Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: A communal catalogue reveals Earth’s multiscale microbial diversity

Journal Article · · Nature (London)
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, we find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE; W.M. Keck Foundation; National Science Foundation (NSF); Australian Research Council; National Oceanic and Atmospheric Administration (NOAA)
Contributing Organization:
The Earth Microbiome Project Consortium
Grant/Contract Number:
AC05-76RL01830; AC02-06CH11357
OSTI ID:
1411914
Alternate ID(s):
OSTI ID: 1467890
Report Number(s):
PNNL-SA-123888
Journal Information:
Nature (London), Vol. 551; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 1285 works
Citation information provided by
Web of Science

References (91)

A Mathematical Theory of Communication journal July 1948
Global patterns in bacterial diversity journal June 2007
Uberon, an integrative multi-species anatomy ontology journal January 2012
Microbial diversity in the deep sea and the underexplored "rare biosphere" journal July 2006
A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies journal February 2016
Determinants of community structure in the global plankton interactome journal May 2015
Decreases in average bacterial community rRNA operon copy number during succession journal November 2015
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies journal July 2016
Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys journal December 2015
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences journal August 2013
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications journal May 2011
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea journal December 2011
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project journal January 2010
Quantifying human impact on Earth's microbiome journal August 2016
A consumer's guide to nestedness analysis journal January 2009
Worlds within worlds: evolution of the vertebrate gut microbiota journal October 2008
The environment ontology: contextualising biological and biomedical entities journal January 2013
Global marine bacterial diversity peaks at high latitudes in winter journal March 2013
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample journal June 2010
Investigating causality of nestedness of insular communities: selective immigrations or extinctions? journal September 1996
The Earth Microbiome project: successes and aspirations journal August 2014
Ironing out the wrinkles in the rare biosphere through improved OTU clustering: Ironing out the wrinkles in the rare biosphere journal March 2010
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton journal June 2015
Simple and efficient fully-functional succinct trees journal December 2016
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses journal November 2014
Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences journal January 2014
A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement journal August 2008
Ribosomal Database Project: data and tools for high throughput rRNA analysis journal November 2013
Conservation evaluation and phylogenetic diversity journal January 1992
Microbial Ecology and Evolution: A Ribosomal RNA Approach journal October 1986
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses journal December 2012
Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales journal June 2017
Marine bacterial, archaeal and protistan association networks reveal ecological linkages journal March 2011
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies journal January 2014
Going back to the roots: the microbial ecology of the rhizosphere journal September 2013
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools journal November 2012
pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution journal January 2017
Building Predictive Models in R Using the caret Package journal January 2008
An ontology for microbial phenotypes journal November 2014
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation journal September 2016
Pasteurella multocida—The major cause of hand infections following domestic animal bites journal January 1982
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data journal October 2012
Low diversity of planktonic bacteria in the tropical ocean journal January 2016
Spatial Gaps in Global Biodiversity Information and the Role of 
Citizen Science journal March 2016
VSEARCH: a versatile open source tool for metagenomics journal January 2016
The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta-analyses: Mass Production of Systematic Reviews and Meta-analyses journal September 2016
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies journal October 2015
The measure of order and disorder in the distribution of species in fragmented habitat journal December 1993
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity journal February 2016
Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches journal September 2012
A new view of the tree of life journal April 2016
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome journal July 2012
A meta-analysis of changes in bacterial and archaeal communities with time journal April 2013
QIIME allows analysis of high-throughput community sequencing data journal April 2010
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data journal August 2009
Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes: Bacterial biogeography in arctic soils journal November 2010
Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals journal July 2016
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria journal April 2000
