A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
A order of gram-negative bacteria whose members are found in a variety of aquatic habitats as well as animal hosts.
The genetic complement of a BACTERIA as represented in its DNA.
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.
The relationships of groups of organisms as reflected by their genetic makeup.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.
The variety of all native living organisms and their various forms and interrelationships.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
Generally refers to the digestive structures stretching from the MOUTH to ANUS, but does not include the accessory glandular organs (LIVER; BILIARY TRACT; PANCREAS).
A group of different species of microorganisms that act together as a community.
An order of photosynthetic bacteria representing a physiological community of predominantly aquatic bacteria.
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.
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.
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).
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
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.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.
The systematic study of the complete DNA sequences (GENOME) of organisms.
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.
Refuse liquid or waste matter carried off by sewers.
A genus of SPONGES in the family Chalinidae characterized by unispicular secondary lines in the choanosomal skeleton.
A genus of shallow-cupped SPONGES with a broad base in the family Theonellidae. They are characterized by ectosomal spicules dominated by phyllotriaenes.
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).
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.
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.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Organisms that live in water.
Databases devoted to knowledge about specific genes and gene products.
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)
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.
A phylum of bacteria comprised of three classes: Bacteroides, Flavobacteria, and Sphingobacteria.
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.
The discarding or destroying of liquid waste products or their transformation into something useful or innocuous.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
Enzymes which catalyze the endohydrolysis of 1,4-beta-D-xylosidic linkages in XYLANS.
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.
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.
Physiological processes and properties of BACTERIA.
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.
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.
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.
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.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
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)
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).
Sequential operating programs and data which instruct the functioning of a digital computer.
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)
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.
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.
The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.
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.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
Software designed to store, manipulate, manage, and control data for specific uses.
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.
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)
Viruses whose hosts are bacterial cells.
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.
Proteins found in any species of bacterium.
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).
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
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.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Genotypic differences observed among individuals in a population.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Excrement from the INTESTINES, containing unabsorbed solids, waste products, secretions, and BACTERIA of the DIGESTIVE SYSTEM.
The portion of an interactive computer program that issues messages to and receives commands from a user.
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 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.
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
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 ...
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: ...
The goal of the Human Microbiome Project is to characterize the human microbiome and analyze its role in human health and disease.
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
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 ...
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
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. ...
via +Humberto González-Díaz *NIH Human Microbiome Project*Data Portalhttp://bit.ly/LhsWi2 | Complex Insight - Understanding our world
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
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
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 ...
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 ...
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
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 ...
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
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
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 ...
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 ...
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 ...
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 ...
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 ...
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
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
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 ...
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 ...
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
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 ...
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 ...
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 ...
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
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 ...
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.. ...
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 ...
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
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 ...
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 ...
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...
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
Gelatin tannate ameliorates acute colitis in mice by reinforcing mucus layer and modulating gut microbiota composition: Emerging role for gut barrier protectors in IBD? ...
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. ...
Interrelationship between gut microbiota composition and host metabolic parameters significantly modified by arabinoxylan supplementation.Green connections indi
To characterize gene expression in the gut microbiome, we analyzed cDNA and DNA datasets obtained from sequencing total community cDNA and DNA prepared from the two fecal samples of TS28 and TS29. All sequencing reads were mapped against the database of 122 gut microbial genomes and the microbiome bins (Metatranscriptome analysis in SI Text). The results revealed marked differences in gene abundance and expression (Figs. S6 and S7). In all cases, technical replicates of each microbiome and metatranscriptome (n = 3-4) clustered together; this clustering was robust to subsampling by COG functional categories (Fig. S6). Microbiome profiles showed the highest average correlation between individuals (R2 = 0.37), relative to metatranscriptomes (R2 = 0.12) and the relative abundance of species-level phylotypes (R2 = 0.18). As with the microbiome, rarefaction analysis of the metatranscriptome revealed that the number of expressed genes and gene clusters continues to increase even after 500,000 mapped ...
DUBLIN--(BUSINESS WIRE)--The Human Microbiome Market - Growth, Trends, COVID-19 Impact and Forecast (2021 - 2026) report has been added to ResearchAndMarkets.coms offering.The global human microbiome market is expected to register a CAGR of nearly 17% over the forecast period.In recent times, the human microbiome...
A pleiotropic missense variant in SLC39A8 is associated with Crohns disease and human gut microbiome composition. Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, DAmato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Buning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan S, Torkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DPB, Duerr RH. A pleiotropic missense variant in SLC39A8 is associated with Crohns disease and human gut microbiome composition. Gastroenterology 2016;151:724-732 ...
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.
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 ...
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 ...
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 ...
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 …
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...
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 ...
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 ...
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
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 ...
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), ...
What is Vaginal Microbiome Dysbiosis? Does it matter, Yes…The vaginal microbiome is a symbiotic relationship between good & bad bacteria.
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
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
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
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 ...
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 ...
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, ...
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...
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 ...
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 ...
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
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 ...
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.
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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.
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 ...
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 ...
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 ...
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 ...
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 ...
