes that make up the ecosystem, how and why it varies from one infant to another, and how the composition of this ecosystem influences human physiology, development, and disease are still poorly understood. As a step toward systematically investigating these questions, we designed a microarray to detect and quantitate the small subunit ribosomal RNA (SSU rRNA) gene sequences of most currently recognized species and taxonomic groups of bacteria. We used this microarray, along with sequencing of cloned libraries of PCR-amplified SSU rDNA, to profile the microbial communities in an average of 26 stool samples each from 14 healthy, full-term human infants, including a pair of dizygotic twins, beginning with the first stool after birth and continuing at defined intervals throughout the first year of life. To investigate possible origins of the infant microbiota, we also profiled vaginal and milk samples from most of the mothers, and stool samples from all of the mothers, most of the fathers, and two siblings. The composition and temporal patterns of the microbial communities varied widely from baby to baby. Despite considerable temporal variation, the distinct features of each baby's microbial community were recognizable for intervals of weeks to months. The strikingly parallel temporal patterns of the twins suggested that incidental environmental exposures play a major role in determining the distinctive characteristics of the microbial community in each baby. By the end of the first year of life, the idiosyncratic microbial ecosystems in each baby, although still distinct, had converged toward a profile characteristic of the adult gastrointestinal tract.  (+info)

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. (3/1707)

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.  (+info)

The human microbiome project. (4/1707)

A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.  (+info)

Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. (5/1707)

 (+info)

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. (6/1707)

 (+info)

Skin microbiota: a source of disease or defence? (7/1707)

 (+info)

The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii. (8/1707)

 (+info)

The Integrative Human Microbiome Project | NatureThe Integrative Human Microbiome Project | Nature
The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between humans and their microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host-microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the human microbiome. Over ten years, the Human Microbiome Project has provided resources for studying the microbiome and its relationship to disease; this Perspective summarizes the key achievements and findings of the project and its relationship to the broader field.
https://www.nature.com/articles/s41586-019-1238-8?error=cookies_not_supported&code=82c00854-4806-4181-ba7b-130ac6a2648e
Frontiers | Correlations of Host Genetics and Gut Microbiome Composition | MicrobiologyFrontiers | Correlations of Host Genetics and Gut Microbiome Composition | Microbiology
The human gut microbiome has a considerable impact on host health. The long list of microbiome-related health disorders raises the question of what in fact determines microbiome composition. In this review we sought to understand how the host itself impacts the structure of the gut microbiota population, specifically by correlations of host genetics and gut microbiome composition.Host genetic profile has been linked to differences in microbiome composition, thus suggesting that host genetics can shape the gut microbiome of the host. However, cause-consequence mechanisms behind these links are still unclear. A survey of the possible mechanisms allowing host genetics to shape microbiota composition in the gut demonstrated the major role of metabolic functions and the immune system. A considerable impact of other factors, such as diet, may outweigh the effects of host genetic background. More studies are necessary for good understanding of the relations between the host genetic profile, gut microbiome
https://www.frontiersin.org/articles/10.3389/fmicb.2016.01357/full
Effect of Dietary Fiber Supplement on the Intestinal Microbiota Among Schizophrenia Patients - Full Text View - ClinicalTrials...Effect of Dietary Fiber Supplement on the Intestinal Microbiota Among Schizophrenia Patients - Full Text View - ClinicalTrials...
Background There has been much interest in the relationship between the types of gut microbiota and the development of obesity in recent years. It has been reported that the proportions of Firmicutes and Bacteroidetes differ between obese and normal weight human subjects. Human intestinal microbiota compositions have been found to be associated with long-term dietary habits and lifestyle. However, an increasing number of researches show that intestinal microbiota composition may be affected after short-term diet intervention. Importantly, obesity and metabolic problems play important roles in morbidity and mortality of schizophrenia patients. Human intestinal microbiota compositions related with obesity may impact the heath of this population. Therefore, we searched current advances about the connection of obesity, intestinal microbiota compositions, and diet in schizophrenia to conduct a clinical research focus on the effect of high fiber diet on the intestinal microbiota of schizophrenia ...
https://clinicaltrials.gov/show/NCT03552237
Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats<...
TY - JOUR. T1 - Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats. AU - Posteraro, Brunella. AU - Paroni Sterbini, Francesco. AU - Petito, Valentina. AU - Rocca, Stefano. AU - Cubeddu, Tiziana. AU - Graziani, Cristina. AU - Arena, Vincenzo. AU - Vassallo, Gabriele A.. AU - Mosoni, Carolina. AU - Lopetuso, Loris. AU - Lorrai, Irene. AU - Maccioni, Paola. AU - Masucci, Luca. AU - Martini, Cecilia. AU - Gasbarrini, Antonio. AU - Sanguinetti, Maurizio. AU - Colombo, Giancarlo. AU - Addolorato, Giovanni. PY - 2018/12/1. Y1 - 2018/12/1. N2 - Background: There is strong evidence that alcoholism leads to dysbiosis in both humans and animals. However, it is unclear how changes in the intestinal microbiota (IM) relate to ethanol (EtOH)-induced disruption of gut-liver homeostasis. We investigated this issue using selectively bred Sardinian alcohol-preferring (sP) rats, a validated animal model of excessive EtOH consumption. Methods: ...
https://moh-it.pure.elsevier.com/en/publications/liver-injury-endotoxemia-and-their-relationship-to-intestinal-mic
The Human Microbiome Project | Baylor College of Medicine | Houston, TexasThe Human Microbiome Project | Baylor College of Medicine | Houston, Texas
The goal of the Human Microbiome Project is to characterize the human microbiome and analyze its role in human health and disease.
https://www.bcm.edu/departments/molecular-virology-and-microbiology/research/the-human-microbiome-project
Change of the duodenal mucosa-associated microbiota is related to intestinal metaplasia | BMC Microbiology | Full TextChange of the duodenal mucosa-associated microbiota is related to intestinal metaplasia | BMC Microbiology | Full Text
In this study, we aimed to investigate the characteristics of the duodenal mucosal microbiota of patients with intestinal metaplasia (IM) and compare it with those of the gastric mucosal microbiota. We collected the duodenal and gastric mucosal samples from 10 adult patients with IM and 10 healthy controls (HC). The V3-V4 region of the bacterial 16S rRNA gene was examined by high throughput sequencing method. The diversity of the HC duodenal microbiota was higher than that of IM patient based on the Shannon and Simpson index while the Chao indices of IM duodenal mucosal microbiota was significantly higher than that of gastric mucosal microbiota of patients with IM. There was a marked difference in the duodenal microbiota structure between patients with IM and HC (ANOSIM, R = 1, P = 0.001). We also found that the Helicobacter pylori infection in gastric mucosa did not influence the structure of duodenal mucosal microbiota. The gastric mucosal microbiota structure significantly differed between patients
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-019-1666-5
Gut Microbiota Composition Reflects COVID-19 Severity - Taurine May Help Prevent Bacterial Infection | Beauty WithinGut Microbiota Composition Reflects COVID-19 Severity - Taurine May Help Prevent Bacterial Infection | Beauty Within
Gut Microbiota Composition Reflects Disease Severity and Dysfunctional Immune Responses in Patients with COVID-19. Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus…. What are the new findings?. Composition of the gut microbiota in patients with COVID-19 is concordant with disease severity and magnitude of plasma concentrations of several inflammatory cytokines, chemokines and blood markers of tissue damage.. Patients with COVID-19 were depleted in gut bacteria with known immunomodulatory potential, such as Faecalibacterium prausnitzii, Eubacterium rectale and several bifidobacterial species.. The dysbiotic gut microbiota composition in patients with COVID-19 persists after clearance of the ...
http://mybeautywithin.com/gut-microbiota-composition-reflects-covid-19-severity-taurine-may-help-prevent-bacterial-infection/
ASMscience | The Human Microbiome
The human microbiome includes bacteria, viruses, and small eukaryotes, such as fungi, and this chapter focuses on the bacterial members of the microbiome. The Human Microbiome Project (HMP) aims at developing tools and resources for characterization of the human microbiota and to relate this microbiota to human health and disease. The goals of the jumpstart phase have been to sequence 900 reference genomes to provide a catalog of genomes for metagenomic studies, to sample at least 300 healthy adults between 18 and 40 years of age at five body sites, and to develop sequencing and analysis protocols for the samples derived from human subjects. The second phase of the HMP includes human microbiome studies that target particular disease states. In a recent study, four phyla comprised 92.3% of bacterial DNA sequences analyzed from multiple human sources, including hair, oral cavity, skin, genitourinary, and gastrointestinal tract. A study by Pei et al. showed that the distal esophageal microbiomes of four
http://www.asmscience.org/content/book/10.1128/9781555816728.chap13
2014-15: Bioinformatics: Discovering Patterns in Human Microbiome Data (HMD): March 16-18, 2015 - SAMSI2014-15: Bioinformatics: Discovering Patterns in Human Microbiome Data (HMD): March 16-18, 2015 - SAMSI
The human microbiome is the community of microorganisms that reside in different body habitats. Host-microbiome interactions play an important but poorly-characterized role in health. Advances in high-throughput technologies including next-generation sequencing and mass spectroscopy allow us to query the population of micro-organisms and observe the interactions in greater detail. The effect of choices in measurement protocols, the multivariate longitudinal nature of data, and combining measurements on different scales pose difficulties in discovering and confirming significant relationships in the human microbiome.. The aim of this workshop was to create a forum for ideas for overcoming current and future challenges in the analysis of human microbiome data. In this workshop, participants learned how metagenomic (sequence-based) and metabolomic (mass spectroscopy-based) data are generated and the implications for analysis. Gaps in the current state-of-the-art methods were highlighted, ...
https://www.samsi.info/programs-and-activities/research-workshops/2014-15-bioinformatics-discovering-patterns-in-human-microbiome-data-hmd-march-16-18-2015/
Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly...Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly...
Omega-3 fatty acids may influence human physiological parameters in part by affecting the gut microbiome. The aim of this study was to investigate the links between omega-3 fatty acids, gut microbiome diversity and composition and faecal metabolomic profiles in middle aged and elderly women. We analysed data from 876 twins with 16S microbiome data and DHA, total omega-3, and other circulating fatty acids. Estimated food intake of omega-3 fatty acids were obtained from food frequency questionnaires. Both total omega-3and DHA serum levels were significantly correlated with microbiome alpha diversity (Shannon index) after adjusting for confounders (DHA Beta(SE) = 0.13(0.04), P = 0.0006 total omega-3: 0.13(0.04), P = 0.001). These associations remained significant after adjusting for dietary fibre intake. We found even stronger associations between DHA and 38 operational taxonomic units (OTUs), the strongest ones being with OTUs from the Lachnospiraceae family (Beta(SE) = 0.13(0.03), P = 8 × 10−7). Some
https://www.nature.com/articles/s41598-017-10382-2.epdf?author_access_token=tP5uN9a9sb6pxgpJ5nVRi9RgN0jAjWel9jnR3ZoTv0MjHLZPF7T5gVQz0Wa5FGCDI2G8h9cClxy8Q9Wt5xbFAgeE_qcnnSTbnXXFEyTr6U_LdfXN1FCcCvZOX2RnxvtK_RKKEg5z4RAOFMe4qhJWGA%3D%3D&error=cookies_not_supported&code=118548be-a1a9-4394-8f13-cfd6f63f6d2f
VIROME: a standard operating procedure for analysis of viral metagenome sequencesVIROME: a standard operating procedure for analysis of viral metagenome sequences
The one consistent finding among viral metagenomics studies has been the high proportion of sequences having no significant homology to a known sequence within one of the large sequence databases (e.g., GenBank, UniRef etc.). Those viral metagenome libraries having the highest frequency of hits to known sequences typically come from marine environments where the hit frequency for longer Sanger reads is around 30% (at a BLAST e-score of ≤0.001) [12]. Sanger libraries from soils show even lower hit rates at ~20%. The lack of homology to known sequences is only exacerbated by the shorter read lengths of next-generation sequencing technology [33] where libraries sequenced using the longest average read length next generation sequencing technology (i.e., 450 bp for the 454 pyrosequencing Ti FLX chemistry) yield hit rates to known sequence databases of less than 20%. In contrast, microbial shotgun metagenome libraries analyzed using the same databases and approaches will yield hit frequencies of ca. ...
http://standardsingenomics.org/content/6/3/427/
Human Microbiome Project DACC - HMPDACC Data Br...Human Microbiome Project DACC - HMPDACC Data Br...
via +Humberto González-Díaz *NIH Human Microbiome Project*Data Portalhttp://bit.ly/LhsWi2 | Complex Insight - Understanding our world
https://www.scoop.it/t/complex-insight/p/1974777400/2012/06/16/human-microbiome-project-dacc-hmpdacc-data-browser
Development of the preterm infant gut microbiome: a research priority | Microbiome | Full TextDevelopment of the preterm infant gut microbiome: a research priority | Microbiome | Full Text
The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role of the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early
https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-38
Frontiers | Correlation of Gut Microbiota Composition with Resistance to Experimental Autoimmune Encephalomyelitis in Rats |...Frontiers | Correlation of Gut Microbiota Composition with Resistance to Experimental Autoimmune Encephalomyelitis in Rats |...