Controlling False Discoveries in Multidimensional Directional Decisions, with Applications to Gene Expression Data on Ordered Categories journal July 2009
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree journal October 2010
The diversity and biogeography of soil bacterial communities journal January 2006
Temperature mediates continental-scale diversity of microbes in forest soils journal July 2016
Cython: The Best of Both Worlds journal March 2011
A unified initiative to harness Earth's microbiomes journal October 2015
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms journal March 2012
EMPeror: a tool for visualizing high-throughput microbial community data journal November 2013
Diet-induced extinctions in the gut microbiota compound over generations journal January 2016
On the Generality of the Latitudinal Diversity Gradient journal February 2004
Bayesian community-wide culture-independent microbial source tracking journal July 2011
A latitudinal diversity gradient in planktonic marine bacteria journal May 2008
Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss journal April 2014
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies journal December 2011
DNA Sequencing as a Tool to Monitor Marine Ecological Status journal May 2017
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis journal July 2017
A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity [Supplemental Data]
  • Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
  • Zenodo-Supplementary information for journal article at DOI: 10.1038/nature24621, 33 files (47.3 GB) https://doi.org/10.5281/zenodo.890000
dataset November 2017
A communal catalogue reveals Earth's multiscale microbial diversity dataset November 2017
Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula journal June 2020
The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change journal April 2021
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. text January 2014
A Mathematical Theory of Communication journal October 1948
pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution text January 2017
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree preprint January 2010
VSEARCH: a versatile open source tool for metagenomics text January 2016
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms journal March 2012
Worlds within worlds: evolution of the vertebrate gut microbiota journal October 2008
The diversity and biogeography of soil bacterial communities journal January 2006
Global patterns in bacterial diversity journal June 2007
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data journal October 2012
A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies journal February 2016
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project journal January 2010
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree preprint January 2010

Cited By (260)

Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing journal January 2020
Structural changes of the microplankton community following a pulse of inorganic nitrogen in a eutrophic river journal January 2020
Evaluation of accuracy and precision in an amplicon sequencing workflow for marine protist communities journal December 2019
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia ( Oreochromis shiranus ) and North African catfish ( Clarias gariepinus ) journal March 2018
Oxic Methane Cycling: New Evidence for Methane Formation in Oxic Lake Water book January 2019
Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses journal April 2019
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists journal February 2020
Salt Marsh Greenhouse Gas Fluxes and Microbial Communities Are Not Sensitive to the First Year of Precipitation Change journal May 2019
Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide journal March 2019
How sample heterogeneity can obscure the signal of microbial interactions journal June 2019
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy journal May 2019
Bacterial adaptation is constrained in complex communities journal February 2020
Bacterial diversification through geological time journal July 2018
Community richness of amphibian skin bacteria correlates with bioclimate at the global scale journal February 2019
Transmission of human-associated microbiota along family and social networks journal March 2019
Community profiling of the urinary microbiota: considerations for low-biomass samples journal October 2018
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases journal May 2019
Striped UniFrac: enabling microbiome analysis at unprecedented scale journal October 2018
Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling journal July 2019
Nutrient-based diet modifications impact on the gut microbiome of the Javan slow loris (Nycticebus javanicus) journal March 2019
Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study journal February 2020
A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns journal February 2020
Restoring subtidal marine macrophytes in the Anthropocene: trajectories and future-proofing journal January 2019
Changes in bacterial community composition across natural grassland and pine forests in the Bunya Mountains in subtropical Australia journal January 2019
Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments journal February 2018
Redox traits characterize the organization of global microbial communities journal February 2019
Chemical and microbial diversity covary in fresh water to influence ecosystem functioning journal November 2019
Initial Evidence of the Relationships between the Human Postmortem Microbiome and Neighborhood Blight and Greening Efforts journal February 2019
Methods for automatic reference trees and multilevel phylogenetic placement journal August 2018