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
Using DNA Microarrays to Study Host-Microbe Interactions, info about Medicine: Medical Specialties: Microbiology: Using DNA Microarrays to Study Host-Microbe Interactions
Title:Colorectal Cancer Microenvironment: Among Nutrition, Gut Microbiota, Inflammation and Epigenetics. VOLUME: 19 ISSUE: 4. Author(s): Paolo Garagnani, Chiara Pirazzini and Claudio Franceschi. Affiliation:Department of Experimental Pathology, Alma Mater Studiorum, University of Bologna, via S.Giacomo 14, 40126 Bologna, Italy; Interdept. Centre for Bioinformatics, Biophysicsand Biocomplexity L. Galvani, Alma Mater Studiorum, University of Bologna, via Selmi 3, 40126 Bologna, Italy; via San Giacomo 12, 40126 Bologna, Italy.. Keywords:Colorectal cancer, inflammation, aging, gut microbiota, epigenetic, nutrition. Abstract:Colorectal cancer (CRC) is a major health problem causing significant morbidity and mortality. During the last decade, results from different studies indicate that the pathogenetic mechanisms of CRC encompass tumour microenvironment, emphasizing a tight correlation with aging, inflammation, nutrition, gut microbiome composition and epigenetic modifications. Aging is one of the ...
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. ...
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 ...
"Pfam alignment: PF03377 metagenome (auto-generated match)". Retrieved 28 May 2019. CS1 maint: discouraged parameter (link) ... Similar sequences found in metagenomes include EBN19408 and ECR81667. Whilst repeats of MOrTL1 and 2 both conform structurally ...
"Info - Symbiochloris reticulata Africa extracted metagenome v1.0". genome.jgi.doe.gov. Retrieved 2018-07-31. Prochnik SE, Umen ...
Jaenicke, S; Albaum, SP; Blumenkamp, P; Linke, B; Stoye, J; Goesmann, A (2018). "Flexible metagenome analysis using the MGX ... Metagenome analysis) and many more. de.NBI tools are also registered and searchable in the ELIXIR Tools and Data Services ...
Ward TL, Hosid S, Ioshikhes I, Altosaar I (May 2013). "Human milk metagenome: a functional capacity analysis". BMC Microbiology ...
"A catalog of the mouse gut metagenome". Nature Biotechnology. 33 (10): 1103-1108. doi:10.1038/nbt.3353. ISSN 1087-0156. PMID ...
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 ...
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( ...
Ghai, Rohit (2012). "Metagenomes of Mediterranean Coastal Lagoons". Scientific Reports. 2: 490. doi:10.1038/srep00490. PMC ...
Further genomes were resolved by culture-independent metagenome binning. The two Nitrospina species are, however, distantly ...
"Assembling the Marine Metagenome, One Cell at a Time". PLOS ONE. 4 (4): e5299. Bibcode:2009PLoSO...4.5299W. doi:10.1371/journal ...
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 demonstrate that ... "Symptomatic atherosclerosis is associated with an altered gut metagenome". Nat Commun. 3: 1245. Bibcode:2012NatCo...3.1245K. ...
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
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, ...
"Scaling metagenome sequence assembly with probabilistic de Bruijn graphs". Proceedings of the National Academy of Sciences. 109 ...
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/ ...
Based on metagenome data, microbial genomes can be reconstructed. While first metagenome-assembled genomes were reconstructed ... The term microbiome is also sometimes confused with the metagenome. Metagenome is, however, clearly defined as a collection of ... 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. Microbes interact with one another, and ...
... in addition to phages and cow rumen metagenomes, as mentioned above. Within the Firmicutes, they are present in a few species ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
"Effects of Dietary Fiber on the Feline Gastrointestinal Metagenome". Journal of Proteome Research. 11 (12): 5924-5933. doi: ...
... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. ISSN ...
"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 ...
PAPRICA is a metagenome prediction tool based on placing input 16S rRNA gene sequences into a known phylogenetic tree based ... This gives a prediction for the contribution of each OTU to the overall gene content of the sample (the metagenome). Finally, ... Okuda et al., 2012 published a similar method that used a bounded k-Nearest Neighbor approach to predict virtual metagenomes. ... Piphillin is a tool produced by the company Second Genome that produces metagenome predictions based on nearest-neighbour ...
Initial work in this area detected homologs of known bacterial RNAs in such metagenome samples. Many of these RNA sequences ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-9. doi:10.1038/ ...
Luckily, there are metagenome-specific assemblers to help, since, if hundreds of strains are present, the sequencing depth ... Once a metagenome is assembled, it is possible to infer the functional potential of the microbiome. The computational ... It is argued that this is the definition of metagenome, which combined with the environment constitutes the microbiome. ... the term human metagenome has the same meaning. Humans are colonized by many microorganisms, with approximately the same order ...
... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17 (1): 132. doi:10.1186/s13059-016-0997-x. PMC ...
GOLLD RNAs were originally detected based on metagenome sequences of DNA isolated from Lake Gatun in Panama. However, they are ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
... data and the second using metagenome (DNA) data. These RNAs are present in environmental sequences, and as of 2009 are not ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-659. doi:10.1038/ ...