Multiple sclerosis is a chronic inflammatory disease of the central nervous system (CNS). It is widely accepted that autoimmune response against the antigens of the CNS is the essential pathogenic force in the disease. It has recently become increasingly appreciated that activated encephalitogenic cells tend to migrate toward gut associated lymphoid tissues (GALTs) and that interrupted balance between regulatory and inflammatory immunity within the GALT might have decisive role in the initiation and propagation of the CNS autoimmunity. Gut microbiota composition and function has the major impact on the balance in the GALT. Thus, our aim was to perform analyses of gut microbiota in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Albino Oxford (AO) rats that are highly resistant to EAE induction and Dark Agouti (DA) rats that develop EAE after mild immunization were compared for gut microbiota composition in different phases after EAE induction. Microbial analyses
https://www.frontiersin.org/articles/10.3389/fmicb.2016.02005/full
Report from #IHMC2016: International microbiome community discusses advances and challenges in human microbiome science - Gut...Report from #IHMC2016: International microbiome community discusses advances and challenges in human microbiome science - Gut...
The 6th Congress of the International Human Microbiome Consortium took place on November 9-11, 2016 in Houston, TX. This first IHMC congress to be held in the USA attracted a wide international audience with attendees from Africa, Asia, Latin America, Australia, Europe, and the United States. This unique community of scientists came together to discuss a wide range of topics in the field of human microbiome science, including crosstalk of environmental microbes with the human microbiome, the importance of microbial communities outside the gut, the role of maternal-infant interactions in the early establishment of the microbiome, and the importance of microbiome science in global health. In this post, we highlight a few key topics that generated significant discussion at the conference.. Sequencing the microbiome: 16S or WGS - or both? On the first day of the conference, an important question was posed to the audience which generated significant debate thereafter: as the field of microbiome ...
https://www.gutmicrobiotaforhealth.com/en/report-ihmc2016-international-microbiome-community-discusses-advances-challenges-human-microbiome-science/
The Inuit gut microbiome is dynamic over time and shaped by traditional foods | Microbiome | Full TextThe Inuit gut microbiome is dynamic over time and shaped by traditional foods | Microbiome | Full Text
The human gut microbiome is a diverse community of microbial eukaryotes, viruses, archaea, and mostly bacteria [1-3], many of which play important roles in immunity, metabolism and nutrition [4-6]. The community structure of the microbiome is determined by many factors, including geography, sex, host genetics, and age [7-11].. Microbiome composition and structure may also vary within individuals over time, although most individuals have a relatively stable microbiome [12, 13]. Individuals with highly diverse microbiomes tend to be more stable through time [12]. Other studies have shown that individuality is preserved through time, underlying an overall stable and personalized microbiome [14]. On time scales of days to weeks, diet is the main factor driving composition and structure of the gut microbiome [13]. For example, some types of dietary fiber transits through the digestive tract without being assimilated by the human body, providing a food source for fermentative bacteria [15]. High fiber ...
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0370-7
RAPD Primer Design from Metagenomes 1.0 - RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying...RAPD Primer Design from Metagenomes 1.0 - RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying...
RAPD Primer Design from Metagenomes RPDM scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA RAPD assays
http://www.filetransit.com/view.php?id=215312
Intestinal Microbiota Composition Modulates Choline Bioavailability from Diet and Accumulation of the Proatherogenic Metabolite...Intestinal Microbiota Composition Modulates Choline Bioavailability from Diet and Accumulation of the Proatherogenic Metabolite...
A major role played by the intestinal microbiota is to aid in the harvest of nutrients from the diet (1). Dietary components that are not readily absorbed in the small intestine serve as growth substrates for members of the gut microbiota, which in turn can modify the bioavailability and nutritional properties of those same dietary components (1). For example, many of the beneficial effects associated with consumption of whole grains, vegetables, and fruits are at least in part mediated by end products of microbial metabolism, including short-chain fatty acids (e.g., butyrate) and phenolic acids (e.g., protocatechuic acid) (2-6). Likewise, gut microbes can also convert otherwise beneficial dietary compounds, such as choline, into metabolites that are detrimental to human health (7-10).. Choline is required for a wide range of biological activities, including maintaining the structural integrity of cell membranes, supporting cholinergic neurotransmission, and donating methyl groups in a number of ...
https://mbio.asm.org/content/6/2/e02481-14
HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota | Microbiome | Full TextHIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota | Microbiome | Full Text
Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establishment of one of the largest HIV reservoirs. Here we test the prediction that HIV infection modifies the composition and function of the mucosal commensal microbiota. Rectal mucosal microbiota were collected from human subjects using a sponge-based sampling methodology. Samples were collected from 20 HIV-positive men not receiving combination anti-retroviral therapy (cART), 20 HIV-positive men on cART and 20 healthy, HIV-negative men. Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing). Microbial metagenomic information for the samples was imputed using the bioinformatic tools PICRUST and HUMAnN. Microbial composition and imputed function in
https://0-microbiomejournal-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/2049-2618-1-26
Mendeley Data - Human Skin Microbiome Data (16S rRNA sequencing) dataset #2Mendeley Data - Human Skin Microbiome Data (16S rRNA sequencing) dataset #2
16S rRNA sequencing data on human skin microbiome samples collected before and after swimming in the ocean. This dataset contains raw sequencing data contained in fasta and qual files produced from an Ion Torrent PGM sequencer. There were 2 sampling occurrences (041218 and 092718) and each occurrence has an associated fasta and qual file. This dataset contains the 092718 sampling data only due to storage restrictions. The other dataset is published separately. Our research has shown that the human skin microbiome is altered after swimming in the ocean. Normal commensals were washed off and simultaneously, exogenous bacteria were deposited on the skin. QIIME was used for initial analysis and indicated that the abundance and diversity of microbial communities on the skin increased after swimming and these changes persisted for more than 24 hours. Downstream analysis using PICRUSt to predict functional metagenomics indicated that there was an increase in antibiotic resistance genes, antibiotic biosynthesis
https://data.mendeley.com/datasets/hjnfzm949y
A framework for human microbiome research. | Sharpton Lab
A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human ...
http://sharptonlab.cgrb.oregonstate.edu/?q=node/36
human microbiome in health and disease pdf
Interest toward the human microbiome, particularly gut microbiome has flourished in recent decades owing to the rapidly advancing sequence-based screening and humanized gnotobiotic model in interrogating the dynamic operations of commensal microbiota. Available data indicates multiple factors have contributed to discrepancies between studies. The study of the human microbiome is important, and it gives an in-depth understanding of the interplay between humans and its indigenous microbiota. Using stool samples (n = 298; aged 1-11 months) from a US birth cohort and 16S rRNA sequencing, neonates (median age, 35 d) were divisible into three microbiota composition states (NGM1-3). The authors declare no conflicts of interest. Due to the coevolution of the human microbiota and the immune system, a balanced and systematic interaction occurs over time. It is important to note that the continuous use of broad-spectrum antibiotics may disrupt the human microbiota. Genome Medicine is pleased to present a ...
http://ww2.ppgteg.ufrpe.br/gordon-ramsay-fnpbr/human-microbiome-in-health-and-disease-pdf-ab30f6
Structure, function and diversity of the healthy human microbiome. | Sharpton Lab
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitats signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of ...
http://sharptonlab.cgrb.oregonstate.edu/?q=node/35
The indian tribal gut microbiota unravelled - Gut Microbiota for HealthThe indian tribal gut microbiota unravelled - Gut Microbiota for Health
The latest revelation in human gut microbiome research is the gut bacterial profiles of fifteen tribal populations representing four geographic regions (Assam, Telangana, Manipur and Sikkim) from India. The study by Dehingia, et al. (2015), Gut bacterial diversity of the tribes of India and comparison with the worldwide data (see References), is a good addition to the knowledge base of gut microbiome profiles across various human populations (Dehingia et al., 2015).. Why is this study relevant and important? Because most of the tribes around the world represent a gut microbiome profile of human ancestral lifestyle, one that was unaffected by junk food and was more physically active. Several lifestyle-associated disorders/diseases like type 2 diabetes, metabolic syndrome, and obesity have been linked to variations in human gut microbiome composition and function. Thus, having the knowledge of our ancestral gut microbiome is a good starting point to identify what changes have occurred since the ...
http://www.gutmicrobiotaforhealth.com/en/indian-tribal-gut-microbiota-unravelled/
Prophage: Summary of the 2016 International Human Microbiome Congress
The theme for the meeting was frontiers of microbiome science and metagenomic medicine. This meant that there was a heavy focus on microbiome studies that utilized metagenomic shotgun sequencing to understand the human microbiome. I honestly felt throughout the meeting that this choice might have been a little too restrictive and had the focus too much on the method and not enough on the actual biology and medicine. There was certainly some excellent science, but it would have been nice to have the focus more on how we can use tools to answer important questions instead of looking for questions we can answer with a tool. But I could do a whole post on this so for now I am going to leave it at that. In the end, I think that the next meeting could really benefit from a broader theme that focuses less on a specific method. For example, I preferred the broad theme last year: future directions for human microbiome research in health and disease ...
http://prophage.blogspot.hr/2016/11/summary-of-2016-international-human.html
The Human Gut Chip HuGChip, an explorative phylogenetic microarray for determining gut microbiome diversity at family levelThe Human Gut Chip HuGChip, an explorative phylogenetic microarray for determining gut microbiome diversity at family level
Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearsons correlation coefficients were obtained between ...
https://cora.ucc.ie/handle/10468/2377
Age-stratified comparative analysis of the differences of gut microbiota associated with blood glucose level | BMC Microbiology...Age-stratified comparative analysis of the differences of gut microbiota associated with blood glucose level | BMC Microbiology...
Gut bacteria are an important component of the microbiota ecosystem in humans and other animals, and they play important roles in human health. The aim of this study was to investigate the relationship between gut microbiota and multiple demographical-, behavioral-, or biochemical-related factors in subjects with chronic disease. Subjects with a very wide age range who participated in community-based chronic disease prevention and screening programs in China were enrolled. We analyzed the intestinal microbiota composition using 16S rRNA-based high-throughput sequencing of fecal samples, analyzed the association between gut microbiota structure and multiple demographical, behavioral, and biochemical factors, and compared the differences in microbiota composition in age-stratified groups with different blood glucose levels. Our results showed that both age and blood glucose levels had a significant impact on the gut microbiota structure. We also identified several taxa showed distinct abundance in groups
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-019-1466-y/email/correspondent/c1/new
A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the MatterA Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter
Obesity is an important and intractable public health problem. In addition to the well-known risk factors of behavior, diet, and genetics, gut microbial communities were recently identified as another possible source of risk and a potential therapeutic target. However, human and animal-model studies have yielded conflicting results about the precise nature of associations between microbiome composition and obesity. In this paper, we use publicly available data from the Human Microbiome Project (HMP) and MetaHIT, both surveys of healthy adults that include obese individuals, plus two smaller studies that specifically examined lean versus obese adults. We find that inter-study variability in the taxonomic composition of stool microbiomes far exceeds differences between lean and obese individuals within studies. Our analyses further reveal a high degree of variability in stool microbiome composition and diversity across individuals. While we confirm the previously published small, but statistically
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084689
06. Microbiome in COPD: Pitfalls and Progress | BRN06. Microbiome in COPD: Pitfalls and Progress | BRN
Microbiome studies of respiratory secretions have provided exciting new observations regarding the bacterial causation of exacerbations of COPD, and the impact of treatment of the exacerbation on the airway microbiome. Bacterial exacerbations likely represent abrupt major changes in the microbiome with resultant large increases in airway and systemic inflammation. Microbiome studies could lead to discovery of new pathogens that have been difficult to obtain with standard culture techniques.. The Vicious Circle Hypothesis embodies the likely contribution of an altered microbiome to COPD progression, with an unhealthy microbiome driving the inflammatory process in stable COPD. While studies with conventional microbiology found potential pathogenic bacteria to be virtually absent in bronchoscopic samples in healthy controls, smoking and development of COPD was associated with 35-50% incidence of isolation of pathogenic bacteria. In contrast, recent microbiome studies have found no or minor ...
http://brn.cat/microbiome2016/06-microbiome-in-copd-pitfalls-and-progress/
Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant...