Rapid alignment-free phylogenetic identification of metagenomic sequences journal January 2019
Interaction between ferruginous clay sediment and an iron-reducing hyperthermophilic Pyrobaculum sp. in a terrestrial hot spring journal August 2018
Inevitable future: space colonization beyond Earth with microbes first journal August 2019
Untapped sponge microbiomes: structure specificity at host order and family levels journal August 2019
HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes journal February 2020
Host identity and symbiotic association affects the taxonomic and functional diversity of the clownfish-hosting sea anemone microbiome journal February 2020
Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14
  • Kochetkova, Tatiana V.; Zayulina, Kseniya S.; Zhigarkov, Vyacheslav S.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2 https://doi.org/10.1099/ijsem.0.003902
journal February 2020
Selection, succession and stabilization of soil microbial consortia posted_content January 2019
A high-resolution pipeline for 16S-sequencing identifies bacterial strains in human microbiome posted_content March 2019
In Search of Model Ecological Systems for Understanding Specialized Metabolism journal March 2018
Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes journal September 2019
SEDE-GPS: socio-economic data enrichment based on GPS information journal November 2018
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data journal November 2019
Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol journal August 2018
tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies journal December 2019
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men journal November 2018
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces journal April 2019
Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets journal May 2019
Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance journal January 2020
Microbial communities from arid environments on a global scale. A systematic review journal July 2020
Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements journal November 2019
A census-based estimate of Earth's bacterial and archaeal diversity journal February 2019
High-order interactions distort the functional landscape of microbial consortia journal December 2019
Latent environment allocation of microbial community data journal June 2018
Erythritol as a single carbon source improves cultural isolation of Burkholderia pseudomallei from rice paddy soils journal October 2019
The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities journal January 2019
Microbial Community Analysis of Sauerkraut Fermentation Reveals a Stable and Rapidly Established Community journal May 2018
Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils journal June 2018
Comparison of extraction methods for recovering ancient microbial DNA from paleofeces journal November 2019
Think global, act local: The small‐scale environment mainly influences microbial community development and function in lake sediment journal January 2020
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles journal January 2020
Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea journal August 2018
Microbial assemblages and bioindicators as proxies for ecosystem health status: potential and limitations journal June 2019
Clinician Guide to Microbiome Testing journal September 2018
Evolutionary constraints on species diversity in marine bacterioplankton communities journal January 2019
Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov journal August 2019
Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity journal March 2019
Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences journal August 2019
Global diversity and biogeography of bacterial communities in wastewater treatment plants journal May 2019
FEAST: fast expectation-maximization for microbial source tracking journal June 2019
Differences in the fecal microbiota of neonates born at home or in the hospital journal October 2018
Uncovering the hidden marine sponge microbiome by applying a multi-primer approach journal April 2019
Current challenges and best-practice protocols for microbiome analysis journal December 2019
Characterization of the microbiome and bioluminescent symbionts across life stages of Ceratioid Anglerfishes of the Gulf of Mexico journal September 2019
Bacterial–fungal interactions: ecology, mechanisms and challenges journal February 2018
From hairballs to hypotheses–biological insights from microbial networks journal July 2018
Systematic processing of ribosomal RNA gene amplicon sequencing data journal December 2019
Mechanisms of soil bacterial and fungal community assembly differ among and within islands journal December 2019
Interactome‐based abiotic and biotic impacts on biodiversity of plankton communities in disturbed wetlands journal June 2019
Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants journal May 2019
Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis journal January 2018
Introduction: The host-associated microbiome: Pattern, process and function journal April 2018
Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose journal February 2019
The power of crowds: Grand challenges in the Asia-Pacific region journal September 2019
EMPeror: a tool for visualizing high-throughput microbial community data journal November 2013
Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks journal November 2019
DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products journal July 2019
Charting the diversity of uncultured viruses of Archaea and Bacteria journal December 2019
Expanding the scope and scale of microbiome research journal September 2019
