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

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

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

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

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

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

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

The human microbiome project. (4/1707)

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

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

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

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

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

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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
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*
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http://bit.ly/LhsWi2 | Complex Insight - Understanding our world
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
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
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
The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters. Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven
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 ...
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 ...
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? ...
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 ...
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 ...
Taken together, the topological features that were found to vary with obesity and IBD suggest a characteristic mode of deviation from a normal microbiome organization that may be associated with a disease state. This suggests that in addition to, or potentially as a consequence of, alterations in the abundance of individual genes or functional classes, disease may be associated with higher order modes of deviation in the microbiome. Clearly, such associations alone cannot directly implicate a mechanism for disease; both obesity and IBD are poorly understood diseases and embody extremely complex phenotypes. Accordingly, the system-level observations reported in this study can have multiple alternative interpretations and stem from mechanisms that are yet unknown. These observations, however, allow us to posit intriguing hypotheses for further study.. Specifically, we find that enzymes typifying various host states tend to have low centrality and are found mostly in the periphery of the network. ...
To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human bodys greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites. The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral
2. The gut microbiome of the mother. As discussed by the authors, stool microbiome of the mother was unfortunately not investigated. During the first year, the gut microbiome of infants become increasingly similar to the gut microbiome of their mothers 4. It could be speculated that a significant proportion of the unknown source of the infants stool microbiome (,70%, Figure 4b) could be the mothers gut. Importantly, low diversity of gut microbiome has been reported in several HIV cohorts, in part associated with immune dysfunction and use of ART 5-9 . The authors discuss maternal ART as a contributing factor, and it is noteworthy that we reported decreased alpha diversity and reduction in Prevotella few months after ART initiation 7, the same findings as reported in HIV-exposed children in the present study ...
Neither ART nor immune reconstitution affect the vaginal microbiome of HIV-infected women, according to the results of an observational study published in Open Forum Infectious Diseases. “To our knowledge, this is the first study that examines the vaginal microbiome during ART initiation,” Cindy M. Liu, MD, PhD, MPH, associate professor of environmental and occupational health at
The symbiotic gut microbiota modulate health and disease of the host through a series of transgenomic metabolic and immune regulatory axes. We explore connections between microbiome composition and function related to individual metabolic phenotypes and consider these interactions as possible targets for developing new personalized therapies and clinical management strategies.. ...
To address these questions, the researchers used a high-throughput sequencing technology to characterize the gut microbiota associated with multiple members of the firebug family and its sister family, the bordered plant bugs or Largidae. They discovered that many different members of the firebug family share the same core microbiota. Interestingly, all the insect taxa that harbored the core microbiota were confined to a single clade within the Pyrrhocoridae, while the core microbes were completely absent from their sister family, the Largidae.. According to phylogenetic analyses, the association between firebugs and the core microbiota originated around 81 million years ago (in the late Cretaceous) which coincided with the emergence of their host plants, the Malvales. "The acquisition of the gut-associated core microbiota apparently enabled firebugs to successfully overcome the plants defenses and nutritional shortcomings and utilize the Malvales seeds as a food source," explains Sailendharan ...
Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host
Commensal microbes must control viral infection by facilitating web host immune system defenses often. germfree (GF) and injected intraperitoneally (we.p.) with an sent retrovirus, the pets became contaminated but didnt transmit infectious trojan with their offspring (6). As a result, very similar compared to that of reoviruses and picornaviruses, transmission of the milk-borne retrovirus in prone animals depends completely over the hosts microbiota. Unlike retrovirus-susceptible mice, retrovirus-resistant mice usually do not move infectious trojan also in the current presence of microbiota; these animals generate antivirus immune reactions capable of removing the disease (7, 8). With this current work, we set out to determine if production of protecting retrovirus-specific immune reactions in retrovirus-resistant mice requires the microbiota. GF mice show normal production of antigen-specific antibodies (Abs) in response to immunization. There have been conflicting reports concerning the ...