A distinct bacterial signature of the placenta was reported, providing evidence that the fetus does not develop in a sterile environment. The oral microbiome was suggested as a possible source of the bacterial DNA present in the placenta based on similarities to the oral non-pregnant microbiome. Here, the possible origin of the placental microbiome was assessed, examining the gut, oral and placental microbiomes from the same pregnant women. Microbiome profiles from 37 overweight and obese pregnant women were examined by 16SrRNA sequencing. Fecal and oral contributions to the establishment of the placental microbiome were evaluated. Core phylotypes between body sites and metagenome predictive functionality were determined. The placental microbiome showed a higher resemblance and phylogenetic proximity with the pregnant oral microbiome. However, similarity decreased at lower taxonomic levels and microbiomes clustered based on tissue origin. Core genera: Prevotella, Streptococcus and Veillonella ...
https://espace.library.uq.edu.au/view/UQ:634121
Processes | Free Full-Text | Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut MicrobiomeProcesses | Free Full-Text | Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome
The gut microbiome is a highly complex microbial community that strongly impacts human health and disease. The two dominant phyla in healthy humans are Bacteroidetes and Firmicutes, with minor phyla such as Proteobacteria having elevated abundances in various disease states. While the gut microbiome has been widely studied, relatively little is known about the role of interspecies interactions in promoting microbiome stability and function. We developed a biofilm metabolic model of a very simple gut microbiome community consisting of a representative bacteroidete (Bacteroides thetaiotaomicron), firmicute (Faecalibacterium prausnitzii) and proteobacterium (Escherichia coli) to investigate the putative role of metabolic byproduct cross feeding between species on community stability, robustness and flexibility. The model predicted coexistence of the three species only if four essential cross-feeding relationships were present. We found that cross feeding allowed coexistence to be robustly maintained for
http://www.mdpi.com/2227-9717/5/1/13
Grant Abstract: DIET, GENETIC FACTORS, AND THE GUT MICROBIOME IN CROHNS DISEASEGrant Abstract: DIET, GENETIC FACTORS, AND THE GUT MICROBIOME IN CROHNS DISEASE
Abstract: We propose to investigate the hypothesis that consistent changes in the human gut microbiome are associated with Crohns disease, a form of inflammatory bowel disease, and that altered microbiota contributes to pathogenesis. Analysis of this problem is greatly complicated by the fact that multiple factors influence the composition of the gut microbiota, including diet, host genotype, and disease state. For example, data from others and us document a drastic impact of diet on the composition of the gut microbiome. No amount of sequencing will yield a useful picture of the role of the microbiota in disease if samples are confounded with uncontrolled variables. Our proposed project will take advantage of our experience with deep sequencing to characterize the composition of the gut microbiome, but also control diet, host genotype, and disease state. Diet will be controlled by analyzing children treated for Crohns disease by placing them on a standardized elemental diet, and by testing ...
https://ods.od.nih.gov/Funding/abstract.aspx?g=1UH2DK083981-01
Microbial modulation of the gut microbiome for treating autoimmune diseases. | GenX SocialHubMicrobial modulation of the gut microbiome for treating autoimmune diseases. | GenX SocialHub
PMID: Expert Rev Gastroenterol Hepatol. 2018 Oct ;12(10):985-996. Epub 2018 Sep 3. PMID: 30146910 Abstract Title: Microbial modulation of the gut microbiome for treating autoimmune diseases. Abstract: Many studies have shown the relationship between autoimmune diseases and the gut microbiome in humans: those with autoimmune conditions display gut microbiome dysbiosis. The big question that needs to be addressed is if restoring eubiosis of the gut microbiota can help suppress the autoimmune condition by activating various immune regulatory mechanisms. Inducing these self-healing mechanisms should prolong good health in affected individuals. Area covered: Here, we review the available clinical and preclinical studies that have used selective bacteria for modulating gut microbiota for treating autoimmune diseases. The potential bacterial candidates and their mechanism of action in treating autoimmune diseases will be discussed. We searched for genetically modified and potential probiotics for ...
https://genx-digital.com/2019/06/10/microbial-modulation-of-the-gut-microbiome-for-treating-autoimmune-diseases/
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice | Science Translational...The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice | Science Translational...
Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a persons gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donors microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a ...
http://stm.sciencemag.org/content/1/6/6ra14.long
A Metagenomic Study of Met52s Effects on the Bacterial Microbiome by Matthew Rusling LampeterA Metagenomic Study of Met52s Effects on the Bacterial Microbiome by Matthew Rusling Lampeter
In an effort to reduce Lyme transmission in Dutchess county, the Carry Institute of Ecosystem Studies is evaluating various vector management strategies for their safety and efficacy. One strategy under consideration is treatment of voluntarily enrolled residential areas with Met52, a biopesticide which kills Ixodes scapularis, a principle Lyme vector. The goal of this Senior Project is to evaluate how application of Metarhizium anisopliae F52, commonly known as Met52, changes the soil bacterial microbiome of plots representative of residential areas. We analyzed the microbiomes of 55 samples using the QIIME pipeline. We found that the edge effect was not detectable at distances of 1 m. This allowed us to pool inner and edge samples for comparisons of how lawn and forest microbiomes responded to Met52. We found that despite greater macro scale diversity, the lawn microbiome actually harbored a more diverse soil microbiome. Surprisingly, this complexity was not correlated with greater microbiome
https://digitalcommons.bard.edu/senproj_s2017/103/
Human Microbiome Project - Home | NIH Common FundHuman Microbiome Project - Home | NIH Common Fund
Microscopic study of the healthy human body has demonstrated that microbial cells outnumber human cells by about ten to one. Prior to the start of the HMP, this abundant community of human-associated microbes remained largely unstudied, leaving their influence upon human development, physiology, immunity, and nutrition almost entirely unknown. The HMP was established with the mission of generating research resources, which were rapidly and broadly shared, enabling comprehensive characterization of the human microbiota and their metabolic capabilities and analysis of their role in human health and disease. The information generated by HMP is now available worldwide for use by investigators and others in efforts to understand and improve human health.. The first phase of HMP was focused on the development of DNA sequence datasets and computational tools for characterizing the microbiome in healthy adults and in people with specific microbiome-associated diseases. An Ethical, Legal and Societal ...
http://commonfund.nih.gov/hmp/
Role of host genetics on gut microbiome is ne | EurekAlert!Role of host genetics on gut microbiome is ne | EurekAlert!
Taken together, the bacteria, viruses, fungi and other microbes that live in our intestines form the gut microbiome, which plays a key role in the health of people and animals. In new research from the University of Minnesota, University of Notre Dame and Duke University, scientists found that genetics nearly always plays a role in the composition of the gut microbiome of wild baboons.. In humans, research has shown that family members share a significant portion of microbes in their gut, but its hard to answer if our microbiome is shaped more by nature, such as those we inherit from our family, or nurture, such as the similar diets, environments and behaviors families share, said lead author Laura Grieneisen, a postdoctoral fellow in the College of Biological Sciences. Many human diseases and other markers of health have a genetic component. The number and types of bacteria in the gut are no different. By understanding the heritability of the gut microbiome will help us better link genes, ...
https://www.eurekalert.org/news-releases/854415
Immigrating to the U.S. leads to loss of microbiome diversityImmigrating to the U.S. leads to loss of microbiome diversity
The researchers compared the microbiome composition of four groups of participants: Hmong and Karen people living in Thailand, Hmong and Karen people who immigrated to the U.S., U.S.-born children of Hmong immigrants, and U.S. Americans with European ancestry. The team also measured participants body mass index and asked them to report what they had eaten in the past 24 hours. In a subset of participants, they tracked changes in microbiome composition, diet, and weight at several time points before and after the people arrived in the U.S.. ...
https://cen.acs.org/biological-chemistry/microbiome/Immigrating-US-leads-loss-microbiome/96/i44?utm_source=YMAL&utm_medium=YMAL&utm_campaign=CEN&utm_content=pos3
Hospital Microbiome Project | Hospital Microbiome ProjectHospital Microbiome Project | Hospital Microbiome Project
In 2012, we began working on a new project at the University of Chicagos new hospital facility: the Center for Care and Discovery. The Hospital Microbiome Project was designed to collect microbial samples from surfaces, air, staff, and patients from the University of Chicagos new hospital pavilion in order to better understand the factors that influence bacterial population development in healthcare environments. Of particular importance and interest are the microbes and viruses that may influence the spread of hospital acquired infections.. We were involved on this project as a subcontract to the University of Chicago to collect data for a number of building environmental and operational parameters - collectively called building science measurements or built environment data that may influence microbial communities in the hospital. The PI on the project is Dr. Jack Gilbert, who is dually appointed in the Department of Ecology & Evolution at U of C and as an Environmental Microbiologist at ...
http://hospitalmicrobiome.com/hospital-microbiome-project/
Compression-Based Distance (CBD): Microbiota Composition | Society for Mucosal ImmunologyCompression-Based Distance (CBD): Microbiota Composition | Society for Mucosal Immunology
Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying
http://www.socmucimm.org/compression-based-distance-cbd-simple-method-for-microbiota-composition-comparison/
Prophage: Recent Publication: The Skin Microbiome in Health and Disease
In short, the paper goes over the history of skin microbial community studies, an overview of how the skin microbiome has been implicated in contributing to health and disease, and some ways our understanding of the skin microbiome has contributed to therapeutic interventions. We focused primarily on the bacterial, fungal, and viral communities associated with the skin, and how they contribute to health and disease. We go over potential roles of microbes in diseases including atopic dermatitis, psoriasis, acne, dandruff, and skin cancer. So go ahead and check it out ...
http://prophage.blogspot.hr/2013/12/recent-publication-skin-microbiome-in.html
Ocasys: Toon vak Microbiome and HealthOcasys: Toon vak Microbiome and Health
The microbiome is a community of microbes that inhabit various surfaces of different hosts, including mammals. Recent developments in genomics and the human microbiome project have fostered the awareness that microbes are key organisms despite their minute size. A balanced microbiome plays a major role in digesting the diet but also in keeping pathogens at bay, controlling metabolism, shaping the immune system and promoting mental health. In accord, changes in the human microbiome have been linked to a variety of diseases. Understanding the microbiome and its crosstalk with the diet and host systems is undoubtedly crucial to maintain host health and prevent disease ...
https://www.rug.nl/ocasys/rug/vak/show?code=WMBM16001
Researchers find clues to inconsistent microbiome findings in ASD, see longitudinal effects - Autism Research InstituteResearchers find clues to inconsistent microbiome findings in ASD, see longitudinal effects - Autism Research Institute
In the study, Jennifer Fouquier and colleagues compared fecal samples from individuals with ASD and controls in Arizona and Colorado, using standardized DNA extraction and sequencing methods. The Arizona participants included 36 children with ASD and 38 age-matched neurotypical controls who did not have first-degree relatives with autism. The Colorado participants included 13 children with ASD and 16 matched neurotypical controls; five of the controls had siblings with ASD.. The researchers found that gut microbiomes differed between individuals in Arizona and those in Colorado. Moreover, in Arizona but not Colorado, gastrointestinal symptoms were higher in individuals with ASD than in controls. Gut microbiome composition was significantly associated with ASD when the researchers controlled for study site location but not when they controlled for gastrointestinal symptoms.. Taken together, the researchers say, these results suggest that geographical differences in gut microbiome composition ...
https://www.autism.org/researchers-find-clues-to-inconsistent-microbiome-findings-in-asd-see-longitudinal-effects/
Science Daily - Immune system, skin microbiome complement one anotherScience Daily - Immune system, skin microbiome complement one another
Researchers demonstrate for the first time that the immune system influences the skin microbiome. A new study found that the skin microbiome a collection of microorganisms inhabiting the human body is governed, at least in part, by an ancient branch of the immune system called complement.http://feeds.feedburner.com/~r/sciencedaily/health_medicine/~4/VKXbSZandvU More...
https://rosaceagroup.org/The_Rosacea_Forum/showthread.php?29458-Science-Daily-Immune-system-skin-microbiome-complement-one-another
Approaches and developments in studying the human microbiome network » Brill OnlineApproaches and developments in studying the human microbiome network » Brill Online
The human microbiome is dynamic and unique to each individual, and its role is being increasingly recognized in healthy physiology and in disease, including gastrointestinal and neuropsychiatric disorders. Therefore, characterizing the human microbiome and the factors that shape its bacterial population, how they are related to host-specific attributes, and understanding the ways in which it can be manipulated and the phenotypic consequences of such manipulations are of great importance. Characterization of the microbiome so far has been mostly based on compositional studies alone, where relative abundances of different species are compared in different conditions, such as health and disease. However, inter-relationships among the bacterial species, such as competition and cooperation over metabolic resources, may be an important factor that affects the structure and function of the microbiome. Here we review the network-based approaches in answering such questions and explore the first attempts that
http://booksandjournals.brillonline.com/content/journals/10.1080/15659801.2015.1042768
Gelatin tannate ameliorates acute colitis in mice by reinforcing mucus layer and modulating gut microbiota composition:...Gelatin tannate ameliorates acute colitis in mice by reinforcing mucus layer and modulating gut microbiota composition:...