Challenges in the construction of knowledge bases for human microbiome-disease associations journal September 2019
A conceptual framework for the phylogenetically constrained assembly of microbial communities journal October 2019
Chemical and microbial diversity covary in fresh water to influence ecosystem functioning text January 2019
Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment journal February 2019
Does Soil Contribute to the Human Gut Microbiome? journal August 2019
A hierarchy of environmental covariates control the global biogeography of soil bacterial richness text January 2019
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance text January 2019
Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate text January 2020
The effect of captivity on the primate gut microbiome varies with host dietary niche journal November 2019
Response and driving factors of soil microbial diversity related to global nitrogen addition journal October 2019
Oxic Methane Cycling: New Evidence for Methane Formation in Oxic Lake Water book January 2018
Cross-Biome Drivers of Soil Bacterial Alpha Diversity on a Worldwide Scale journal January 2019
Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy journal June 2019
Home chemical and microbial transitions across urbanization journal November 2019
The hunt for the most-wanted chemolithoautotrophic spookmicrobes journal April 2018
Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju journal July 2020
MGnify: the microbiome analysis resource in 2020 journal November 2019
Contrasting patterns of plant and microbial diversity during long-term ecosystem development journal January 2019
Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest journal December 2019
Towards a systematic understanding of differences between archaeal and bacterial diversity: Systematic understanding of differences journal November 2018
Host genetic determinants of the gut microbiota of wild mice journal June 2019
The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution journal September 2019
Inferring macro‐ecological patterns from local presence/absence data journal August 2019
Metagenome Sequences of Sediment from a Recovering Industrialized Appalachian River in West Virginia journal May 2018
Microbiomes In Natura : Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions journal April 2018
Metagenomic Approaches for Understanding New Concepts in Microbial Science journal August 2018
Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions journal January 2019
Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice journal December 2019
Parasite microbiome project: Grand challenges journal October 2019
Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition journal June 2018
Global Observational Needs and Resources for Marine Biodiversity journal July 2019
A Response to Scientific and Societal Needs for Marine Biological Observations journal July 2019
Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function journal August 2018
Optimal Microbiome Networks: Macroecology and Criticality journal May 2019
Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling journal June 2019
Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes text January 2020
Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis journal October 2018
Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework text January 2019
The gut microbiome of nonhuman primates: Lessons in ecology and evolution journal June 2018
Advancements in Microbial Genome Sequencing and Microbial Community Characterization book January 2019
Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity journal July 2018
Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome journal January 2020
Community-level signatures of ecological succession in natural bacterial communities journal May 2020
Polarization of microbial communities between competitive and cooperative metabolism journal January 2021
Soil microbiomes and climate change journal October 2019
Marchantia liverworts as a proxy to plants’ basal microbiomes journal August 2018
The known and the unknown in soil microbial ecology journal January 2019
Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis journal March 2019
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments journal May 2018
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data journal October 2018
Conserving the holobiont journal April 2020
Microbial diversity and biogeography in Arctic soils: Microbial diversity and biogeography journal August 2018
Impacts of indoor surface finishes on bacterial viability journal May 2019
Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study
  • Saborío‐Montero, Alejandro; Gutiérrez‐Rivas, Mónica; García‐Rodríguez, Aser
  • Journal of Animal Breeding and Genetics, Vol. 137, Issue 1 https://doi.org/10.1111/jbg.12444
journal August 2019
DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions journal April 2019
Identifying and Predicting Novelty in Microbiome Studies journal December 2018
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease journal February 2019
Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner journal April 2019
High-throughput DNA sequencing technologies for water and wastewater analysis journal October 2019
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus journal November 2018
Coexistence and cooperation in structured habitats journal March 2020
A global survey of arsenic-related genes in soil microbiomes journal May 2019
CAMISIM: simulating metagenomes and microbial communities journal February 2019
Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities journal February 2019