"Assembling the marine metagenome, one cell at a time". PLOS ONE. 4 (4): e5299. Bibcode:2009PLoSO...4.5299W. doi:10.1371/ ... "Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes". Microbiome. 6 (1): ...
urban metagenome[Taxonomy ID: 1591089]. unclassified sequences; metagenomes; ecological metagenomes; urban metagenome ... urban metagenome. New York City MTA subway samples Metagenome. A survey of the NYC subway system to study the microbiome of a ...
microbial mat metagenome[Taxonomy ID: 527640]. unclassified sequences; metagenomes; ecological metagenomes; microbial mat ... microbial mat metagenome microbial mat metagenome. Metagenome isolated from subsurface mine microbial mat ... microbial mat metagenome. Metagenome isolated from subsurface mine microbial mat. Microbial mat flourished along with the hot ...
Bioinformatics tool for metagenome analysis. Los Alamos creates bioinformatics tool for metagenome analysis. Scientists have ... In a paper this week in the journal Nucleic Acids Research, "Accurate read-based metagenome characterization using a ... metagenome datasets that can be used to re-validate any current or future tools; and 3) addresses the issue of false positives ... and then it classifies the individual metagenome sequences or "reads." They have established a unique method to query these ...
Novel cold-adapted esterase MHlip from an Antarctic soil metagenome. Biology. 2013;2:177-88.CrossRefGoogle Scholar ... Cloning the metagenome: culture-independent access to the diversity and functions of the uncultivated microbial world. In: ... Searching the "Needle in the Haystack" in the Antarctic Soil Metagenome. Once the soil-derived metagenomic library is finally ... Daniel R. The soil metagenome-a rich resource for the discovery of novel natural products. Curr Opin Biotechnol. 2004;15(3):199 ...
Relating the metatranscriptome and metagenome of the human gut. Eric A. Franzosa, Xochitl C. Morgan, Nicola Segata, Levi ... 5E). Thus, although subjects share a highly conserved gut metagenome derived from microbial contributors that are quite ... Functional diversity at the transcriptional level suggests a pattern of subject-specific metagenome regulation. (A) The 10 most ... We next investigated possible global models for metagenome vs. metatranscriptome regulation in the gut microbiota. Among the ...
The indoor atmosphere is an ecological unit that impacts on public health. To investigate the composition of organisms in this space, we applied culture-independent approaches to microbes harvested from the air of two densely populated urban buildings, from which we analyzed 80 megabases genomic DNA sequence and 6000 16S rDNA clones. The air microbiota is primarily bacteria, including potential opportunistic pathogens commonly isolated from human-inhabited environments such as hospitals, but none of the data contain matches to virulent pathogens or bioterror agents. Comparison of air samples with each other and nearby environments suggested that the indoor air microbes are not random transients from surrounding outdoor environments, but rather originate from indoor niches. Sequence annotation by gene function revealed specific adaptive capabilities enriched in the air environment, including genes potentially involved in resistance to desiccation and oxidative damage. This baseline index of air
... is a partial list of those usages pertaining to biology or the overall biological metagenome. ... Retrieved from "https://en.wikiversity.org/w/index.php?title=Dominant_group/Metagenome/Term_test&oldid=2146513" ...
More about Cloning the Metagenome to Access the Biodiversity of Unculturable Bacteria * biodiversity Essay. 476 Words , 2 Pages ... Cloning the Metagenome to Access the Biodiversity of Unculturable Bacteria 1461 Words 6 Pages ...
Pande Putu Erawijantari, Sayaka Mizutani, Hirotsugu Shiroma, Satoshi Shiba, Takeshi Nakajima, Taku Sakamoto, Yutaka Saito, Shinji Fukuda, Shinichi Yachida, Takuji Yamada ...
Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. Environmental Microbiology ...
tr,A0A0W8FA01,A0A0W8FA01_9ZZZZ Arsenate reductase OS=hydrocarbon metagenome OX=938273 GN=ASZ90_012621 PE=4 SV=1 ...
Phase Genomics Pushes Forward With Hi-C-Based Metagenome Deconvolution Kit, Service. Oct 06, 2017 ... Home » Phase Genomics Pushes Forward With Hi-C-Based Metagenome Deconvolution Kit, Service ...
The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified ... To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from ... Metagenome-based relative abundance of NCLDV and cellular genomes in the TOP data set. Seventeen TOP metagenomes (0.2-1.6 μm ... Metagenome-based relative abundance of NCLDV families. (a) Representation of different viral groups in the whole TOP ...
... PLoS One. 2007 Aug 29;2(8):e800. doi: ... Importantly, ICEs accounted for 41% of the new GAS metagenome gene content identified in these four genomes. Two large ICEs, ... The data provide new information about the GAS metagenome and will assist studies of pathogenesis, antimicrobial resistance, ... Cumulatively, 242 new GAS metagenome genes were identified that were not present in the previously sequenced genomes. ...
The analysis of these vast amounts of data is complicated by the fact that reconstructing large genomic segments from metagenomic reads is a formidable computational challenge. Even for single organisms, the assembly of genome sequences from sequencing reads is a complex task, primarily due to ambiguities in the reconstruction that are caused by genomic repeats. In metagenomic data, additional challenges arise from the non-uniform representation of genomes in a sample as well as from the genomic variants between the sequences of closely related organisms. ...