Gelatin tannate ameliorates acute colitis in mice by reinforcing mucus layer and modulating gut microbiota composition: Emerging role for gut barrier protectors in IBD? ...
http://www.crohnsforum.com/showthread.php?t=67411
Fermented green tea extract alleviates obesity and related complications and alters gut microbiota composition in diet-induced...
Fingerprint Dive into the research topics of Fermented green tea extract alleviates obesity and related complications and alters gut microbiota composition in diet-induced obese mice. Together they form a unique fingerprint. ...
https://koreauniv.pure.elsevier.com/en/publications/fermented-green-tea-extract-alleviates-obesity-and-related-compli/fingerprints/
Gut microbiome composition is associated with age and memory performance in pet dogsGut microbiome composition is associated with age and memory performance in pet dogs
Our gut microbiota can crucially influence our behavior and neurodevelopment. New research from the Ethology Department at the Faculty of Science at Eötvös Loránd University indicates that dogs aging mechanism and memory performance are also linked to their gut microbiome composition. According to the study, dogs and humans may have similar mechanisms in cognitive aging.
https://phys.org/news/2020-09-gut-microbiome-composition-age-memory.html
Gut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis | IOVS | ARVO JournalsGut Microbiota Composition and Fecal Metabolic Phenotype in Patients With Acute Anterior Uveitis | IOVS | ARVO Journals
In the present study, we found that AAU patients had a characteristic fecal metabolite profile, irrespective of the presence of AS or their HLA-B27 status. Although the alpha analysis or abundance of gut microbiota between patients and controls failed to show any significant differences, we revealed significant alterations in microbiota composition in AAU patients compared with healthy controls following analysis of PCoA plots of unweighted UniFrac distances. Our findings are, by and large, in agreement with recent observations showing that the development of ocular inflammation during experimental autoimmune uveitis in mice is dependent on the presence of certain bacteria in the gut of these animals.14 To our knowledge this is the first report concerning the analysis of gut microbiota composition and fecal metabolite profile in clinical AAU, although we are aware of the fact that due to the various limitations of our study, one should see this report as a preliminary observation in an important ...
https://iovs.arvojournals.org/article.aspx?articleid=2675703
Advances in computational analysis of metagenome sequences - Davenport - 2012 - Environmental Microbiology - Wiley Online...Advances in computational analysis of metagenome sequences - Davenport - 2012 - Environmental Microbiology - Wiley Online...
Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. Environmental Microbiology, 15: 1-5. doi: 10.1111/j.1462-2920.2012.02843.x ...
http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02843.x/references?globalMessage=0
こちら - 宮崎大学こちら - 宮崎大学
宮崎大学ハイステップ研究者 表彰者リスト（2014.10.27） 代表者氏名 林 哲也 所 属 論文タイトル 受賞者名 NATURE 473 2011 An extensive repertoire of type III secretion effectors in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 2006 1494114946 林 哲也 DNA RESEARCH 14 2007 169-181 林 哲也 小椋義俊 Vol.59 No.SP1 2007 S1-S7 フロンティア科学実験総 Escherichia coli O157 and the role of lambdoid phages in 合センター長 Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes 情報統括機構情報基盤 The X-Ray Observatory Suzaku センター長 The COMPASS experiment at CERN 松田 達郎 Vol. 発刊年 ページ番号 Enterotypes of the human gut microbiome their dissemination 廿日出 勇 ジャーナル名 工学教育研究部工学基 Evidence for the Theta(+) in the gamma d -, K(+)K(-)pn 礎教育センター教授 reaction by detecting K+K- pairs Publications of ...
http://exploredoc.com/doc/391030/%E3%81%93%E3%81%A1%E3%82%89---%E5%AE%AE%E5%B4%8E%E5%A4%A7%E5%AD%A6
Lactulose Differently Modulates the Composition of Luminal and Mucosal Microbiota in C57BL/6J MiceLactulose Differently Modulates the Composition of Luminal and Mucosal Microbiota in C57BL/6J Mice
In this study, C57BL/6J mice were fed diets supplemented with different proportions of lactulose (0%, 5%, and 15%) for 2 weeks to study its effects on the luminal and mucosal microbiota. The luminal and mucosal samples of cecum and colon were investigated. After high-lactulose treatment (15%), pH of …
https://pubmed.ncbi.nlm.nih.gov/27438677/
NIH to host workshop on advances, future needs in human microbiome research
Microbes inhabit just about every part of the human body outnumbering human cells by 10 to 1. The 10-year, National Institutes of Health Common Fund Human Microbiome Project was established to understand how microbial communities impact human...
http://taggatore.com/articolo/nih-to-host-workshop-on-advances-future-needs-in-human-microbiome
Fecal Microbiota Composition Differs Between Children With β-Cell Autoimmunity and Those Without | DiabetesFecal Microbiota Composition Differs Between Children With β-Cell Autoimmunity and Those Without | Diabetes
The role of the intestinal microbiota as a regulator of autoimmune diabetes in animal models is well-established, but data on human type 1 diabetes are tentative and based on studies including only a few study subjects. To exclude secondary effects of diabetes and HLA risk genotype on gut microbiota, we compared the intestinal microbiota composition in children with at least two diabetes-associated autoantibodies (n = 18) with autoantibody-negative children matched for age, sex, early feeding history, and HLA risk genotype using pyrosequencing. Principal component analysis indicated that a low abundance of lactate-producing and butyrate-producing species was associated with β-cell autoimmunity. In addition, a dearth of the two most dominant Bifidobacterium species, Bifidobacterium adolescentis and Bifidobacterium pseudocatenulatum, and an increased abundance of the Bacteroides genus were observed in the children with β-cell autoimmunity. We did not find increased fecal calprotectin or IgA as ...
http://diabetes.diabetesjournals.org/content/62/4/1238.short
whale gut microbiome - Annabel Beichman, UCLAwhale gut microbiome - Annabel Beichman, UCLA
Next-generation sequencing has allowed us to characterize cetacean gut microbial communities and discover surprising similarities to the microbiomes of terrestrial herbivores and carnivores.. I am thrilled to announce the publication of our paper on the whale gut microbiome in Nature Communications.. By sequencing the bacterial genomes contained in whale fecal samples, we explore the gut community of baleen whales and its functional potential. We find a remarkable fusion microbiome that, while highly diverged overall from that of terrestrial mammals, contains functional elements characteristic of both terrestrial carnivore and terrestrial herbivore gut microbiomes. We find evidence to support the hypothesis that whales (which are descended from herbivorous terrestrial mammals, but are carnivores, eating small crustaceans and small fish) may use foregut fermentation to break down their food, much as ruminants do. In particular, the need to break down recalcitrant chitin in the exoskeletons of ...
http://annabelbeichman.com/tag/whale-gut-microbiome/
Reshaped fecal gut microbiota composition by the intake of high molecular weight persimmon tannin in normal and high...Reshaped fecal gut microbiota composition by the intake of high molecular weight persimmon tannin in normal and high...
It has been proposed that the gut microbiome may be related to obesity, and diet-induced obesity may induce changes in the gut microbiota composition. Our previous studies suggested that persimmon tannin (PT), which is highly polymerized and non-absorbable in the intestine, showed anti-hyperlipidemic and cholestero
http://pubs.rsc.org/en/content/articlelanding/2018/fo/c7fo00995j/unauth
Circadian disruption changes gut microbiome taxa and functional gene composition<...
TY - JOUR. T1 - Circadian disruption changes gut microbiome taxa and functional gene composition. AU - Deaver, Jessica A.. AU - Eum, Sung Y.. AU - Toborek, Michal. N1 - Funding Information: We would like to acknowledge the assistance of Second Genome (San Francisco, CA, United States) in metatranscriptome analyses. The current study was supported in part by grants from the National Institutes of Health (CA133257) and Alltech Nutrigenomics. Publisher Copyright: © 2018 Deaver, Eum and Toborek.. PY - 2018/4/13. Y1 - 2018/4/13. N2 - Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light-dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool ...
https://miami.pure.elsevier.com/en/publications/circadian-disruption-changes-gut-microbiome-taxa-and-functional-g
Antibiotic Exposure Has Sex-Dependent Effects on the Gut Microbiota and Metabolism of Short-Chain Fatty Acids and Amino Acids...Antibiotic Exposure Has Sex-Dependent Effects on the Gut Microbiota and Metabolism of Short-Chain Fatty Acids and Amino Acids...
The gut microbiota has the capability to generate a series of metabolites and thereby regulate homeostasis of the host metabolism (1). Antibiotic treatment, as an important therapeutic approach in clinical practice, can adversely affect the gut microbiota, inevitably giving rise to metabolic disorders (19). However, whether antibiotics have sex-dependent effects on the gut microbiota and host metabolism is unknown.. In the present study, at first we found that the gut microbiome and metabolome are influenced by gender. Results showed that male mice had higher abundances of Adlercreutzia, AF12, Anaeroplasma, Bacteroides, Dehalobacterium, Dorea, Mucispirillum, Roseburia, and Ruminococcus as well as lower levels of Lactobacillus, Prevotella, and Sutterella than female mice. In fact, sex-dependent differences in the gut microbiota have been reported due to hormonal effects (20), but many other factors may also affect microbial composition changes, such as genotype (21), age (22), body weight (23), ...
https://msystems.asm.org/content/4/4/e00048-19
What is Vaginal Microbiome Dysbiosis? Does it matter, Yes | BiomWhat is Vaginal Microbiome Dysbiosis? Does it matter, Yes | Biom
What is Vaginal Microbiome Dysbiosis? Does it matter, Yes…The vaginal microbiome is a symbiotic relationship between good & bad bacteria.
https://www.biomprobiotics.com/what-is-vaginal-microbiome-dysbiosis-does-it-matter-yes/
Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota | SpringerLinkToothbrush microbiomes feature a meeting ground for human oral and environmental microbiota | SpringerLink
While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were
https://rd.springer.com/article/10.1186/s40168-020-00983-x?error=cookies_not_supported&error=cookies_not_supported&code=875b8d72-81ae-48b2-927a-ad279e021791&code=2be8e5e1-3698-448f-8e60-c6ffed6df53e
Ritter Pharmaceuticals, Inc. Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published In PNAS | BioSpaceRitter Pharmaceuticals, Inc. Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published In PNAS | BioSpace
Ritter Pharmaceuticals, Inc. Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published In PNAS - read this article along with other careers information, tips and advice on BioSpace
https://www.biospace.com/article/releases/ritter-pharmaceuticals-inc-phase-2a-lactose-intolerance-clinical-trial-microbiome-data-published-in-pnas-/
Intestinal Microbiota Diversity of Pre-Smolt Steelhead (<i>Oncorhynchu by Christina Carrell...Intestinal Microbiota Diversity of Pre-Smolt Steelhead (<i>Oncorhynchu by Christina Carrell...
The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this
https://pdxscholar.library.pdx.edu/open_access_etds/3709/
Alteration of the Intestinal Microbiome | Healing Alopecia AreataAlteration of the Intestinal Microbiome | Healing Alopecia Areata
Karlsson and colleagues draw a parallel between intestinal microbiota becoming pro-inflammatory resulting in increased mucosal permeability and the oxidative stress-induced subclinical inflammation that leads to chronic inflammation within arteries as seen in atherosclerosis.[83] Although difficult to prove, ongoing research suggests increased translocation of intestinal microbiota into the bloodstream through disruption of epithelial tight junctions. Karlsson performed a randomized controlled trial with 16 male patients diagnosed with carotid wall atherosclerotic plaques. Nine patients were given a 4-week trial of a L. plantarum-fermented oat drink and seven patients were in the placebo arm (unfermented oat drink without L. plantarum). Study patients demonstrated increased intestinal microbiome diversity and lower concentrations of fecal carboxylic acids, specifically isovaleric (p = 0.006) and valeric (p = 0.029) acid, surrogate markers for inflammatory disease. There were no significant ...
https://polardash.org/alteration-of-the-intestinal-microbiome/
Aberrant intestinal microbiota in individuals with prediabetes - DTU OrbitAberrant intestinal microbiota in individuals with prediabetes - DTU Orbit
Aims/hypothesis: Individuals with type 2 diabetes have aberrant intestinal microbiota. However, recent studies suggest that metformin alters the composition and functional potential of gut microbiota, thereby interfering with the diabetes-related microbial signatures. We tested whether specific gut microbiota profiles are associated with prediabetes (defined as fasting plasma glucose of 6.1-7.0 mmol/l or HbA1c of 42-48 mmol/mol [6.0-6.5%]) and a range of clinical biomarkers of poor metabolic health. Methods: In the present case-control study, we analysed the gut microbiota of 134 Danish adults with prediabetes, overweight, insulin resistance, dyslipidaemia and low-grade inflammation and 134 age- and sex-matched individuals with normal glucose regulation. Results: We found that five bacterial genera and 36 operational taxonomic units (OTUs) were differentially abundant between individuals with prediabetes and those with normal glucose regulation. At the genus level, the abundance of Clostridium ...