The Microbial Landscape of Sea Stars and the Anatomical and Interspecies Variability of Their Microbiome journal August 2018
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands journal January 2019
Species abundance information improves sequence taxonomy classification accuracy journal October 2019
A meta-analysis of global fungal distribution reveals climate-driven patterns journal November 2019
Insect herbivory reshapes a native leaf microbiome journal January 2020
Airborne microbial transport limitation to isolated Antarctic soil habitats journal March 2019
Global change microbiology — big questions about small life for our future journal May 2019
Soil nematode abundance and functional group composition at a global scale journal July 2019
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions journal October 2019
Dormancy dynamics and dispersal contribute to soil microbiome resilience journal March 2020
Elucidating the ecological networks in stone‐dwelling microbiomes journal April 2020
Interdomain ecological networks between plants and microbes journal September 2019
Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate journal February 2020
Biogeography of soil bacteria and archaea across France journal July 2018
Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019 journal October 2019
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota journal January 2020
Microbiome of vineyard soils is shaped by geography and management journal November 2019
Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities journal November 2019
Microbial Diversity Exploration of Marine Hosts at Serrana Bank, a Coral Atoll of the Seaflower Biosphere Reserve journal June 2019
Simultaneous Metabarcoding of Eukaryotes and Prokaryotes to Elucidate the Community Structures within Tardigrade Microhabitats journal March 2020
Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models journal February 2018
Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents journal January 2019
Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage journal August 2019
Streaming histogram sketching for rapid microbiome analytics journal March 2019
The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities journal August 2019
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz journal January 2020
The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics journal January 2018
Latitudinal gradient of cyanobacterial diversity in tidal flats journal November 2019
Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere journal December 2019
The Community Simulator: A Python package for microbial ecology journal March 2020
The Role of Soil Fungi in K+ Plant Nutrition journal June 2019
Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota journal January 2020
A practical introduction to microbial molecular ecology through the use of isolation chips journal December 2018
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia ( Oreochromis shiranus ) and North African catfish ( Clarias gariepinus ) journal March 2018
Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles journal February 2019
The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks journal January 2019
Linking bacterial community composition to soil salinity along environmental gradients journal November 2018
Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide journal March 2019
Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov journal August 2019
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy journal May 2019
Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences journal August 2019
A meta-analysis of global fungal distribution reveals climate-driven patterns journal November 2019
Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes journal January 2020
Bacterial adaptation is constrained in complex communities journal February 2020
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases journal May 2019
Qiita: rapid, web-enabled microbiome meta-analysis journal October 2018
Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents journal January 2019
A hierarchy of environmental covariates control the global biogeography of soil bacterial richness journal August 2019
Metaphylogenetic analysis of global sewage reveals that bacterial strains associated with human disease show less degree of geographic clustering journal February 2020
Redox traits characterize the organization of global microbial communities journal February 2019
Quantifying Crop Rhizosphere Microbiome Ecology: The Next Frontier in Enhancing the Commercial Utility of Agricultural Microbes journal June 2018
Methods for automatic reference trees and multilevel phylogenetic placement journal August 2018
Biogeographical patterns in soil bacterial communities across the Arctic region journal August 2019
Characterization of the microbiome and bioluminescent symbionts across life stages of Ceratioid Anglerfishes of the Gulf of Mexico journal September 2019
Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic journal July 2019
HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes journal February 2020
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments journal May 2018
Systematic processing of ribosomal RNA gene amplicon sequencing data journal December 2019
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data journal October 2018
Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants journal May 2019
Impacts of indoor surface finishes on bacterial viability journal May 2019
Biogeography of soil bacteria and archaea across France journal July 2018
Asexual Reproduction Can Account for the High Diversity and Prevalence of Rare Taxa Observed in Microbial Communities journal May 2019