... per gigabase of metagenome than vOTUs derived from bulk-soil metagenomes from the same site (J. B. Emerson, S. Roux, J. R. Brum ... CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal, May 2015 * ... CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes journal, May 2015 * ... Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy journal, May 2018 * Sieber, ...
To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wi … ... A metagenome-wide association study of gut microbiota in type 2 diabetes Nature. 2012 Oct 4;490(7418):55-60. doi: 10.1038/ ... To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide ...
The metagenome was purified, fragmented by partial digestion with Sau3AI, and ligated into a p18GFP vector at the BamHI site, ... Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome. Taku Uchiyama1, Katusro Yaoi1 and Kentaro Miyazaki1,2* ... Citation: Uchiyama T, Yaoi K and Miyazaki K (2015) Glucose-tolerant β-glucosidase retrieved from a Kusaya gravy metagenome. ... Uchiyama, T., and Watanabe, K. (2008). Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat. Protoc ...
... 7th February 2015 - BioRxiv. Given a massive collection of ... to reduce large sequences to a representative sketch and rapidly estimate pairwise distances between genomes or metagenomes. ...
Hi-C metagenome deconvolution prod,Phase,Genomics,Announces,Availability,of,Kit-based,ProxiMeta™,Hi-C,Metagenome,Deconvolution, ... Researchers can use the ProxiMeta Hi-C kit and accompanying cloud-based bioinformatics software to perform Hi-C metagenome ... Phase Genomics, the industry leader in Hi-C-based genomic technologies, launched its ProxiMeta™ Hi-C metagenome deconvolution ... Phase Genomics Announces Availability of Kit-based ProxiMeta™ Hi-C Metagenome Deconvolution ...
The metagenome skimming approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and ... In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural ... which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina ... of scaffolds mapped to the same genomic site revealed intra-and/or intergenomic variation within a metagenome pool. ...
National Laboratory recently completed a study that compared more than 14 million microbial sequences from 90 metagenomes ... Using this database, the researchers then isolated matches between the metagenomes and the sequences in SEED. Up until the ... a high-throughput pipeline designed specifically for metagenome sequencing by researchers at Argonne. In order to make sense of ... Eventually the researchers found that more than 1 million sequences from the microbial metagenomes, and over 500,000 from the ...
Center for Genome and Metagenome Studies. James Madison University. 951 Carrier Drive. Bioscience Building, loading dock. ... Center for Genome and Metagenome Studies. James Madison University. MSC 7801. Harrisonburg VA 22807 ...
... ... "Application of Universal Stress Proteins in Probing the Dynamics of Potent Degraders in Complex Terephthalate Metagenome," ...
Both metagenomes curves rise very quickly at first, but the activated sludge then levels off as more new species are found per ... The metagenomes were compared at the levels of phylum, class, genus, and species including their functional attributes using ... To gain insight into the pathways, we annotated the reads from each metagenome to the KEGG and SEED terms mapped in MEGAN. The ... A metagenome analysis has been proven as an effective method for retrieving interesting microbial populations from complex ...
Biosynthesis of terpenoids and polyketides Terpenoid backbone biosynthesis M00096 C5 isoprenoid biosynthesis, non-mevalonate pathway [PATH:T30731_00900 T30731_01100 T30731_01110 ...
Marine metagenome Metagenomic library Esterase Cold adaptation Salt resistance Polyester hydrolysis Electronic supplementary ... Kourist R, Hari Krishna S, Patel JS, Bartnek F, Hitchman TS, Weiner DP, Bornscheuer UT (2007) Identification of a metagenome- ... Steele HL, Jaeger KE, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol ... The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes. ...
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. By Vaughn Iverson, Robert M. Morris ... Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota. By Vaughn Iverson, Robert M. Morris ... Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota Message Subject. (Your Name) has ... Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain ...
Ribonucleotide reductase, Phage, Metagenome, Phage metadata, Phylogenetics, Evolution, Split gene National Category Medical and ... RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the ... A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. Dwivedi, Bhakti ... and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes ...