https://orbit.dtu.dk/en/publications/aberrant-intestinal-microbiota-in-individuals-with-prediabetes
RePub, Erasmus University Repository: The Gut Microbiome in Patients with Intestinal FailureRePub, Erasmus University Repository: The Gut Microbiome in Patients with Intestinal Failure
Intestinal failure (IF) is the reduction of gut function or mass below a minimum needed to absorb nutrients and fluids, such that patients are dependent on parenteral nutrition (PN). Patients with IF have an altered gut microbiome. Our aim was to review and evaluate the current evidence on gut microbiome and its metabolic activity, as well as its association with disease characteristics in adults and children with IF. We performed a PubMed literature search for articles published after 2000 using the following terms: intestinal, microbiome, microbiota, short‐chain fatty acids, short bowel syndrome, and PN. Literature search was restricted to human studies only. The gut microbiome diversity is remarkably reduced, and community structure is altered with a noticeable overabundance of Proteobacteria, especially the Enterobacteriaceae family. A substantial increase in Lactobacillus level is often reported in patients with IF. Gut microbiome characteristics have been associated with poor growth, ...
https://repub.eur.nl/pub/115272
Taconic Launches Exciting New Website in Support of Translational Microbiome ResearchTaconic Launches Exciting New Website in Support of Translational Microbiome Research
HUDSON, NY--(Marketwired - May 8, 2014) - Today, Taconic announced the launch of the Translational Microbiome Research Forum website, which provides an opportunity for investigators worldwide to access and exchange information in the emerging field of microbiome research. The Translational Microbiome Research Forum website provides up-to-date news, publications, events, and...
http://www.marketwired.com/press-release/taconic-launches-exciting-new-website-support-translational-microbiome-research-1908283.htm
Human microbiome - Simple English Wikipedia, the free encyclopediaHuman microbiome - Simple English Wikipedia, the free encyclopedia
The human microbiome (or human microbiota) is the collection of microorganisms which live on us. They live on the skin, in the saliva and mouth, in the eyes, and in the gut and the rest of the gastrointestinal tract. They include bacteria, archaea, fungi and single-celled eukaryotes (protozoa).[1] Everyone carries around far more of these microbes than the number of human cells in the body. The human body has about 100 trillion cells, and carries about ten times as many microorganisms in the intestines alone.[2][3][4][5] The microbiome is the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.[6][7] The term was originally coined by Joshua Lederberg. He thought the microorganisms living in the human body in health and disease were important. Many scientific articles distinguish microbiome and microbiota to describe either the collective genomes of the microorganisms that live in an environmental niche or the microorganisms ...
https://simple.wikipedia.org/wiki/Human_microbiota
The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. | Broad...The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. | Broad...
To address how the microbiome might modify the interaction between diet and cardiometabolic health, we analyzed longitudinal microbiome data from 307 male participants in the Health Professionals Follow-Up Study, together with long-term dietary information and measurements of biomarkers of glucose homeostasis, lipid metabolism and inflammation from blood samples. Here, we demonstrate that a healthy Mediterranean-style dietary pattern is associated with specific functional and taxonomic components of the gut microbiome, and that its protective associations with cardiometabolic health vary depending on microbial composition. In particular, the protective association between adherence to the Mediterranean diet and cardiometabolic disease risk was significantly stronger among participants with decreased abundance of Prevotella copri. Our findings advance the concept of precision nutrition and have the potential to inform more effective and precise dietary approaches for the prevention of ...
https://www.broadinstitute.org/publications/broad768586
Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic SyndromeAnalysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome
Obesity has been linked to the human gut microbiota; however, the contribution of gut bacterial species to the obese phenotype remains controversial because of conflicting results from studies in different populations. To explore the possible dysbiosis of gut microbiota in obesity and its metabolic complications, we studied men and women over a range of body mass indices from the Old Order Amish sect, a culturally homogeneous Caucasian population of Central European ancestry. We characterized the gut microbiota in 310 subjects by deep pyrosequencing of bar-coded PCR amplicons from the V1-V3 region of the 16S rRNA gene. Three communities of interacting bacteria were identified in the gut microbiota, analogous to previously identified gut enterotypes. Neither BMI nor any metabolic syndrome trait was associated with a particular gut community. Network analysis identified twenty-two bacterial species and four OTUs that were either positively or inversely correlated with metabolic syndrome traits, suggesting
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043052
Plus itPlus it
Background: The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here, we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk.. Methods: We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA. We compared oral microbiota from buccal cells with that from eight other oral sample types collected by following the protocols of the Human Microbiome Project. Microbiota profiles were determined by sequencing 16S rRNA gene V3-V4 region.. Results: Compared with each of the eight other oral samples, the buccal cell samples had significantly more observed species (P , 0.002) and higher alpha diversity (Shannon index, P , 0.02). The ...
http://cebp.aacrjournals.org/content/26/2/249
About the CMR | Center for Microbiome ResearchAbout the CMR | Center for Microbiome Research
The UMass Center for Microbiome Research was created to accelerate our understanding of how the microbes that live in and on us influence our lives, our health and our environment. Our missions are to: • Educate and inform Research generates the discoveries that change our lives. We want to communicate these discoveries to you. Human microbiome research is creating new therapies and new approaches to understanding disease. We want to make our research accessible so everyone can share our excitement.
https://www.umassmed.edu/microbiome/ccts1/about/
Blog - Swette Center for ​Environmental BiotechnologyBlog - Swette Center for ​Environmental Biotechnology
ASM had organized lots of interesting presentations and the size of the venue was such that it took more than 15 minutes to walk from one side to the other side of the conference. Due to the time overlap of presentations and posters and the huge size of the venue, I was only able to attend a certain number of oral presentations. One of the best parts of the ASM conference was that I was able to see the trend of current research. To me, working on the human microbiome study, it was quite impressive because the number of talks and posters on human microbiome was significantly increased compared with my previous ASM meeting in San Francisco 2 years back. The microbiome studies was not limited to understanding microbial communities by 16S rRNA gene sequencing any more, but expanded their scope at the functional level with more mechanistical and practical approaches. One interesting session, for example, was on fecal microbiota transplantation. The talks were about successful trials on Clostridium ...
http://www.environmentalbiotechnology.org/blog/category/conferences
Intestinal Microbiota of Infants With Colic: Development and Specific Signatures | Articles | PediatricsIntestinal Microbiota of Infants With Colic: Development and Specific Signatures | Articles | Pediatrics
In this study we followed the temporal development of the intestinal microbiota from birth onward in infants with and without colic by using the HITChip, a phylogenetic microarray that allows a highly reproducible and comprehensive analysis of the known intestinal microbiota.18 Colic was determined at 6 weeks of age with a cry diary. The infants with colic were characterized by a microbiota that developed slower than that of the control infants and that also showed a reduced temporal stability. Infants with colic also showed a significantly reduced microbiota diversity at 14 and 28 days of life. In addition, already in the first 2 weeks of life, specific significant differences between both groups were found; proteobacteria were increased in infants with colic, with a more than doubled relative abundance, whereas bifidobacteria and lactobacilli were increased in control infants. Moreover, samples from infants with colic were found to contain fewer bacteria related to butyrate-producing ...
http://pediatrics.aappublications.org/content/131/2/e550
A Robust Longitudinal Co-culture of Obligate Anaerobic Gut Microbiome With Human Intestinal Epithelium in an Anoxic-Oxic...
The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. These anaerobic gut bacteria constantly crosstalk with the colonic epithelium in a mucosal anoxic-oxic interface (AOI). However, in vitro recreation of the metabolically mismatched colonic AOI has been technically challenging. Furthermore, stable co-culture of the obligate anaerobic commensal microbiome and epithelial cells in a mechanically dynamic condition is essential for demonstrating the host-gut microbiome crosstalk. Here, we developed an anoxic-oxic interface-on-a-chip (AOI Chip) by leveraging amodified human gut-on-a-chip to demonstrate a controlled oxygen gradient in the lumen-capillary transepithelial interface by flowing anoxic and oxic culture medium at various physiological milieus. Computational simulation and experimental results revealed that the presence of the epithelial cell layer and the flow-dependent conditioning in the lumen ...
https://www.leehicam.com/portfolio/a-robust-longitudinal-co-culture-of/
Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.
Esberg A, Haworth S, Hasslöf P, Lif Holgerson P, Johansson I Nutrients 12 (3) - [2020-03-03; online 2020-03-03] Oral microbiota ecology is influenced by environmental and host conditions, but few studies have evaluated associations between untargeted measures of the entire oral microbiome and potentially relevant environmental and host factors. This study aimed to identify salivary microbiota cluster groups using hierarchical cluster analyses (Wards method) based on 16S rRNA gene amplicon sequencing, and identify lifestyle and host factors which were associated with these groups. Group members ( n = 175) were distinctly separated by microbiota profiles and differed in reported sucrose intake and allelic variation in the taste-preference-associated genes TAS1R1 (rs731024) and GNAT3 (rs2074673). Groups with higher sucrose intake were either characterized by a wide panel of species or phylotypes with fewer aciduric species, or by a narrower profile that included documented aciduric- and ...
https://publications.scilifelab.se/publication/fc7a25ffb3114b019ba788d35be80ecc
Toll-like receptor 5 in obesity: The role of gut microbiota and adipose tissue inflammation - Tampere University of Technology
Objective This study aimed at establishing bacterial flagellin-recognizing toll-like receptor 5 (TLR5) as a novel link between gut microbiota composition, adipose tissue inflammation, and obesity. Methods An adipose tissue microarray database was used to compare women having the highest (n = 4, H-TLR) and lowest (n = 4, L-TLR) expression levels of TLR5-signaling pathway genes. Gut microbiota composition was profiled using flow cytometry and FISH. Standard laboratory techniques were used to determine anthropometric and clinical variables. In vivo results were verified using cultured human adipocytes. Results The H-TLR group had higher flagellated Clostridium cluster XIV abundance and Firmicutes-to-Bacteroides ratio. H-TLR subjects had obese phenotype characterized by greater waist circumference, fat %, and blood pressure (P , 0.05 for all). They also had higher leptin and lower adiponectin levels (P , 0.05 for both). Six hundred and sixty-eight metabolism-and inflammation-related adipose tissue ...
https://tutcris.tut.fi/portal/en/publications/tolllike-receptor-5-in-obesity-the-role-of-gut-microbiota-and-adipose-tissue-inflammation
Experimental NeurobiologyExperimental Neurobiology
The microbiota profile assessed from urine EVs might reflect a large part of the gut microbiota. Nonetheless, we do believe that the microbiota profile assessed from urine EVs is not likely a simple alternative for microbiota profile assessed from stool. Possible sources for metagenome analysis of bodily microbiota may include stool bacteria, stool EVs, gut (ex, stomach and/or specific regions of the small and large intestines) bacteria, respiratory exhale EVs, oral/nasal bacteria and EVs, urinary system bacteria and EVs, and blood EVs. Generally speaking, microbiota in stool represents the intestinal compartment, whereas microbiota in urine or blood reflects the whole body including the intestinal compartments, oral system, respiratory system, and urinary system. Nonetheless, among the body parts, the gut is the major source of bodily microbiota. It was reported that the metabolites of intestinal microbiota activities, including phenyllactate, p-cresol sulfate, concentrations, and serotonin in ...
https://www.en-journal.org/journal/view.html?doi=10.5607/en.2017.26.5.307
Keeping the peace: aryl hydrocarbon receptor signaling modulates the mucosal microbiotaKeeping the peace: aryl hydrocarbon receptor signaling modulates the mucosal microbiota
In this issue of Immunity, Zelante et al. (2013) and Qiu et al. (2013) provide mechanistic insights into functional interactions between commensal microbes and innate lymphoid cells via the aryl hydrocarbon receptor.
https://pubmed.ncbi.nlm.nih.gov/23973218/?dopt=Abstract
Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal...Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal...
