Metagenome datasets of microbial. Medical search. Frequent questions

Our growing knowledge of microbial contributions to energy metabolism highlights new opportunities for weight management, including the microbiome-aware improvement of existing tools and novel microbiome-targeted therapies. (nature.com)
Recipient factors and donor-recipient complementarity, encompassing entire microbial communities to individual strains, were the main determinants of strain population dynamics, providing insights into the underlying processes that shape the post-FMT gut microbiome. (nature.com)
human gut microbiome, data repositories, large-scale and integrative computational tools, modelling, immunomodulation, drug screening Background The human gastrointestinal tract is a complex ecosystem in which eukaryotic cells continuously interact with nutrients and with the complex microbial population of the gut microbiota [1]. (deepdyve.com)
A key resource which was created was a complete dataset of microbiome and host sequence data from a cohort of 300 adults verified to be free of disease and so considered healthy. (nih.gov)
This reference dataset includes over 2000 metagenomes and over 10 terabytes (TB) of DNA sequence data, making it the largest set of microbiome data from human or any other habitat. (nih.gov)
This resource is the world's most comprehensive reference host/microbiome dataset as it includes the microbial community composition from five major body regions (nasal, oral, skin, gastrointestinal tract, and urogenital tract) of these subjects, and the predicted metabolic pathways of the microbial communities in these body regions. (nih.gov)
Additional attention has been paid to the gut microbiome in this cohort and the research community has used the HMP reference dataset to analyze the mobile gene content, the antibiotic resistome, the bacteriophage composition and the presence of putative pathogens in this key subset of the human microbiome reference dataset. (nih.gov)
Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. (biomedcentral.com)
These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. (biomedcentral.com)
Published in Nature , researchers from the Department of Energy's (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab), the Gladstone Institutes, and the Chan-Zuckerberg Biohub presented nearly 61,000 microbial genomes that were computationally reconstructed from 3,810 publicly available human gut metagenomes, which are datasets of all the genetic material present in a microbiome sample. (regenerativemedicine.net)
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. (nih.gov)
This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics. (nih.gov)
In her commitment to educate about the microbiome, she is also a collaborator of the "Microbiota Vault" effort, a project that seeks to conserve microbial communities around the world for the benefit of future generations. (appliedmicrobiology.org)
The gut microbiome of companion animals (cats and dogs) is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. (harvard.edu)
These are compared with a baseline human population of 238 gut metagenomes from the Human Microbiome Project 1-II processed in an identical manner. (harvard.edu)
This study provides the largest one-health microbiome resource to date of companion animal gut metagenomes, greatly improves the ability to profile additional animal gut microbiomes in the future and contributes to our understanding of how microbes are transmitted between companion animals and humans in the contexts of infectious diseases, immune modulation, and specific genetic elements such as antimicrobial resistance genes. (harvard.edu)
Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. (knaw.nl)
It is also clear that these standards will be vital to exploring the complex interactions that take place in communities - both microbial communities, such as those sampled in marine environments, and host-microbial communities, such as those now being sampled in the Human Microbiome Project. (biomedcentral.com)

Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. (peerj.com)
Finally, the program was also run on ocean surface water metagenomic datasets, through which we demonstrate that the program works on uncultured metagenomic datasets. (bvsalud.org)
Sorted cells from water of Crystal Geyser, Green River, Utah for developing a pipeline for high-throughput recovery of near-complete and complete microbial genomes from complex metagenomic datasets. (nih.gov)
With shotgun metagenomic datasets covering an ever widening range of biomes, multiple studies have been conducted with the aim of recovering the genomes of prokaryotes, viruses and more recently eukaryotes 7 . (researchsquare.com)
However as eukaryotic genomes are generally larger and lower in abundance in shotgun metagenomic datasets, they often go unreported. (researchsquare.com)
Compared to other tools, our benchmarks show that our tool outperforms in the ability to detect BGCs across different classes, and notably retains precision in metagenomic datasets. (x-meeting.com)