  • The tool, named GOTTCHA (for Genomic Origins Through Taxonomic CHAllenge), makes use of a database of reference genomes that have been pre-processed to retain only unique segments of the genomes at any level of taxonomy, and then it classifies the individual metagenome sequences or "reads. (lanl.gov)
  • Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. (wiley.com)
  • Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. (osti.gov)
  • article{osti_1572795, title = {Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost}, author = {Xue, Yaxin and Jonassen, Inge and Øvreås, Lise and Taş, Neslihan}, abstractNote = {ABSTRACT Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. (osti.gov)
  • Our new tool, Mash, uses MinHash locality-sensitive hashing to reduce large sequences to a representative sketch and rapidly estimate pairwise distances between genomes or metagenomes. (nanoporetech.com)
  • Researchers at Argonne National Laboratory recently completed a study that compared more than 14 million microbial sequences from 90 metagenomes collected from nine different biomes or ecosystems. (anl.gov)
  • Using this database, the researchers then isolated matches between the metagenomes and the sequences in SEED. (anl.gov)
  • Eventually the researchers found that more than 1 million sequences from the microbial metagenomes, and over 500,000 from the viral metagenomes, were substantially similar to functional genes within the SEED database. (anl.gov)
  • Better Microbial Genome Binning with MetaBAT An automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. (doe.gov)
  • To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. (osti.gov)
  • Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. (osti.gov)
  • Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels) to assign other reads based on their compositional similarity. (biomedcentral.com)
  • By applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. (biomedcentral.com)
  • Many noncoding RNAs that likely act in trans are also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences. (biomedcentral.com)
  • This method was applied to all available bacterial and archaeal genome sequences, as well as metagenome (that is, environmental) sequences, and identified 104 candidate RNA motifs described in this report. (biomedcentral.com)
  • Metagenome samples consist of several DNA sequences originating from all organisms in the examined environment. (biomedcentral.com)
  • The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared. (biomedcentral.com)
  • However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. (biomedcentral.com)
  • We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. (biomedcentral.com)
  • Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. (biomedcentral.com)
  • The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. (ru.nl)
  • Moreover, mapping of metagenome reads to complete genome sequences of selected pathogenic bacteria revealed that not the pathogenic species itself, but only species that are more or less related to pathogenic ones are present in the fermentation samples analyzed. (uni-bielefeld.de)
  • employ genome-resolved metagenomics to investigate supragingival plaque metagenomes of 88 individuals ( 1 ). (asm.org)
  • In this study deep metagenomics and fluorescence in situ hybridization (FISH) were used to study a full-scale wastewater treatment plant with enhanced biological phosphorus removal (EBPR), and the results were compared to an existing EBPR metagenome. (environmental-expert.com)
  • Furthermore, we discuss and illustrate some of the general pitfalls in metagenomics and stress the need of additional DNA extraction independent information in metagenome studies. (environmental-expert.com)
  • Encyclopedia of Metagenomics: Genes, Genomes and Metagenomes. (iberlibro.com)
  • Portada Nelson, Karen E. (Edited by) Encyclopedia of Metagenomics: Genes, Genomes and Metagenomes. (iberlibro.com)
  • Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. (elsevier.com)
  • What is the difference between Metagenomics and Metagenome Sequencing? (mrdnalab.com)
  • Argonne scientists Folker Meyer and Elizabeth Glass analyzing species and metabolic diversity from NEON soil metagenomics samples using MG-RAST (Metagenome Rapid Annotation using Subsystem Technology) on Argonne's Active Mural Display. (anl.gov)
  • The second position will focus on metagenome analyses as well as integration of datasets of amplicon sequencing. (isme-microbes.org)
  • A comparison of 32 metagenome datasets revealed a similarity in functional profiles between the cryoconite and metagenomes characterized from other cold microbe-mineral aggregates. (figshare.com)
  • How to assemble complex soil metagenome datasets? (biostars.org)
  • I have 27 soil WGS metagenome datasets and I am trying to assemble them into contigs that are at least 1000-2000 kb long. (biostars.org)
  • Read mapping analyses revealed that the depth of coverage within individual genomes is significantly more uneven in PCR-amplified datasets versus unamplified metagenomes, with regions of high depth of coverage enriched in short inserts. (elsevier.com)
  • Here we show that a modified assembly pipeline can lead to an improved de novo genome assembly from PCR-amplified datasets, and enables a better genome recovery from low input metagenomes. (elsevier.com)
  • Using deep sequence metagenome and metatranscriptome datasets in combination with 16S rRNA gene amplicon sequencing from HMY and LMY sheep, we show enrichment of lactate-producing Sharpea spp. (biomedcentral.com)
  • Metagenome datasets of microbial communities from an agricultural biogas plant as well as from anaerobic lab-scale digesters operating at different temperatures and conditions were analyzed for the presence of putative pathogenic bacteria and virulence determinants by various bioinformatic approaches. (uni-bielefeld.de)
  • Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by " genome skimming, " which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. (archives-ouvertes.fr)
  • Analyses of metagenomes can give extensive information about the identity of microbes in the community as well as their functional potential (Kuczynski et al. (aau.dk)
  • A transition from singular snapshots of cryoconite metagenomes to comparative analyses is advocated. (figshare.com)