The gut microbiota is a complex ecosystem that wields great influence over the health of its host.32 Conversely, mammalian hosts use a broad array of mechanisms to shape the microbiota in a way that maximises its benefit and minimises its potential to harm.33 That, at least among healthy persons, intraindividual variance in microbiota composition (ie, repeat sampling of individual subjects) is much smaller than that seen when comparing different individuals33-35 indicates that the ability of host and microbiota to influence each other typically results in a relatively stable equilibrium within specific hosts. Yet, some exogenous factors, for example, pathogens or antibiotics, can dramatically and lastingly disturb this equilibrium in a manner that promotes persistent disease.36 Moreover, even factors that cause relatively modest disturbances of the host-microbiota relationship have been associated with chronic low-grade inflammatory diseases, including metabolic syndrome.36 The genetics of the ...
http://gut.bmj.com/content/66/8/1414
Prakriti phenotypes as a stratifier of gut microbiome: A new frontier in personalized medicine? MAHE Digital RepositoryPrakriti phenotypes as a stratifier of gut microbiome: A new frontier in personalized medicine? MAHE Digital Repository
Ayurveda has a rich history and its significance woven deeply in the Indian culture. The concept of prakriti (a persons nature or constitutional type determined by the proportion of three doshas, namely - vata, pitta and kapha) in Ayurveda is deeply rooted in personalized health management. While the attributes of prakriti has been established to have a genomic basis, there is dearth of elaborate evidences linking prakriti with manifestation of diseases. Next generation sequencing studies have provided a causal link between variation in the gut microbiome and its effect on an individuals fitness. Separately, reports have identified gut microbial patterns associated with several host variables such as geography, age, diet and extreme prakriti phenotypes. Recently, few reports have identified a core gut microbiome consisting of Bacteroides, Faecalibacterium, Prevotella and Ruminococcus prevalent across the Indian population; however, a few bacterial genera were specifically enriched in ...
http://eprints.manipal.edu/155880/
The role of the gut microbiota in development, function and disorders of the central nervous system and the enteric nervous...The role of the gut microbiota in development, function and disorders of the central nervous system and the enteric nervous...
PMID: J Neuroendocrinol. 2019 May ;31(5):e12684. Epub 2019 Feb 1. PMID: 30614568 Abstract Title: The role of the gut microbiota in development, function and disorders of the central nervous system and the enteric nervous system. Abstract: The gut microbiota has emerged as an environmental factor that modulates the development of the central nervous system (CNS) and the enteric nervous system (ENS). Before obtaining its own microbiota, eutherian foetuses are exposed to products and metabolites from the maternal microbiota. At birth, the infants are colonised by microorganisms. The microbial composition in early life is strongly influenced by the mode of delivery, the feeding method, the use of antibiotics and the maternal microbial composition. Microbial products and microbially produced metabolites act as signalling molecules that have direct or indirect effects on the CNS and the ENS. An increasing number of studies show that the gut microbiota can modulate important processes during ...
https://genx-digital.com/2019/06/09/the-role-of-the-gut-microbiota-in-development-function-and-disorders-of-the-central-nervous-system-and-the-enteric-nervous-system/
Gut microbiome regulates the intestinal immune system - SeeraveGut microbiome regulates the intestinal immune system - Seerave
A new study in mice unveils the role of vitamin A in immune system regulation, a finding that could assist in developing treatments for autoimmune and inflammatory diseases as well as vitamin A deficiency.. PROVIDENCE, R.I. [Brown University] - Scientists have long known that bacteria in the intestines, also known as the microbiome, perform a variety of useful functions for their hosts, such as breaking down dietary fiber in the digestive process and making vitamins K and B7.. Yet a new study unveils another useful role the microbiome plays. A team of researchers from Brown University found that in mice, the gut microbiome regulates the hosts immune system - so that rather than the hosts defense system attacking these helpful bacteria, the bacteria can coexist peacefully with the immune system.. Whats the trick to the microbiomes work with the immune system? Vitamin A - the bacteria moderate active vitamin A levels in the intestine, protecting the microbiome from an overactive immune ...
http://www.seerave.org/2018/12/21/gut-microbiome-regulates-the-intestinal-immune-system/
Bifidobacterium - WikipediaBifidobacterium - Wikipedia
The human infant gut is relatively sterile up until birth, where it takes up bacteria from its surrounding environment and its mother.[13] The microbiota that makes up the infant gut differs from the adult gut. An infant reaches the adult stage of their microbiome at around 3 years of age, when their microbiome diversity increases, stabilizes, and the infant switches over to solid foods. When breast-fed, infants are colonized earlier by Bifidobacterium when compared to babies that are primarily formula-fed.[14] Bifidobacterium is the most common bacteria in the infant gut microbiome.[15] There is more variability in genotypes over time in infants, making them less stable compared to the adult Bifidobacterium. Infants and children under 3 years old show low diversity in microbiome bacteria, but more diversity between individuals when compared to adults.[16] Reduction of Bifidobacterium and increase in diversity of the infant gut microbiome occurs with less breast-milk intake and increase of solid ...
https://en.wikipedia.org/wiki/Bifidobacterium
Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response<...
TY - JOUR. T1 - Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response. AU - Sethi, Vrishketan. AU - Kurtom, Saba. AU - Tarique, Mohammad. AU - Lavania, Shweta. AU - Malchiodi, Zoe. AU - Hellmund, Leonor. AU - Zhang, Li. AU - Sharma, Umakant. AU - Giri, Bhuwan. AU - Garg, Bharti. AU - Ferrantella, Anthony. AU - Vickers, Selwyn M.. AU - Banerjee, Sulagna. AU - Dawra, Rajinder. AU - Roy, Sabita. AU - Ramakrishnan, Sundaram. AU - Saluja, Ashok. AU - Dudeja, Vikas. N1 - Publisher Copyright: © 2018 AGA Institute. PY - 2018/7. Y1 - 2018/7. N2 - We studied the effects of gut microbiome depletion by oral antibiotics on tumor growth in subcutaneous and liver metastases models of pancreatic cancer, colon cancer, and melanoma. Gut microbiome depletion significantly reduced tumor burden in all the models tested. However, depletion of gut microbiome did not reduce tumor growth in Rag1-knockout mice, which lack mature T and B cells. Flow cytometry analyses demonstrated that gut microbiome ...
https://miami.pure.elsevier.com/en/publications/gut-microbiota-promotes-tumor-growth-in-mice-by-modulating-immune
Isolation and biochemical characterization of a metagenome-derived 3-deoxy- d -arabino-heptulosonate-7-phosphate synthase gene...Isolation and biochemical characterization of a metagenome-derived 3-deoxy- d -arabino-heptulosonate-7-phosphate synthase gene...
3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iβ-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The
https://amb-express.springeropen.com/articles/10.1186/s13568-019-0742-4/tables/1
Viral metagenomicsViral metagenomics
MEGAN MEtaGenome ANalyzer. A stand-alone metagenome analysis tool. MetaGeneMark MetaGeneMark for MetaGenome Gene Finding ... GOLD Genomes OnLine Database (GOLD). IMG/M The Integrated Microbial Genomes system, for metagenome analysis by the DOE-JGI. ... by metagenomic sequencing of viral nucleic acids and is frequently used to describe environmental shotgun metagenomes. Viral ...
https://en.wikipedia.org/wiki/Viral_metagenomics
MetaproteomicsMetaproteomics
The term was derived from "metagenome". Wilmes and Bond proposed the term "metaproteomics" for the large-scale characterization ... complement approaches that assess community composition based on gene copy counts such as 16S rRNA gene amplicon or metagenome ...
https://en.wikipedia.org/wiki/Metaproteomics
TALE-likesTALE-likes
"Pfam alignment: PF03377 metagenome (auto-generated match)". Retrieved 28 May 2019. Bertonati C, Duchateau P, Juillerat A, Silva ... Similar sequences found in metagenomes include EBN19408 and ECR81667. Whilst repeats of MOrTL1 and 2 both conform structurally ...
https://en.wikipedia.org/wiki/TALE-likes
List of sequenced algae genomesList of sequenced algae genomes
"Info - Symbiochloris reticulata Africa extracted metagenome v1.0". genome.jgi.doe.gov. Retrieved 2018-07-31. Prochnik SE, Umen ...
https://en.wikipedia.org/wiki/List_of_sequenced_algae_genomes
German Network for Bioinformatics InfrastructureGerman Network for Bioinformatics Infrastructure
Jaenicke, S; Albaum, SP; Blumenkamp, P; Linke, B; Stoye, J; Goesmann, A (2018). "Flexible metagenome analysis using the MGX ... Metagenome analysis), ASA³P (automated WGS analysis of bacterial cohorts), Bakta (annotation of bacterial genomes and plasmids ...
https://en.wikipedia.org/wiki/German_Network_for_Bioinformatics_Infrastructure
Human milk microbiomeHuman milk microbiome
Ward TL, Hosid S, Ioshikhes I, Altosaar I (May 2013). "Human milk metagenome: a functional capacity analysis". BMC Microbiology ...
https://en.wikipedia.org/wiki/Human_milk_microbiome
Wang Jun (scientist)Wang Jun (scientist)
"A catalog of the mouse gut metagenome". Nature Biotechnology. 33 (10): 1103-1108. doi:10.1038/nbt.3353. ISSN 1087-0156. PMID ...
https://en.wikipedia.org/wiki/Wang_Jun_(scientist)
K-merK-mer
Zhu, Zheng (2014). "Self-organizing approach for meta-genomes". Computational Biology and Chemistry. 53: 118-124. doi:10.1016/j ... Zhu, Jianfeng; Zheng, Wei-Mou (2014). "Self-organizing approach for meta-genomes". Computational Biology and Chemistry. 53: 118 ... Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino; Polikar, Robi; Sokhansanj, Bahrad (2008). "Metagenome Fragment ...
https://en.wikipedia.org/wiki/K-mer
MicrobiomeMicrobiome
The term microbiome is also sometimes confused with the metagenome. Metagenome is, however, clearly defined as a collection of ... Based on metagenome data, microbial genomes can be reconstructed. While first metagenome-assembled genomes were reconstructed ... Metagenome data provides a playground for new predictions, yet much more data is needed to strengthen the links between ... Viral metagenomes can be suggested as a semantically and scientifically better term. Co-occurrence networks help visualising ...
https://en.wikipedia.org/wiki/Microbiome
Nikos KyrpidesNikos Kyrpides
2006) An Experimental Metagenome Data Management and Analysis System. Bioinformatics 22, e359-67. PMID 16873494 Markowitz VM, ... 2015) Ten years of maintaining and expanding a microbial genome and metagenome analysis system. Trends in Microbiology 23(11): ... 2017) Protein Structure Determination using Metagenome sequence data. Science 355:294-298. PMID 28104891. GSC Board Members ... 2017) Critical Assessment of Metagenome Interpretation - a benchmark of computational metagenomics software. Nature Methods 14( ...
https://en.wikipedia.org/wiki/Nikos_Kyrpides
AlbuferaAlbufera
Ghai, Rohit (2012). "Metagenomes of Mediterranean Coastal Lagoons". Scientific Reports. 2: 490. doi:10.1038/srep00490. PMC ...
https://en.wikipedia.org/wiki/Albufera
Multiple displacement amplificationMultiple displacement amplification
"Assembling the Marine Metagenome, One Cell at a Time". PLOS ONE. 4 (4): e5299. Bibcode:2009PLoSO...4.5299W. doi:10.1371/journal ...
https://en.wikipedia.org/wiki/Multiple_displacement_amplification
Jens NielsenJens Nielsen
Karlsson FH, Tremaroli V, Nookaew I, Bergström G, Behre CJ, Fagerberg B, Nielsen J, Bäckhed F (2013). "Gut metagenome in ... He was involved in early studies on using metagenome sequencing for characterization of the gut microbiota and demonstrating ... "Symptomatic atherosclerosis is associated with an altered gut metagenome". Nat Commun. 3: 1245. Bibcode:2012NatCo...3.1245K. ...
https://en.wikipedia.org/wiki/Jens_Nielsen
IMES-4 RNA motifIMES-4 RNA motif
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
https://en.wikipedia.org/wiki/IMES-4_RNA_motif
Sørensen-Dice coefficientSørensen-Dice coefficient
logDice is also used as part of the Mash Distance for genome and metagenome distance estimation Finally, Dice is used in image ... "Mash: fast genome and metagenome distance estimation using MinHash." Genome biology 17.1 (2016): 1-14. Bray, J. Roger; Curtis, ...
https://en.wikipedia.org/wiki/Sørensen–Dice_coefficient
Computational genomicsComputational genomics
Ondov B, Treangen T, Melsted P, Mallonee A, Bergman N, Koren S, Phillippy A (2016). "Mash: fast genome and metagenome distance ...
https://en.wikipedia.org/wiki/Computational_genomics
Bloom filters in bioinformaticsBloom filters in bioinformatics
"Scaling metagenome sequence assembly with probabilistic de Bruijn graphs". Proceedings of the National Academy of Sciences. 109 ...
https://en.wikipedia.org/wiki/Bloom_filters_in_bioinformatics
Ocean-VII RNA motifOcean-VII RNA motif
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
https://en.wikipedia.org/wiki/Ocean-VII_RNA_motif
Machine learning in bioinformaticsMachine learning in bioinformatics
Databases exist for each type of biological data, for example for biosynthetic gene clusters and metagenomes. The National ... Cao L, Shcherbin E, Mohimani H (August 2019). "A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural ... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. PMC ... an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine ...
https://en.wikipedia.org/wiki/Machine_learning_in_bioinformatics
Solorina croceaSolorina crocea
A metagenome of Solorina crocea was reported in 2022. In addition to the fungal component of the lichen, the metagenome ... "Metagenomes of Lichens Solorina crocea and Peltigera canina". Microbiology Resource Announcements. 11 (1): e01000-21. doi: ...