The impact of the gut microbiota on immune homeostasis within the gut and, importantly, also at systemic sites has gained tremendous research interest over the last few years. The intestinal microbiota is an integral component of a fascinating ecosystem that interacts with and benefits its host on several complex levels to achieve a mutualistic relationship. Host-microbial homeostasis involves appropriate immune regulation within the gut mucosa to maintain a healthy gut while preventing uncontrolled immune responses against the beneficial commensal microbiota potentially leading to chronic inflammatory bowel diseases (IBD). Furthermore, recent studies suggest that the microbiota composition might impact on the susceptibility to immune-mediated disorders such as autoimmunity and allergy. Understanding how the microbiota modulates susceptibility to these diseases is an important step toward better prevention or treatment options for such diseases.. ...
Abstract Colon Cancer is the most common cancer among Inflammatory Bowel Disease (IBD) patients and IBD is one of the three leading high-risk factors for Colon Cancer. In 2012 it was found, by using genetic sequencing of the gut microbiome, that Fusobacteria sequences were enriched in colorectal carcinomas (CRC). To explore this possible link between inflammation, gut microbes, and colon cancer I have turned my own body into a
Overview:. This project has two objectives: to understand the factors that shape symbiotic microbial. communities, and to understand how symbiotic microbial communities interact with invading. pathogens. Animals serve as habitats to complex symbiotic microbial communities (referred. to as the microbiome). The microbiome may interact with pathogens encountered by the host,. and this interaction can affect disease resistance and/or alter the species composition of. the microbiome. This project will examine microbiome assembly and microbiome-pathogen interactions. in a wildlife disease system consisting of a frog species, the symbiotic bacteria inhabiting. its skin, and a fungal pathogen. Molecular methods (16S amplicon sequencing and metagenomics. of bacterial communities; microsatellite analysis of host genotypes) will be combined with. field surveys and laboratory experiments to understand the relative influence of environment. and host on microbial community composition. Mathematical models ...
The human gut microbiome is a highly diverse microbial ecosystem of approximately 400 different species, with most of the species belonging to the phylum Bacteroidetes or Firmicutes. Each person has an unique composition of bacteria, and its also clear that subsets of the population have microbiomes that look more a like, as different diets promote the growth of certain species in the gut, and some health disorders are characterized by a specific microbial profile. By now its well established that obesity is associated with an "obese microbiota" that is quite different than the microbiota of a lean person (1,2).. The first studies looking into the microbiota in overweight and obesity found that obese individuals have a decreased Bacteroidetes/Firmicutes ratio, but recent findings show that this isnt always the case. Also, since both "good" and "bad" bugs belong to both of these major groups of bacteria, the ratio between Bacteroidetes and Firmicutes doesnt necessarily tell us much about the ...
TY - JOUR. T1 - Impact of the gut microbiome on the genome and epigenome of colon epithelial cells. T2 - Contributions to colorectal cancer development 11 Medical and Health Sciences 1112 Oncology and Carcinogenesis. AU - Allen, Jawara. AU - Sears, Cynthia Louise. PY - 2019/2/25. Y1 - 2019/2/25. N2 - In recent years, the number of studies investigating the impact of the gut microbiome in colorectal cancer (CRC) has risen sharply. As a result, we now know that various microbes (and microbial communities) are found more frequently in the stool and mucosa of individuals with CRC than healthy controls, including in the primary tumors themselves, and even in distant metastases. We also know that these microbes induce tumors in various mouse models, but we know little about how they impact colon epithelial cells (CECs) directly, or about how these interactions might lead to modifications at the genetic and epigenetic levels that trigger and propagate tumor growth. Rates of CRC are increasing in ...
If the human gut microbiome contains two times more gene power than that of our total human cells, then the microbiome has a total of 40,000 genes of protein producing ability. Our gastrointestinal tract is awash with a myriad of enzymes, messengers molecules, binding molecules, protein cascade molecules derived from both our human cells and our microbial communitys cells.. This is the arena that the National Institute of Healths Human Microbiome Project is now putting their full attention into understanding. Traditionally, microbiology has focused on the study of individual species as isolated units, making it difficult to develop and inventory all of the microbes in an area such as the human GI tract. However new technologies have emerged which enable scientists to quantify the different organisms present in the milieu of an ecosystem. Instead of isolating and culturing each microbe, all of the DNA within the collected samples will be sequenced and analzyed through PCR technology and ...
"IMG/M: A data management and analysis system for metagenomes". Nucleic Acids Research. 36 (Database issue): D534-D538. doi ... "The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes". BMC ...
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. ...
Metagenomics: Study of metagenomes, i.e., genetic material recovered directly from environmental samples. ...
The gut metagenome is the aggregate of all the genomes of gut microbiota. The gut is one niche that human microbiota inhabit. ...
The term was derived from "metagenome". Wilmes and Bond proposed the term "metaproteomics" for the large-scale characterization ...