  • Tiedje, James M. / Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes . (elsevier.com)
  • The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. (nature.com)
  • We used Bowtie2 ( 11 ) to recruit reads from metagenomes, and anvi'o ( 12 ) to visualize and refine Espinoza et al. (asm.org)
  • As a reference genome exists for clade IIA we used the raw metagenome reads to estimate the Accumulibacter micro-diversity in the metagenomes. (aau.dk)
  • The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. (montana.edu)
  • Basically I have metagenome sequencing samples (i.e. reads) in fastq format, these are paired end reads, the quality was pretty bad at first so I trimmed some of the reads to maintain a certain phred score, both of the pairs were dropped if one of them was below the quality score cut off. (biostars.org)
  • I first mapped this metagenome to representative bacterial genomes using bowtie2 and I used the '-a' argument so that the output keeps multi-mapped reads and not just the best one. (biostars.org)
  • One of the grand challenges in the study of metagenome data involves reconstructing the different microbial genomes from a mixture of sequence reads. (biomedcentral.com)
  • As such,the metagenome assembly problem is complex and challenging [ 6 ] and is often subject to further analysis as a collection of short reads. (biomedcentral.com)
  • We first evaluated coverage bias by mapping reads from PCR-amplified metagenomes onto reference contigs obtained from unamplified metagenomes of the same samples. (elsevier.com)
  • In a paper this week in the journal Nucleic Acids Research , "Accurate read-based metagenome characterization using a hierarchical suite of unique signatures," the researchers present this novel method for shotgun metagenomic read classification, a method that is highly accurate, and outperforms all other most recent methods, they say. (lanl.gov)
  • To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. (nih.gov)
  • Here we use shotgun sequencing of the gut metagenome to demonstrate that the genus Collinsella was enriched in patients with symptomatic atherosclerosis, defined as stenotic atherosclerotic plaques in the carotid artery leading to cerebrovascular events, whereas Roseburia and Eubacterium were enriched in healthy controls. (lu.se)
  • TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. (jcvi.org)
  • Recently, the massive sampling and sequencing effort of the Sorcerer II Global Ocean Sampling (GOS) expedition ( 41 ) has produced the largest shotgun metagenome for any oceanic habitat to date. (asm.org)
  • thus, shotgun sequencing and de novo assembly of a metagenome typically yield a collection of contigs that cannot readily be grouped by species. (g3journal.org)
  • Hi All, I have a large dataset from soil community: shotgun metagenome sequencing, 10 sequencing. (biostars.org)
  • How is shotgun metagenome sequencing different from 16s metagenome sequencing? (mrdnalab.com)
  • Is there a difference between 16s rRNA sequencing and Shotgun metagenome sequencing? (mrdnalab.com)
  • On the other hand, shotgun metagenome sequencing targets all genes from all microbial organisms. (mrdnalab.com)
  • This sequencing method is aptly named 'Shotgun' due to its widespread of targets, whereas targeted resequencing methods could by the same logic be named 'Rifle' metagenome sequencing. (mrdnalab.com)
  • Shotgun metagenome sequencing is able to provide scientists a more full picture of the microbial diversity present in their environmental samples. (mrdnalab.com)
  • Today, with the popularization of next-generation sequencing platforms, these traditional microbiology techniques are no longer necessary, and as a result there is less bias involved in shotgun metagenome studies. (mrdnalab.com)
  • Not only does Shotgun metagenome sequencing provide the ability for researchers to gain insight into the taxonomic makeup of their environmental samples, but because this method is not limited to the 16s rRNA gene, researchers are also able to gain insight into the functional genes present as well as the metabolic pathways. (mrdnalab.com)
  • It is clear to see that Shotgun metagenome sequencing provides the most complete picture of microbial diversity and function in a specified environment. (mrdnalab.com)
  • 16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. (semanticscholar.org)
  • The algorithm is evaluated on synthetic samples and eight targeted 16S rRNA metagenome samples taken from seawater. (biomedcentral.com)
  • In this study, esterase EstA3 was derived from a drinking water metagenome, and esterase EstCE1 was derived from a soil metagenome. (asm.org)
  • Here we report an unconventional mode by which a response regulator derived from a soil metagenome confers resistance to the β-lactam antibiotic carbenicillin in Escherichia coli. (uky.edu)
  • Importantly, ICEs accounted for 41% of the new GAS metagenome gene content identified in these four genomes. (nih.gov)
  • To explore the natural enzyme diversity of these environments and identify new carboxylesterases, we have screened three marine metagenome gene libraries for esterase activity. (springer.com)
  • The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as collections of mobile genetic elements and environmental metagenomes to improve the classification and functional prediction of viral gene products. (jcvi.org)
  • Antarctic Peninsula Bacterioplankton 16S rRNA gene surveys and metagenomes from Winter 2002 and Summer 2006. (gbif.org)
  • Targeted metagenome or 16S rRNA gene sequencing has been widely used for the analysis of genetic diversity estimation, enabling deep views into hundreds of complex microbial communities simultaneously. (biomedcentral.com)
  • This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. (biomedcentral.com)
  • The metagenome-derived AP (mAP) gene composed of 1,824 nucleotides encodes a polypeptide with a calculated molecular mass of 64 kDa. (biomedcentral.com)
  • Metaproteomics can also be used as a tool to assess the composition of a microbial community in terms of biomass contributions of individual members species in the community and can thus complement approaches that assess community composition based on gene copy counts such as 16S rRNA gene amplicon or metagenome sequencing. (wikipedia.org)