https://en.wikipedia.org/wiki/Solorina_crocea
Termite-flg RNA motifTermite-flg RNA motif
March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
https://en.wikipedia.org/wiki/Termite-flg_RNA_motif
Metabolic gene clusterMetabolic gene cluster
Ondov B, Treangen T, Melsted P, Mallonee A, Bergman N, Koren S, Phillippy A (2016). "Mash: fast genome and metagenome distance ...
https://en.wikipedia.org/wiki/Metabolic_gene_cluster
IMES-2 RNA motifIMES-2 RNA motif
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. Bibcode: ...
https://en.wikipedia.org/wiki/IMES-2_RNA_motif
ROOL RNA motifROOL RNA motif
... in addition to phages and cow rumen metagenomes, as mentioned above. Within the Bacillota, they are present in a few species of ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
https://en.wikipedia.org/wiki/ROOL_RNA_motif
Cat foodCat food
"Effects of Dietary Fiber on the Feline Gastrointestinal Metagenome". Journal of Proteome Research. 11 (12): 5924-5933. doi: ...
https://en.wikipedia.org/wiki/Cat_food
Genome skimmingGenome skimming
... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. ISSN ...
https://en.wikipedia.org/wiki/Genome_skimming
HEARO RNA motifHEARO RNA motif
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
https://en.wikipedia.org/wiki/HEARO_RNA_motif
MetatranscriptomicsMetatranscriptomics
"Relating the metatranscriptome and metagenome of the human gut". Proceedings of the National Academy of Sciences of the United ... "Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes". Briefings in ... "Species-level functional profiling of metagenomes and metatranscriptomes". Nature Methods. 15 (11): 962-968. doi:10.1038/s41592 ...
https://en.wikipedia.org/wiki/Metatranscriptomics
ManA RNA motifManA RNA motif
March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
https://en.wikipedia.org/wiki/ManA_RNA_motif
MinHashMinHash
... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. ISSN ...
https://en.wikipedia.org/wiki/MinHash
KEGG MGENOME: T30366 (Metagenome)
Number of protein genes: ...
https://www.genome.jp/entry/gn:T30366
GitHub - voutcn/megahit: Ultra-fast and memory-efficient (meta-)genome assemblerGitHub - voutcn/megahit: Ultra-fast and memory-efficient (meta-)genome assembler
if the metagenome is complex (i.e., bio-diversity is high, for example soil metagenomes) ... It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single- ... MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Methods. ...
https://github.com/voutcn/megahit
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 | Nature CommunicationsPrecise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 | Nature Communications
Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 ... The increasing amount of sequenced microbial genomes and metagenomes requires platforms for efficient integrated analysis. Here ... as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. ... 3: Phylogenetic analysis of MAGs from 50 rural Ethiopian metagenomes.. a Occurrence of the 20 most prevalent SGBs among 50 ...
https://www.nature.com/articles/s41467-020-16366-7?error=cookies_not_supported&code=9a92fab5-818e-4783-a563-11f82fc81dde
British Library EThOS: Functional metagenomics : metagenome mining for industrial biocatalysisBritish Library EThOS: Functional metagenomics : metagenome mining for industrial biocatalysis
In total 100 genes were identified for retrieval from the two metagenomes, 69 of which were successfully cloned. From the 69 ... Retrieval of targeted genes from the two metagenomes and the assay of active enzymes stand as proof of principle, that a ... in order to maximise the number of active enzymes that could be retrieved from the metagenome. ... sequence directed method gives constructive access to metagenomes and importantly improves on the numbers, types and diversity ...
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.779108
KEGG Metagenome: T30065KEGG Metagenome: T30065
Genes and Proteins Orthologs, modules and networks 00001 KEGG Orthology (KO) ...
https://www.kegg.jp/kegg-bin/show_organism?menu_type=gene_catalogs&org=T30065
talks.cam : Challenges in pathogen detection with metagenome classification techniquestalks.cam : Challenges in pathogen detection with metagenome classification techniques
Challenges in pathogen detection with metagenome classification techniques. Add to your list(s) Download to your calendar using ... University of Cambridge , Talks.cam , Isaac Newton Institute Seminar Series , Challenges in pathogen detection with metagenome ...
http://talks.cam.ac.uk/talk/index/66183
Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT) - LTEREcological Metagenome-derived Reference Genomes and Traits (EMERGENT) - LTER
The Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT) synthesis project connects genomic information about ...
https://lternet.edu/working-groups/emergent/
Sequenced genes (ureC gene) and a metagenome from Archaea in Arctic and Antarctic marine environmentsSequenced genes (ureC gene) and a metagenome from Archaea in Arctic and Antarctic marine environments
... Citation. Alonso-Saez L, ... and a metagenome from Archaea in Arctic and Antarctic marine environments. Version 1.1. SCAR - Microbial Antarctic Resource ... as well as a metagenome (454 pyrosequencing) the Beaufort Sea. Sampling Description. Study Extent. Water samples were collected ...
https://www.gbif.org/dataset/53fb0f04-3ba5-4fe8-8ea4-0511914bd0c3
Our early life microbial metagenome guides developmental phenotypes - The Evolution and Medicine ReviewOur early life microbial metagenome guides developmental phenotypes - The Evolution and Medicine Review
Our early life microbial metagenome guides developmental phenotypes" ...
https://evmedreview.com/our-early-life-microbial-metagenome-guides-developmental-phenotypes/
BIOCHEMICAL AND BIOPHYSICAL PROPERTIES OF A METAGENOME-DERIVED GH5 ENDOGLUCANASE DISPLAYING AN UNCONVENTIONAL DOMAIN...BIOCHEMICAL AND BIOPHYSICAL PROPERTIES OF A METAGENOME-DERIVED GH5 ENDOGLUCANASE DISPLAYING AN UNCONVENTIONAL DOMAIN...
The aim of this work was to perform the biochemical and biophysical characterization of CelE2, a soil metagenome derived ... Home / KnowledgeBase Articles / BIOCHEMICAL AND BIOPHYSICAL PROPERTIES OF A METAGENOME-DERIVED GH5 ENDOGLUCANASE DISPLAYING AN ... BIOCHEMICAL AND BIOPHYSICAL PROPERTIES OF A METAGENOME-DERIVED GH5 ENDOGLUCANASE DISPLAYING AN UNCONVENTIONAL DOMAIN ... BIOCHEMICAL AND BIOPHYSICAL PROPERTIES OF A METAGENOME-DERIVED GH5 ENDOGLUCANASE DISPLAYING AN UNCONVENTIONAL DOMAIN ...
https://jascoinc.com/knowledgebase/biochemical-and-biophysical-properties-of-a-metagenome-derived-gh5-endoglucanase-displaying-an-unconventional-domain-architecture/
MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly | BMC Bioinformatics | Full TextMetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly | BMC Bioinformatics | Full Text
MetaVelvet-SL is a short-read de novo metagenome assembler that partitions a multi-species de Bruijn graph into single-species ... MetaVelvet-DL provides more accurate de novo assemblies of whole metagenome data. The authors believe that this improvement can ... Assembly of the Critical Assessment of Metagenome Interpretation (CAMI) dataset showed that after removing chimeric assemblies ... The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the ...
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03737-6/figures/4
Bergen Open Research Archive: Metagenome-assembled genome distribution and key functionality highlight importance of aerobic...Bergen Open Research Archive: Metagenome-assembled genome distribution and key functionality highlight importance of aerobic...
Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard ...
https://bora.uib.no/bora-xmlui/handle/11250/2757061
JYX - Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight WomenJYX - Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women
Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women. ... We determined whether six-weeks endurance exercise, without changing diet, affected the gut metagenome and systemic metabolites ... Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women. Frontiers ... studies in larger cohorts to determine whether exercise types other than endurance exercise also modify the gut metagenome.. ...
https://jyx.jyu.fi/handle/123456789/59950
GenomePeek - An online tool for prokaryotic and metagenome analysis [PeerJ Preprints]GenomePeek - An online tool for prokaryotic and metagenome analysis [PeerJ Preprints]
The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing ... GenomePeek - An online tool for prokaryotic and metagenome analysis. Katelyn McNair​1,2, Rob Edwards1,2,3,4 ... genome, metagenome, taxonomic, bacteria, sequencing, population, distribution, archaea, abundance. Copyright. © 2014 McNair et ... The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing ...
https://peerj.com/preprints/525/
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and...Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and...
Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can ... Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes ... spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous ... rectale in 146 publicly available metagenomes from wild non-hominid primates as well as 29 metagenomes from wild non-human ...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02042-y
Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow...Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow...
From: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a ...
https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-016-0534-x/tables/5
Critical assessment of metagenome interpretation - A benchmark of metagenomics software<...Critical assessment of metagenome interpretation - A benchmark of metagenomics software<...
Critical assessment of metagenome interpretation - A benchmark of metagenomics software. Nature Methods. 2017 Nov 1;14(11):1063 ... Critical assessment of metagenome interpretation - A benchmark of metagenomics software. / Sczyrba, Alexander; Hofmann, Peter; ... Critical assessment of metagenome interpretation - A benchmark of metagenomics software. Alexander Sczyrba, Peter Hofmann, ... Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about ...
https://research-portal.uea.ac.uk/en/publications/critical-assessment-of-metagenome-interpretation-a-benchmark-of-m
Approaches to scaling and improving metagenome sequence assembly | MSU LibrariesApproaches to scaling and improving metagenome sequence assembly | MSU Libraries
We evaluate the algorithm with an E. coli dataset as well as a mock human gut metagenome dataset and find that the error ... we develop approaches to tackle the current shortcomings in metagenome sequence assembly. First, we devise the novel use of a ...
https://d.lib.msu.edu/etd/1869
PRJNA410099 - marine metagenome - OmicsDI
marine metagenome. Project description:Metatranscriptome of deep ocean microbial communities from Pacific Ocean - MP1785 ... marine metagenome. Project description:Metatranscriptome of deep ocean microbial communities from Pacific Ocean - MP2049 ... marine metagenome. Project description:Metatranscriptome of deep ocean microbial communities from Pacific Ocean - MP2156 ... marine metagenome. Project description:Metatranscriptome of deep ocean microbial communities from Pacific Ocean - MP1602 ...
https://www.omicsdi.org/dataset/omics_ena_project/PRJNA410099
R16M crust metagenome (ID: SAMD00110608) - DeepseaDBR16M crust metagenome (ID: SAMD00110608) - DeepseaDB
Keywords: GSC:MIxS;MIMS:5.0 PRJDB6686: Fe-Mn crust metagenome
https://db.cngb.org/deepseadb/samples/SAMD00110608
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling | Sage...A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling | Sage...
A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling. Posted on ... The authors present a restriction enzyme reduced representation sequencing (RE-RRS) method for metagenome profiling of ...
https://sagescience.com/citation/a-restriction-enzyme-reduced-representation-sequencing-approach-for-low-cost-high-throughput-metagenome-profiling/
An Exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.An Exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.
Shotgun metagenome sequencing of a Sudanese toombak snuff tobacco: genetic attributes of a high tobacco-specific nitrosamine ... Title : Shotgun metagenome sequencing of a Sudanese toombak snuff tobacco: genetic attributes of a high tobacco-specific ... An Exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis.. ... These results present novel findings from the first combined metagenome and metatranscriptome of a commercial tobacco product. ...
https://stacks.cdc.gov/view/cdc/84046
Station and train surface microbiomes of Mexico Citys metro (subway/underground) | Scientific ReportsStation and train surface microbiomes of Mexico City's metro (subway/underground) | Scientific Reports
Releases · mmassaviol / microbial metagenome · GitLabReleases · mmassaviol / microbial metagenome · GitLab
Bio-GO-SHIP: Generating high resolution surface ocean metagenomes through international collaboration | Research Data at...Bio-GO-SHIP: Generating high resolution surface ocean metagenomes through international collaboration | Research Data at...
This work builds upon the success of previous ocean metagenome projects such as the Global Ocean Survey, Tara Oceans, and ... At the same time, our dataset highlights significant gaps in our measurements of the global ocean metagenome. For example, high ... Bio-GO-SHIP: Generating high resolution surface ocean metagenomes through international collaboration Sampling the biology of ... Bio-GO-SHIP: Generating high resolution surface ocean metagenomes through international collaboration Sampling the biology of ...
https://researchdata.springernature.com/posts/bio-go-ship-generating-high-resolution-surface-ocean-metagenomes-through-international-collaboration?user_id=alyse-larkin
Benchmarking different approaches for Norovirus genome assembly in metagenome samples | BMC Genomics | Full TextBenchmarking different approaches for Norovirus genome assembly in metagenome samples | BMC Genomics | Full Text
Not all metagenome assemblies are equal and the choice in the workflow depends on the species studied and the prior steps to ... or from metagenome samples, poses a challenge for the scientific community due to the coexistence of several viral quasispecies ...