Important components of the HMP were culture-independent methods of microbial community characterization, such as metagenomics (which provides a broad genetic perspective on a single microbial community), as well as extensive whole genome sequencing (which provides a "deep" genetic perspective on certain aspects of a given microbial community, i.e. of individual bacterial species). (wikipedia.org)
Cow Rumen and the Early Days of Metagenomics Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities. (doe.gov)
Rhometa extends the capabilities of conventional sequence-based composite likelihood population recombination rate estimators to include modern aligned metagenomic read datasets with diverse sequencing depths, thereby enabling the effective application of these techniques and their high accuracy rates to the field of metagenomics. (bvsalud.org)
The field of metagenomics has expanded rapidly over the past decade, both in terms of the number and diversity of different datasets. (x-meeting.com)
Metagenomics, as a culture-independent approach, enables the exploration of complex heterogeneous microbial communities under natural conditions by massive sequencing of community-specific DNA. (uni-goettingen.de)
Her research is at the frontier of Microbial Ecology with Physiology, Metagenomics and Bioinformatics. (appliedmicrobiology.org)
After her NSF-funded postdoc studying with metagenomics an herbivorous bird -Hoatzin- at the DOE-JGI, she founded her first Microbial Ecology laboratory in Puerto Rico in 2012. (appliedmicrobiology.org)
Metagenomics studies microbial genomes in an ecosystem such as the gastrointestinal tract of a human. (nsf.gov)

In contrast, the microbial metabolomes, intestinal element and metal profiles, the diversity of bacterial, archaeal and fungal microbial communities were not significantly affected. (frontiersin.org)
This increase in the body of data on virophage not only revealed the diversity of the virophage group, but also the relevant ecological impact of these small viruses and their potential role in the dynamics of the microbial network. (mdpi.com)
Hence, an in-depth study of the diversity and functional mechanisms of microbial communities in AS is beneficial for improving wastewater treatment technology. (biomedcentral.com)
CD and UC patients showed a reduction in phylogenetic diversity and shifts in microbial composition, comparable to previous studies using conventional mucosal biopsies. (escholarship.org)
The metagenome-assembled genomes (MAGs) included 2,058 previously unknown species, thereby bringing the number of known human gut species to 4,558 and increasing the phylogenetic diversity of sequenced gut bacteria by 50 percent. (regenerativemedicine.net)
Discovery of new bacterial species shows little sign of abating, demonstrating the continued need to improve the experimental methods and informatics tooling used to produce metagenome assembled genomes (MAGs) thereby allowing the full microbial diversity to be described. (researchsquare.com)
While eukaryotes are often present in lower numbers, and are yet to show the same level of diversity in the microbial space, they are found in many biomes and interact with other members of those communities 10 - 13 . (researchsquare.com)
Mining JGI data portals for microbial and metagenome datasets allows researchers to learn more about the planet's known microbial diversity - and find viruses that impact microbial health and the planet's nutrient cycles. (energy.gov)
In order to investigate microbial contribution to HS degradation in freshwater ecosystems, we investigated the genomic and metabolic diversity of natural microbial communities using next-generation sequencing technologies. (europa.eu)
Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats. (knaw.nl)
Analysis of metagenomes from across the globe reveals the spectrum of soil microbial functional diversity based on community aggregated traits. (springernature.com)
It can be used to explore the diversity, function, and ecology of microbial communities. (bioinformatics.ca)

A global dataset of microbial community in ticks from metagenome study. (cdc.gov)
By assessing genomic traits of soil bacteria using a global dataset of soil metagenomes, our study could be an important step towards filling this knowledge gap. (springernature.com)
A characterisation of the dominant trait dimensions, using a global dataset, as it has been done for plant 4 , was lacking. (springernature.com)

We quantified strain-level dynamics of 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. (nature.com)

A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. (glbrc.org)
The recovery of metagenome assembled genomes (MAGs) of these organisms enables in-depth analysis of the functional potential of these, often elusive, organisms. (researchsquare.com)
To address this, we developed new approaches to improve the recovery of eukaryotic MAGs and applied these to large collections of assembled metagenomes in an effort to systematically identify both prokaryotic and eukaryotic MAGs. (researchsquare.com)
The goal of this study was to identify the combination of assembly and binning approaches that result in high-quality and -quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. (nsf.gov)
Furthermore, a combination of metaSPAdes coassembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. (nsf.gov)

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. (glbrc.org)
To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. (glbrc.org)
A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. (researchgate.net)
Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. (peerj.com)
Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
For instance, an expression time-series performed on microbial communities living in surface oceanic showed that processes of energy production were active in hours with light, while anabolic housekeeping processes were predominant during the night [ 4 ]. (biomedcentral.com)
Anonymous Reviewer ( 2017 ) Peer Review #1 of 'HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities (v0.2)' . (peerj.com)
Metagenome WGS assemblies consisting entirely of long reads have yet to be fully characterized, particularly those from complex, multi-kingdom symbiotic communities. (biomedcentral.com)
These metagenomic studies have been central to our understanding of microbial communities from both functional and genomic perspectives. (researchsquare.com)
The assembly of microbial communities and understanding the metabolic roles of each population is an important step to engineering microbial communities to carry out a desired function. (frontiersin.org)
ABSTRACT Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. (nsf.gov)
In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. (nsf.gov)
Using cultivation-independent metagenomic and metatranscriptomic approaches, we aimed to resolve the structural and functional biodiversity of freshwater microbial communities on a very fine scale. (europa.eu)
To enable comparative analysis between different microbial communities, we sampled two lakes in northeastern Germany at various occasions: Lake Stechlin and Lake Grosse Fuchskuhle. (europa.eu)
In addition to the molecular samples, we also measured a variety of environmental parameters for multivariate statistical analysis to link microbial communities to certain biogeochemical functions in the lakes. (europa.eu)

It comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. (cosmeticsandtoiletries.com)
Repetitive content contributes to difficulty in multicellular Eukaryotic genome assembly as well [ 4 ], but the problem becomes more complicated in metagenome assembly [ 5 ] due to the wide range of abundance among bacterial species and strains, and the presence of other environmental DNA (e.g., plants, protists). (biomedcentral.com)
The bovine rumen is an organ that serves as the site of symbiosis between the cow and microbial species from all three taxonomic superkingdoms of life that are dedicated to the degradation of highly recalcitrant plant polymers [ 13 ]. (biomedcentral.com)
While much attention has been given to the prokaryotic species and their functional capacity 2 - 4 , microbial eukaryotes such as fungi also perform key roles in many environments, for example by making carbon available and by creating new environments 5 . (researchsquare.com)
Even if cultivation were possible, isolation of all microbial species would be problematic due to the sheer number of species involved 6 . (researchsquare.com)
Identification of novel microbial species and quantification of their distributional variations among different samples that are sequenced using next-generation-sequencing technology hold the key to the success of most metagenomic studies. (nsf.gov)
The binary matrix can be used to separate microbial species and the nonnegative matrix quantifies the species distributions in different samples. (nsf.gov)

In this study, we assessed the performance of a combination of assembly and binning strategies for time series drinking water metagenomes that were collected over 6 months. (nsf.gov)

Here we conducted a meta-analysis of novel and published metagenomes from fecal samples collected before and after FMT to compare the fate of donor and recipient strain populations across multiple disease indications. (nature.com)
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. (mbl.edu)
Moreover, it is well recognized that the excessive use of broad-spectrum antibiotics can affect the relative proportions of gut microbial populations and foster bacterial resistance [24]. (deepdyve.com)
By infecting and lysing host cells, viruses can affect the composition of microbial populations and facilitate the transfer of organic matter from cells to the dissolved organic matter pool via the "viral shunt" [ 9 ], and when consumed by small phagotrophs, viruses facilitate the movement of organic matter into the classical food web, which is called the "viral sweep" [ 10 ]. (biomedcentral.com)
Here, we present a comprehensive analysis of cat and dog gut microbiomes, incorporating 2,423 stool shotgun metagenomes (2,056 dog and 367 cat) spanning 12 publicly available datasets (n=513) and 7 populations newly presented in this study (n=1,910). (harvard.edu)

More recently, as throughput and accuracy have increased, it has been possible to consider work involving more complex genomes and metagenomes. (earlham.ac.uk)

However, the high complexity and low inter-individual overlap of intestinal microbial composition are formidable barriers to identifying microbial taxa representing this dysbiosis. (escholarship.org)

Microbial modules thus provide an integrative view of microbial ecology relevant to IBD. (escholarship.org)

Shotgun metagenomes were analyzed at various taxonomic and functional levels, 1 H- and 13 C -metabolomes were processed using standard quantitative and human expert approaches, whereas metals were assessed using X-ray fluorescence spectrometry. (frontiersin.org)

While the sequencing of metagenomes provides an overview of the genes present in specific environments that can potentially play a role in adaptation, the analysis of expression provides a more precise picture of what functions are expressed and active in a particular moment of the environment. (biomedcentral.com)

In the published work, the authors combined bacterial cultivation and metagenomic sequencing to create the Skin Microbial Genome Collection (SMGC). (cosmeticsandtoiletries.com)
All microbial members (bacterial, archaeal, bacteriophage, viral, and fungal) have been included in this baseline dataset and both phylogenetic marker gene sequence [e.g. 16S rRNA, 18S rRNA, and internal transcribed spacer region (ITS)] and metagenomic whole genome shotgun sequence data were generated. (nih.gov)
Our efforts in these areas should lead to (i) fundamental advances in metagenomic binning, (ii) development and refinement of technology for the rapid identification and quantification of microbial distributions and (iii) finding of potential probiotics or reliable pathogenic bacterial strains. (nsf.gov)