  • Each concentric circle represents one of the 88 metagenomes in the original study, dendrograms show hierarchical clustering of contigs based on sequence composition and differential mean coverage across metagenomes (using Euclidean distance and Ward's method), and each data point represents the read recruitment statistic of a given contig in a given metagenome. (asm.org)
  • For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. (diva-portal.org)
  • Then, we compared different assembly pipelines in terms of assembly size (number of bp in contigs ≥ 10 kb) and error rates to evaluate which are the best suited for PCR-amplified metagenomes. (elsevier.com)
  • We found that a pipeline combining read deduplication and an assembly algorithm originally designed to recover genomes from libraries generated after whole genome amplification (single-cell SPAdes) frequently improved assembly of contigs ≥10 kb by 10 to 100-fold for low input metagenomes. (elsevier.com)
  • A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3,738 apparently complete phage genomes that represent 451 putative genera. (researchsquare.com)
  • We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. (biomedcentral.com)
  • From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. (biomedcentral.com)
  • As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes. (biomedcentral.com)
  • That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis. (biomedcentral.com)
  • The metagenome assembly yielded 12,264 total contigs (12,332,388 bp), with an N 50 of 4,275 and a GC% of 56.52 (SRA accession no. (asm.org)
  • The metagenome was binned with VizBin ( 2 ) and 22.5% of the contigs were assigned to the genus Pseudomonas . (asm.org)
  • DAS Tool for Genome Reconstruction from Metagenomes Through the JGI's Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. (doe.gov)
  • metagenome sequence data was automatically annotated at the Joint Genome Institute (see Grzymski et al. (gbif.org)
  • metagenome analysis, cloud, distributed workflows Introduction The ever-increasing amount of DNA sequence data [1] has motivated significant developments in biomedical research. (deepdyve.com)
  • The draft genome sequence of Pseudomonas stutzeri strain K35 was separated from a metagenome derived from a produced water microbial community of a coalbed methane well. (asm.org)
  • Analysis was performed with RAST (Rapid Annotation using Subsystem Technology), a high-throughput pipeline designed specifically for metagenome sequencing by researchers at Argonne. (anl.gov)
  • Metagenome Annotation using massively parallel undergrads. (blogspot.com)
  • They do this as part of a course on metagenome annotation. (blogspot.com)
  • Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively. (diva-portal.org)
  • Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. (diva-portal.org)
  • But as our knowledge of the genes associated with the disease states expands, we understand that humans must be viewed as superorganisms in which a plethora of bacterial genomes - a metagenome - work in tandem with our own. (edu.au)
  • Researchers can use the ProxiMeta Hi-C kit and accompanying cloud-based bioinformatics software to perform Hi-C metagenome deconvolution using their own facilities, supplementing the company's full-service ProxiMeta offering launched in May 2017. (bio-medicine.org)
  • Publication of sequenced and annotated metagenomes obtained with already available and new bioinformatics tools. (europa.eu)
  • MetaGenome Analytics (MGA) provides simple solutions to these barriers with commercial-scale software that unites bioinformatics, statistics, data sciences, with the power of cloud-based computing and delivers it to your fingertips in seamless, easy to use applications that are affordable. (metagenomeanalytics.com)
  • These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. (elsevier.com)
  • Further characterization of the functional capacity of the metagenomes revealed that patient gut metagenomes. (lu.se)
  • This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. (mdpi.com)
  • However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. (biomedcentral.com)
  • Thus, it is difficult to differentiate the functional potentials between different genomes and metagenomes by analysis based on COG classification. (biomedcentral.com)
  • The EBPR plants form a distinct group when compared to metagenomes from a wide range of environments, both on phylogenetic and functional level (Fig. 1). (aau.dk)
  • Functional metagenomic analysis of soil metagenomes is a method for uncovering as-yet unidentified mechanisms for antibiotic resistance. (uky.edu)
  • Research on gut metagenome of patients with Crohn's disease elucidates how it influences the taxonomic and functional composition of intestinal microbiota. (fomatmedical.com)
  • To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses. (biomedcentral.com)
  • Conclusions: This comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. (diva-portal.org)
  • Analysis of phage genomes identified in whole-community human gut metagenomes resulted in the delineation of at least three new candidate families of Caudovirales and revealed diverse putative mechanisms underlying phage-host interactions in the human gut. (researchsquare.com)
  • The megx.net portal for Marine Ecological GenomiX is a web site for specialized georeferenced databases and tools for the analysis of marine bacterial, archaeal, and phage genomes and metagenomes. (megx.net)
  • Here, we report on the first isolation and biochemical characterization of a thermolabile AP from a metagenome. (biomedcentral.com)
  • To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2-1.6 μm size range) collected during the Tara Oceans Expedition. (nature.com)
  • To better characterize members of these communities, we developed methods to reconstruct genomes directly from mate-paired short-read metagenomes. (sciencemag.org)
  • The method developed in this study could characterize the functionome harbored in genomes and metagenomes. (biomedcentral.com)
  • As the NIH Human Microbiome Project continues to better characterize the human metagenome, new insights into autoimmune pathogenesis are beginning to emerge. (edu.au)
  • GRASPx was also applied to a human saliva metagenome dataset and shows superior performance for both recall and precision rates. (ku.edu)