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08067-2/tables/3
Minimal Metagenome Sequence Analysis Standard | BiŌkeanósMinimal Metagenome Sequence Analysis Standard | BiŌkeanós
metagenome metasource: Fairsharing.org version: FAIRsharing.org: MINIMESS; Minimal Metagenome Sequence Analysis Standard; DOI: ... Minimal Metagenome Sequence Analysis Standard Names. More detailed information about this field from each metasource. × ... Get the most out of your metagenome: computational analysis of environmental sequence data PubMed citations: 59. 59 articles ... Minimal Metagenome Sequence Analysis Standard metasource: Fairsharing.org version: FAIRsharing.org: MINIMESS; Minimal ...
https://biokeanos.com/source/Minimal%20Metagenome%20Sequence%20Analysis%20Standard
Status - Population metagenomics of uncultured photosynthetic marine eukaryotes: Uncultured metagenome CN11 C50 N6 SortRC 1Status - Population metagenomics of uncultured photosynthetic marine eukaryotes: Uncultured metagenome CN11 C50 N6 SortRC 1
Population metagenomics of uncultured photosynthetic marine eukaryotes: Uncultured metagenome CN11_C50_N6_SortRC_1 ...
https://genome.jgi.doe.gov/portal/pages/projectStatus.jsf?db=Uncmet6_SortRC_1_2
Home - Lobaria pulmonaria Switzerland extracted metagenome v1.0Home - Lobaria pulmonaria Switzerland extracted metagenome v1.0
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Critical Assessment of Metagenome Interpretation (CAMI) - Workshop - Microbiome COSICritical Assessment of Metagenome Interpretation (CAMI) - Workshop - Microbiome COSI
The interpretation of metagenomes relies on sophisticated computational methods for read assembly, binning, and taxonomic ... In 2014, the Critical Assessment of Metagenome Interpretation (CAMI) initiative was founded to address this need.. Based on the ...
https://www.microbiome-cosi.org/cami/cami2-workshop
Critical Assessment of Metagenome InterpretationMetagenomicsObtaining metagenome-assembled genomesGenesHigh-throughput metagenomeGenomes from metagenomesBacterialReference genomesMetatranscriptomeGenome assemblySequenceShotgunIsolatesV1.0Single genomeMicrobial genomesGenomicTaxonomicSequencingAnnotationSoilAnalysisMethodsViralShowGlobal
Critical Assessment of Metagenome Interpretation2
  • The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. (uea.ac.uk)
  • In 2014, the Critical Assessment of Metagenome Interpretation (CAMI) initiative was founded to address this need. (microbiome-cosi.org)
Metagenomics2
  • One thought on "Open Metagenomics Highlight - Metagenome Annotation using massively parallel undergrads. (phylogenomics.me)
  • Functional metagenomics is a powerful tool to identify novel enzymes followed by the construction of metagenome-based enzyme libraries. (who.int)
Obtaining metagenome-assembled genomes1
  • Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. (nature.com)
Genes11
  • A variety of cloning methodologies were tested, to streamline the process between identification, amplification and expression of the genes, in order to maximise the number of active enzymes that could be retrieved from the metagenome. (bl.uk)
  • In total 100 genes were identified for retrieval from the two metagenomes, 69 of which were successfully cloned. (bl.uk)
  • Retrieval of targeted genes from the two metagenomes and the assay of active enzymes stand as proof of principle, that a sequence directed method gives constructive access to metagenomes and importantly improves on the numbers, types and diversity of enzymes produced when compared with other metagenomic screening methods. (bl.uk)
  • Microbial dataset containing sequenced genes (ureC gene) from Thaumarchaeota from the Beaufort Sea (Arctic) and the Amundsen Sea (Antarctica), as well as a metagenome (454 pyrosequencing) the Beaufort Sea. (gbif.org)
  • From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. (biokeanos.com)
  • The analysis of both the metagenome of the consortium and the reconstructed metagenome-assembled genomes show that the most abundant bacterial genus in the consortium, Acidocella , possess many of the genes required for the degradation of diesel fuel aromatic hydrocarbons, which are often the most toxic component. (springeropen.com)
  • Functional orthologues for peroxisome proliferator-activated receptor (PPAR) pathway in endocrine system were analyzed from gut bacterial metagenome with Kyoto Encyclopaedia of Genes and Genomes. (luke.fi)
  • Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilit ate intra- and intercellular gene transfer. (cdc.gov)
  • The recent success gut microbial genes, obtained after has fantastic potential, it has only of faecal microbiota transplantation, sequencing whole faecal microbiota been about 10 years since the sci- especially in the context of Clostridi- metagenomes from 124 European indi- entific community first realized its im- um difficile infection, argues for such viduals [4]. (who.int)
  • Barrier agains t pathogen s gut bacterial genes in the MetaHIT ation when attempting to extrapolate [10], although Proteobacteria, Ver- catalogue were also well represent- results obtained in mouse models to rucomicrobia, and Fusobacteria are ed in the other metagenomes that the situation in humans. (who.int)
  • In 2014, the MetaHIT consortium by bacteria of the genera Lacto- alytical method used: 66 from 16S published an integrated catalogue bacillus , Prevotella , and Sneathia , rDNA sequencing [11] or 57 from of 10 million bacterial genes de- whereas for infants delivered by whole-metagenome sequencing [5]. (who.int)
High-throughput metagenome1
  • As current read clustering approaches cannot handle the large datasets arising from high-throughput metagenome sequencing, a novel read clustering approach is needed. (nih.gov)
Genomes from metagenomes1
  • Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. (biomedcentral.com)
Bacterial1
  • The large number of publicly available metagenomic cohorts and accurate methods for genome reconstruction from metagenomes thus provide an unprecedented opportunity to gain insights into this otherwise relatively poorly investigated bacterial species using metagenomic data at a global scale. (biomedcentral.com)
Reference genomes4
  • 10,000 metagenomes, and while GToTree automatically retrieves reference genomes from public resources, it does not provide access to MAGs or phylogenetic markers for species-level clades. (nature.com)
  • The Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT) synthesis project connects genomic information about the soil microbiome with the broader ecological context. (lternet.edu)
  • Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. (bvsalud.org)
  • We introduce the operational genomic unit (OGU) method , a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. (bvsalud.org)
Metatranscriptome1
  • An Exploration of smokeless tobacco product nucleic acids: a combined metagenome and metatranscriptome analysis. (cdc.gov)
Genome assembly1
  • It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly. (github.com)
Sequence3
  • Despite these algorithmic advances, DNA sequence assembly still scales poorly due to errors and computer memory inefficiency.In this dissertation, we develop approaches to tackle the current shortcomings in metagenome sequence assembly. (msu.edu)
  • The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. (gfz-potsdam.de)
  • To test this hypothesis we propose to exome-sequence 400 severely obese (BMI>35kg/m2) patients and 100 lean controls benefiting from an existing project (EU-MetaCardis) in which 80% of participants have their gut metagenomes currently in sequencing. (france-genomique.org)
Shotgun2
  • Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing. (biomedcentral.com)
  • In this article, we propose OGRE, an Overlap Graph-based Read clustEring procedure for high-throughput sequencing data, with a focus on shotgun metagenomes. (nih.gov)
Isolates2
  • Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses. (nature.com)
  • This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission. (cdc.gov)
V1.02
  • MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. (github.com)
  • Please confirm that you want to SAVE all your changes for 'Lobaria pulmonaria Switzerland extracted metagenome v1.0' . (doe.gov)
Single genome1
  • The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. (peerj.com)
Microbial genomes1
  • With such a volume of microbial genomes generated at a wide range of qualities and completeness, however, there are no scalable phylogenetic methods that can easily tackle these challenges for investigators studying genomes and metagenomes. (nature.com)
Genomic2
  • The microbes that live in an environment can be identified from the combined genomic material, also referred to as the metagenome. (nih.gov)
  • 7468 /organism="Norovirus GII.6" /mol_type="genomic RNA" /isolation_source="stool" /host="Homo sapiens" /db_xref="taxon:499193" /clone="V4B" /environmental_sample /country="Venezuela" /collection_date="2015" /metagenome_source="gut metagenome" /note="metagenomic" gene 5. (cdc.gov)
Taxonomic2
  • Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. (uea.ac.uk)
  • The interpretation of metagenomes relies on sophisticated computational methods for read assembly, binning, and taxonomic classification. (microbiome-cosi.org)
Sequencing5
  • Metagenome sequencing of a coastal marine microbial community from monterey bay, california. (omicsdi.org)
  • The authors present a restriction enzyme reduced representation sequencing (RE-RRS) method for metagenome profiling of livestock rumen microbial communities. (sagescience.com)
  • Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. (biokeanos.com)
  • A study that benchmarks six high molecular weight DNA extraction strategies (commercially available kits, phenol-chloroform extraction, and agarose encasement followed by agarase digestion) for long-read sequencing of metagenomes with MinION. (merenlab.org)
  • Sequencing a metagenome can result in large volumes of sequencing reads. (nih.gov)
Annotation2
Soil1
  • The aim of this work was to perform the biochemical and biophysical characterization of CelE2, a soil metagenome derived endoglucanase. (jascoinc.com)
Analysis2
  • In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. (gfz-potsdam.de)
  • Our consortium (ICAN, CNG, MGP) has the right set of expertise (clinical, genome, metagenome, data analysis and integration) to conduct this project C-METAGENOB. (france-genomique.org)
Methods1
  • Many methods exist for more targeted microbial genome and metagenome phylogenetics. (nature.com)
Viral1
  • We studied the marine viral metagenome (virome) of four oceanic regions. (plos.org)
Show1
  • Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. (frontiersin.org)
Global1
  • This work builds upon the success of previous ocean metagenome projects such as the Global Ocean Survey , Tara Oceans , and bioGEOTRACES . (springernature.com)
Station and train surface microbiomes of Mexico City's metro (subway/underground) | Scientific Reports
Station and train surface microbiomes of Mexico City's metro (subway/underground) | Scientific Reports (nature.com)
How does eukaryotic gene prediction work? | Nature Biotechnology
How does eukaryotic gene prediction work? | Nature Biotechnology (nature.com)
Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships | Nature Microbiology
Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships | Nature Microbiology (nature.com)
Frontiers | Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
Frontiers | Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla (frontiersin.org)
A faecal microbiota signature with high specificity for pancreatic cancer | Gut
A faecal microbiota signature with high specificity for pancreatic cancer | Gut (gut.bmj.com)
Fuels
Fuels (mdpi.com)
Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis | Gut
Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis | Gut (gut.bmj.com)
Program Meetings and Workshops
Program Meetings and Workshops (jgi.doe.gov)
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 | eLife
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 | eLife (elifesciences.org)
The Center's Research Projects
The Center's Research Projects (bgsu.edu)
Sarah STRYCHARZ | Research Biologist | PhD | United States Naval Research Laboratory, DC | NRL | Center for Biomolecular...
Sarah STRYCHARZ | Research Biologist | PhD | United States Naval Research Laboratory, DC | NRL | Center for Biomolecular... (researchgate.net)
Progressive Cactus is a multiple-genome aligner for the thousand-genome era | Nature
Progressive Cactus is a multiple-genome aligner for the thousand-genome era | Nature (nature.com)
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage | Nature Communications
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage | Nature Communications (nature.com)
Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs | BMC Genomics | Full Text
Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs | BMC Genomics | Full Text (bmcgenomics.biomedcentral.com)
Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT) - LTER
Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT) - LTER (lternet.edu)
Characterization of Microsatellite Loci in the Lichen-Forming Fungus Cetraria aculeata (Parmeliaceae, Ascomycota)
Characterization of Microsatellite Loci in the Lichen-Forming Fungus Cetraria aculeata (Parmeliaceae, Ascomycota) (bioone.org)
Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes - Volume 14, Number 10-October 2008 - Emerging Infectious...
Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes - Volume 14, Number 10-October 2008 - Emerging Infectious... (wwwnc.cdc.gov)
Figure 2 - Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes - Volume 14, Number 10-October 2008 - Emerging...
Figure 2 - Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes - Volume 14, Number 10-October 2008 - Emerging... (wwwnc.cdc.gov)
Figure 1 - Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes - Volume 14, Number 10-October 2008 - Emerging...
Figure 1 - Rise and Persistence of Global M1T1 Clone of Streptococcus pyogenes - Volume 14, Number 10-October 2008 - Emerging... (wwwnc.cdc.gov)
Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds |...
Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds |... (nature.com)
Publications | Externwebben
Publications | Externwebben (slu.se)
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale...
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale... (microbiomejournal.biomedcentral.com)
Frontiers | Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern...
Frontiers | Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern... (frontiersin.org)
Permalink
Permalink (scienceblogs.com)
Frontiers | Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland
Frontiers | Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland (frontiersin.org)
APC News | University College Cork
APC News | University College Cork (ucc.ie)