Metagenome Sequences of Sediment from a Recovering Industrialized Appalachian River in West Virginia journal May 2018
Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy” journal August 2019
Identifying and Predicting Novelty in Microbiome Studies journal December 2018
In Search of Model Ecological Systems for Understanding Specialized Metabolism journal March 2018
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease journal February 2019
Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019 journal October 2019
Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes journal September 2019
Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs journal April 2020
Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks journal November 2019
DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products journal July 2019
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus journal November 2018
Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol journal August 2018
Coexistence and cooperation in structured habitats journal March 2020
Charting the diversity of uncultured viruses of Archaea and Bacteria journal December 2019
Expanding the scope and scale of microbiome research journal September 2019
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families journal November 2019
tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies journal December 2019
Host-associated microbiomes are predicted by immune system complexity and climate journal February 2020
Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces journal April 2019
Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets journal May 2019
The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities journal August 2019
Challenges in the construction of knowledge bases for human microbiome-disease associations journal September 2019
A census-based estimate of Earth's bacterial and archaeal diversity journal February 2019
High-order interactions distort the functional landscape of microbial consortia journal December 2019
Low mutational load and high mutation rate variation in gut commensal bacteria journal March 2020
Latent environment allocation of microbial community data journal June 2018
Erythritol as a single carbon source improves cultural isolation of Burkholderia pseudomallei from rice paddy soils journal October 2019
Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere journal December 2019
Parasite microbiome project: Grand challenges journal October 2019
Gut microbial features can predict host phenotype response to protein deficiency journal December 2018
Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition journal June 2018
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal journal April 2018
The Rootstock Regulates Microbiome Diversity in Root and Rhizosphere Compartments of Vitis vinifera Cultivar Lambrusco journal September 2018
The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities journal January 2019
Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius) journal September 2019
Unconventional Oil and Gas Energy Systems: An Unidentified Hotspot of Antimicrobial Resistance? journal October 2019
The Effects of Temperature on Animal Gut Microbiomes journal March 2020
The Role of Soil Fungi in K+ Plant Nutrition journal June 2019
Microbial Transformations of Organically Fermented Foods journal August 2019
Characterizing the Composition of the Pediatric Gut Microbiome: A Systematic Review journal December 2019
The Community Simulator: A Python package for microbial ecology text January 2019
Porting and optimizing UniFrac for GPUs text January 2020
Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets journal January 2019
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands journal January 2019
DISCo-microbe: design of an identifiable synthetic community of microbes journal January 2020

Figures / Tables (11)

Figure 1 | Environment type and provenance of samples.(p. 2)figure Figure 1 | Environment type and provenance of samples.
Figure 2 | Alpha-diversity, beta-diversity, and predicted average 16S rRNA gene copy number(p. 4)figure Figure 2 | Alpha-diversity, beta-diversity, and predicted average 16S rRNA gene copy number
Figure 3 | Nestedness of community composition(p. 5)figure Figure 3 | Nestedness of community composition
Figure 4 | Specificity of sequences and higher taxonomic groups for environment(p. 6)figure Figure 4 | Specificity of sequences and higher taxonomic groups for environment
Extended Data Figure 1 | Physicochemical properties of the EMP samples(p. 14)figure Extended Data Figure 1 | Physicochemical properties of the EMP samples
Extended Data Figure 2 | Sequence length, database effects, and beta-diversity patterns(p. 15)figure Extended Data Figure 2 | Sequence length, database effects, and beta-diversity patterns
Extended Data Figure 3 | Sequence length effects on observed diversity patterns(p. 16)figure Extended Data Figure 3 | Sequence length effects on observed diversity patterns
Extended Data Figure 4 | Tag sequence prevalence patterns(p. 17)figure Extended Data Figure 4 | Tag sequence prevalence patterns
Extended Data Figure 5 | Environmental effect sizes, sample classification, and correlation patterns(p. 19)figure Extended Data Figure 5 | Environmental effect sizes, sample classification, and correlation patterns
Extended Data Figure 6 | NODF scores of nestedness across samples by taxonomic level(p. 20)figure Extended Data Figure 6 | NODF scores of nestedness across samples by taxonomic level
Extended Data Figure 7 | Subsets and EMP trading cards(p. 21)figure Extended Data Figure 7 | Subsets and EMP trading cards

Similar Records

Related Subjects

54 ENVIRONMENTAL SCIENCES
microbiome
Earth
global
59 BASIC BIOLOGICAL SCIENCES