MEta Genome ANalyzer)[29][30]。第一版的程式是2005年用來分析從長毛象骨頭獲得的DNA序列的總體基因體[31]。根據BLAST比較參考的資料庫,這個工具同時表現其分類群和功能性,藉由將判讀的片段分別放到利用a simple ... Metagenome,又稱宏基因組、環境基因組或生態基因組),這些基因確定
"A catalog of the mouse gut metagenome". Nature Biotechnology. 33 (10): 1103-1108. doi:10.1038/nbt.3353. ISSN 1087-0156. Zhang, ...
2013). "Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes". Nat. ...
"Metagenomes of Mediterranean Coastal Lagoons". Scientific Reports. 2. doi:10.1038/srep00490. PMC 3391805 . PMID 22778901. Parc ...
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. doi:10.1038/ncomms2266. PMC ...
"Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-9. doi:10.1038/ ...
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): 656-9. doi:10.1038/ ...
... in addition phages and cow rumen metagenomes, as mentioned above. Within the Firmicutes, they are present in a few species of ... "Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis". Nature. 462 (7273): 656-9. doi:10.1038/ ...
... fast genome and metagenome distance estimation using MinHash". Genome Biology. 17: 132. doi:10.1186/s13059-016-0997-x. ISSN ...
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/ ...
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): 656-9. 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): 656-9. doi:10.1038/ ...
The human metagenome includes all organisms that live on or in us. Viruses contribute to the metagenome and establish chronic ... "Laboratory procedures to generate viral metagenomes". Nature Protocols. 4 (4): 470-483. doi:10.1038/nprot.2009.10. PMID ...
The word is derived from virus and genome and first used by Forest Rohwer and colleagues to describe viral shotgun metagenomes ... Thurber, RV; Haynes, M; Breitbart, M; Wegley, L; Rohwer, F (2009). "Laboratory procedures to generate viral metagenomes". ...
2012). "Metagenomes of Mediterranean Coastal Lagoons". Scientific Reports. 2. doi:10.1038/srep00490. PMC 3391805 . PMID ...
doi:10.1186/s12859-015-0875-7. CS1 maint: Uses authors parameter (link) Zhu, Zheng (2014). "Self-organizing approach for meta- ...
Over 8,000 users now have submitted a total of 50,000 metagenomes to MG-RAST. The Integrated Microbial Genomes/Metagenomes (IMG ... One of the first standalone tools for analysing high-throughput metagenome shotgun data was MEGAN (MEta Genome ANalyzer). A ... The term metagenome referenced the idea that a collection of genes sequenced from the environment could be analyzed in a way ... Functional comparisons between metagenomes may be made by comparing sequences against reference databases such as COG or KEGG, ...
The integrated metagenome data management and comparative analysis system". Nucleic Acids Research. 40 (Database issue): D123- ... a related system that integrates metagenome data sets with isolate microbial genomes from the IMG system; CharProtDB, a ...
The integrated metagenome data management and comparative analysis system". Nucleic Acids Research. 40 (Database issue): D123- ...
Schipper C, Hornung C, Bijtenhoorn P, Quitschau M, Grond S, Streit WR (2009). "Metagenome-Derived Clones Encoding Two Novel ... Gabor EM, Alkema WBL, Janssen DB (2004). "Quantifying the accessibility of the metagenome by random expression cloning ... "Identification and characterization of lipolytic enzymes from a peat-swamp forest soil metagenome". Biosci. Biotechnol. Biochem ... require a good design of probes that detect molecules being synthesized and depend on the ability to express metagenomes in a ...
Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. Environmental Microbiology ...
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 ...
Carnoules arsenic-contaminated mine drainage metagenome, Carnoules bin 1, Contig491a, whole genome shotgun sequence. GenBank: ... Carnoules arsenic-contaminated mine drainage metagenome, Carnoules bin 1, Contig... Carnoules arsenic-contaminated mine ... drainage metagenome, Carnoules bin 1, Contig491a, whole genome shotgun sequence. gi,318099972,emb,CABL01000009.1, ...
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
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 ...
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 ...
... 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, ...
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 ...
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 ...
  • 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)
  • 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)
  • 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)
  • Here, we analyzed the abundance and diversity of both nosZ types in whole-genome shotgun metagenomes from sandy and silty loam agricultural soils that typify the U.S. Midwest corn belt. (asm.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)
  • 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)
  • 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)
  • We used Bowtie2 ( 11 ) to recruit reads from metagenomes, and anvi'o ( 12 ) to visualize and refine Espinoza et al. (asm.org)
  • First, different search algorithms and parameters for detecting nosZ metagenomic reads were evaluated based on in silico -generated (mock) metagenomes. (asm.org)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • Here, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. (asm.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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • Metagenomes provide a fragmented view of such communities, but the ecosystem functions of major groups of organisms remain mysterious. (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)
  • The Pseudomonas stutzeri strain K35 draft genome was extracted in silico from the metagenome of a produced water sample, which was taken from the Pocahontas 3 coal seam in the Central Appalachian Basin at a depth of 1,912 ft. (asm.org)
  • 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)
  • The 34 metagenome-assembled genomes (MAGs) that the authors report include those that resolve to clades that have largely evaded cultivation efforts, such as Gracilibacteria (formerly GN02) and Saccharibacteria (formerly TM7) of the recently described Candidate Phyla Radiation ( 2 ). (asm.org)