The PlanHab wash-out period corresponded to a profound life-style change (i.e., reintroduction of exercise) that resulted in stepwise amelioration of the negative physiological symptoms, indicating that exercise apparently prevented the crosstalk between the microbial physiology, mucin degradation and proinflammatory immune activities in the host. (frontiersin.org)
Thus, research into the fast and complete degradation of BPA, and other compounds via microbial means is of great interest. (rsc.org)
Our current approaches of developing more efficient enzyme cocktails and improving biomass conversion rely largely on expanding our knowledge on the microbial degradation and utilization of plant biomass. (biomedcentral.com)

In this presentation I will describe out latest efforts in understanding the microbial biodiversity found in different environmental samples. (x-meeting.com)

Yu and colleagues (2019) 3 were able to effectively combine multi-omics data to analyze a microbial community's ability to break down bisphenol A (BPA) products. (rsc.org)
Through a clever multi-omics design, the authors were able to use three major types of integrated analyses to identify differences in encoded and expressed microbial functions that were involved in the BPA-degrading microbial community. (rsc.org)
As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. (biomedcentral.com)
A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. (biomedcentral.com)
IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. (biomedcentral.com)

Her laboratory is dedicated to the study of host-microbial symbioses in diverse systems, especially characterizing microbiomes to understand the co-evolution, transmission and functions of microbial-host symbioses in a wide variety of phenotypes and biological systems. (appliedmicrobiology.org)

The presence of organisms from all major superkingdoms in varying degrees of abundance makes the rumen an excellent model for a complex, partially characterized metagenome system. (biomedcentral.com)
These modules were unprecedented, as they were detectable in all individuals, and their composition and abundance was recapitulated in an independent, biopsy-based mucosal dataset 2 modules were associated with healthy, CD, or UC disease states. (escholarship.org)
We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. (knaw.nl)

With efficiency unrivaled by most abiotic industrial processes, the protists, archaea, bacteria, and fungi that make up the rumen microbial community are able to process cellulose and other plant biopolymers into byproducts, such as volatile fatty acids (VFA), that can be utilized by the host. (biomedcentral.com)

We demonstrated the power of our high-speed function annotation method, mi-faser, by analysing ~ 400 shotgun metagenomes in 2 days, with the results recapitulating functional signals of different city subway microbiomes. (biomedcentral.com)

In 2014 the American Academy of Microbiology published a FAQ that emphasized that the number of microbial cells and the number of human cells are both estimates, and noted that recent research had arrived at a new estimate of the number of human cells at around 37 trillion cells, meaning that the ratio of microbial to human cells is probably about 3:1. (wikipedia.org)
In this study now published in Nature Microbiology , we decided to focus on bacteria that dominate the soil metagenomes. (springernature.com)

One area of significant growth has been the assembly of datasets, and the subsequent elucidation of genomes, so called metagenome assembled genomes (MAG). (x-meeting.com)
Many of the initial publications concerning the platform focussed on provision of tools to access and analyse the new sequence formats and then demonstrating the assembly of microbial genomes. (earlham.ac.uk)

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. (biomedcentral.com)
Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. (biomedcentral.com)
We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community. (biomedcentral.com)
Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible. (biomedcentral.com)
Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. (biomedcentral.com)

We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a controlled laboratory environment (circadian rhythm, fluid and dietary intakes, microbial bioburden, oxygen level, exercise). (frontiersin.org)
The epithelium function and the mucosal associated immune system are influenced by direct host-microbiota interactions and through modulation of the microbial metabolism [7]. (deepdyve.com)

We developed an ensemble approach that exploits k-mer and reference-based strategies to improve eukaryotic sequence identification from metagenomes and identified MetaBAT2 as the best performing binning approach for clustering of eukaryotic sequences. (sciety.org)

Microbial community dynamics are dictated by both abiotic environmental conditions and biotic interactions. (researchgate.net)

«MicroScope -- an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data» , Brief Bioinform, 2017 Sep. (cns.fr)
«MicroScope -- an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data» , Nucleic Acids Res. (cns.fr)

These difficulties might be overcome by an ecologic analytic strategy to identify modules of interacting bacteria (rather than individual bacteria) as quantitative reproducible features of microbial composition in normal and IBD mucosa. (escholarship.org)

Microbial consortia represent promising candidates for aiding in the development of plant biomass conversion strategies for biofuel production. (biomedcentral.com)

The highly preserved microbial modules accurately classified IBD status of individual patients during disease quiescence, suggesting that microbial dysbiosis in IBD may be an underlying disorder independent of disease activity. (escholarship.org)

«MicroScope: a platform for microbial genome annotation and comparative genomics» , Database (Oxford), 2009. (cns.fr)

Thus, it can be broadly used to identify disease-related microbial organisms that are not well-studied. (nsf.gov)