  • This dataset includes FASTA formatted files of the metagenomes from the East Pacific Rise seafloor basalt, the Loi'hi Seamount seafloor basalt, and negative control of sterile water. (bco-dmo.org)
  • Metagenome" sequencing involves decoding the DNA of organisms co-existing within ecosystems ranging from ocean, soil and human body. (biomedcentral.com)
  • A Response Regulator from a Soil Metagenome Enhances Resistance to the" by Heather K. Allen, Ran An et al. (uky.edu)
  • Thus, esterases from marine metagenomes are cold-adapted enzymes exhibiting broad biochemical diversity reflecting the environmental conditions where they evolved. (springer.com)
  • Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments. (pubmedcentralcanada.ca)
  • In this study, we examined the taxonomic diversity and saxitoxin production potential of cyanobacteria in the water and sediments of a large river, the North Han River in South Korea, by metagenome analysis using next-generation sequencing (NGS) and molecular biological approaches, respectively. (springer.com)
  • Metagenomic analysis is the analysis of environmental microbial flora, referred to as the metagenome. (peerj.com)
  • however, these studies also have highlighted the need for improved approaches in the analysis of viral metagenomes. (biomedcentral.com)
  • The " metagenome skimming " approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics. (archives-ouvertes.fr)
  • This revealed a much greater micro-diversity than observed through qFISH - also between the two metagenomes. (aau.dk)
  • Here, we provide the first report of a cryoconite metagenome and culture-independent study of alpine cryoconite microbial diversity. (figshare.com)
  • The results indicated that 23 similar prokaryotic phyla were represented in both metagenomes irrespective of their relative abundance. (hindawi.com)
  • In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. (archives-ouvertes.fr)
  • We closed a genome representing the as-yet uncultured marine group II Euryarchaeota , assembled de novo from 1.7% of a metagenome sequenced from surface seawater. (sciencemag.org)
  • The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.Results: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. (umd.edu)
  • Metagenomes obtained by 'deep sequencing' - what do they tell about the enhanced biological phosphorus removal communities? (environmental-expert.com)
  • We sequenced two metagenomes from Aalborg East and West EBPR wastewater treatment plants at a depth of 12 and 8 Gb using Illumina short read sequencing. (aau.dk)
  • 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)
  • However, these libraries require several rounds of PCR amplification before sequencing, and recent data suggest these typically yield smaller and more fragmented assemblies than regular metagenomes. (elsevier.com)
  • Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. (nature.com)
  • These are valid questions and questions that can be resolved with a quick breakdown of metagenome sequencing methods. (mrdnalab.com)
  • Additionally, we provide a mathematical model for estimating the probability of assembling targeted genes in a metagenome for estimating required sequencing depth. (elsevier.com)
  • This is referred to as the metagenome assembly problem. (biomedcentral.com)
  • Here we evaluate de novo assembly methods of 169 PCR-amplified metagenomes, including 25 for which an unamplified counterpart is available, to optimize specific assembly approaches for PCR-amplified libraries. (elsevier.com)
  • Eloe-Fadrosh, Emiley A. / Optimizing de novo genome assembly from PCR-amplified metagenomes . (elsevier.com)
  • yet, the gut phageome is far from being fully characterized, and additional groups of phages, including highly abundant ones, continue to be discovered by metagenome mining. (researchsquare.com)
  • The data provide new information about the GAS metagenome and will assist studies of pathogenesis, antimicrobial resistance, and population genomics. (nih.gov)
  • Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. (diva-portal.org)
  • Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. (diva-portal.org)
  • Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. (diva-portal.org)
  • This week our post is about the Open Metagenome Toolkit because it is a cool opportunity for collaborative programming in our microbiome community. (blogspot.com)
  • Phase Genomics, the industry leader in Hi-C-based genomic technologies, launched its ProxiMeta™ Hi-C metagenome deconvolution product, featuring the first commercially available Hi-C kit. (bio-medicine.org)
  • Originally, the investigators had assumed that the study would reveal similarities in metabolic function between the viral and microbial metagenomes across the different biomes. (anl.gov)
  • 2011). The aim of this study was to compare metagenomes from two full-scale EBPR plants to other environments and to investigate in detail similarities and differences between the two EBPR communities. (aau.dk)
  • A metagenome wide association (MGWA) study of bacterial host association determinants in Drosophila predicted that LPS biosynthesis genes are significantly associated with host colonization. (g3journal.org)
  • To identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (MGWA) approach in two steps. (asm.org)
  • Metagenome-wide association (MGWA) approaches, which associate microbiota genetic content with host trait magnitude, are an emerging systems-level approach for predicting genetic mechanisms of gut microbiota function within a host ( 17 - 20 ). (asm.org)
  • The presented mAP enzyme is the first thermolabile AP found in cold-adapted marine metagenomes and may be useful for efficient dephosphorylation of linearized DNA. (biomedcentral.com)
  • We apply this approach to two synthetic metagenome samples, successfully clustering the genome content of fungal, bacterial, and archaeal species with more than 99% agreement with published reference genomes. (g3journal.org)
  • When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae , while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. (biomedcentral.com)
  • Thus, Mash combines the high specificity of matching-based approaches with the dimensionality reduction of statistical approaches, enabling accurate all-pairs comparisons between many large genomes and metagenomes. (biomedcentral.com)