A high-throughput and low-cost method is needed to achieve industry-wide implementation of metagenome profiles into livestock production. (biomedcentral.com)

Over the past decade, the number of metagenome assemblies available has increased significantly. (researchsquare.com)

which is a web-based platform for microbial comparative genome analysis and manual functional annotation. (cns.fr)
«MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis» , Nucleic Acids Res. (cns.fr)
«MaGe: a microbial genome annotation system supported by synteny results» , Nucleic Acids Res. (cns.fr)

The human sequence dataset are under controlled access but can be requested for appropriate research purposes from NIH's database of genotypes and phenotypes ( dbGaP ). (nih.gov)

A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. (peerj.com)

The datasets presented in this study can be found in online repositories. (glbrc.org)
The authors switched to metagenome assemblers for the simulation study. (peerj.com)
Two of these are notable: the HMP Data Analysis and Coordination Center and the Qiita web-based microbial study management platform. (nih.gov)
Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. (nih.gov)
We present here a comprehensive study on the community structure and enzyme systems of a lignocellulolytic microbial consortium EMSD5 during growth on corn stover, using metagenome sequencing in combination with quantitative metaproteomics. (biomedcentral.com)
Looking at available global datasets, I found the study by Bahram et al. (springernature.com)
The use of the omic approach to study microbial traits was beginning to be used in some studies, including some by my new colleagues at the University of California Irvine 13,14 . (springernature.com)

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. (mbl.edu)
These results highlight the potential impact of gene regulation in the adaptation of bacteria to the different habitats through the distribution of their regulatory potential among specific functions, and point to critical environmental factors that challenge the growth of any microbial community. (biomedcentral.com)
These results demonstrate that the corn stover-adapted microbial consortium EMSD5 harbors a variety of lignocellulolytic anaerobic bacteria and degradative enzymes, especially those implicated in hemicellulose decomposition. (biomedcentral.com)

As a part of the 2018 CAMDA challenge, we functionally profiled the available ~ 400 subway metagenomes and built predictor for city origin. (biomedcentral.com)
For the purposes of the 2018 CAMDA (Critical Assessment of Massive Data Analysis) challenge, we used mi-faser to functionally profile 392 MetaSUB metagenome datasets -- 310 samples from eight cities provided as the training set and 82 samples in need of evaluation/prediction, including eight training city and new city samples. (biomedcentral.com)

Systematic effects were found to have minimal influence on metagenome profiles. (biomedcentral.com)

Here, we performed a meta-analysis of marine metagenomes from pelagic regions of the oceans around the globe, which includes previously published and new metagenomes from the South Atlantic Ocean, a poorly characterized marine realm. (peerj.com)
It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. (bvsalud.org)
Analysis of weighted co-occurrence network revealed 5 microbial modules. (escholarship.org)
Imputed metagenome analysis indicated that these modules displayed distinct metabolic functionality, specifically the enrichment of oxidative response and glycan metabolism pathways relevant to host-pathogen interaction in the disease-associated modules. (escholarship.org)
Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. (nih.gov)
The CBW has developed a 3-day course providing an introduction to metagenomic data analysis followed by hands-on practical tutorials demonstrating the use of metagenome analysis tools. (bioinformatics.ca)

Processes such as host-microbe crosstalk, immune activation and inflammation, microbe-microbe signalling, microbial metabolism and antimicrobial activity are bioactive in the human gut [3]. (deepdyve.com)

Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. (biomedcentral.com)

Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. (researchgate.net)

Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. (frontiersin.org)

Anatomy3

Organisms15

Chemicals and Drugs11

Analytical, Diagnostic and Therapeutic Techniques and Equipment24

Phenomena and Processes36

Disciplines and Occupations10

Technology, Industry, Agriculture2

Humanities1

Information Science28

Health Care21

Geographicals2

Microbiome18

Metagenomic datasets6

Metagenomics8

Diversity12

Global dataset3

Constructed metagenome-assembled genomes1

MAGs5

Communities15

Species7

Drinking water metagenomes1

Populations5

Genomes and metagenomes1

Taxa1

Ecology1

Taxonomic1

Genes1

Bacterial3

Degradation3

Biodiversity1

Multi-omics5

Host-microbial1

Abundance3

Fungi1

Microbiomes1

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Microbiota2

Sequences1

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Genomic and metabolic2

Composition1

Consortia1

Dysbiosis1

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Organisms1

High-throughput1

Assemblies1

Annotation3

Phenotypes1

Microorganisms1

Study7

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20182

Systematic1

Analysis6

Crosstalk1

Metabolism1

Significantly1

Consortium1