ArticleGenome research2010
A global network of coexisting microbes from environmental and whole-genome sequence data.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 211 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
211 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease.Frontiers in physiology · 2022Pooled it
- Spatiotemporal Variations in Microbial Community Structure and Assembly Mechanisms Within Recirculating Aquaculture Systems for Mandarin Fish (Microorganisms · 2026Article
- The Importance ofMicroorganisms · 2026Article
- Plant diversity induces shifts from microbial generalists to specialist by enhancing niche differentiation, microbiome connectivity, and network stability in a temperate grassland.Environmental microbiome · 2026Article
- Single-cell assembled genomes predict enhanced bacterial metabolic cross-feeding potential in carbon-enriched soils.The ISME journal · 2026Article
- N2SIMBA: from Network topology to SIMulation of interactions and BActerial abundance, using microbial consumer resource model.Frontiers in bioinformatics · 2026Article
- Gut Microbiome of Two Rodent Species (Animals : an open access journal from MDPI · 2025Article
- Decoding microbial diversity, biogeochemical functions, and interaction potentials in red sea hydrothermal vents.Environmental microbiome · 2025Article
- Microbiome data integration via shared dictionary learning.Nature communications · 2025Article
- Correlation with viruses enhances network complexity and stability of co-occurrence prokaryotes across the oceans.mSystems · 2025Article
- Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China.Microbial ecology · 2025Article
- Exploring the structure and assembly of seagrass microbial communities in rhizosphere and phyllosphere.Applied and environmental microbiology · 2025Article
- Article
- Temporal profiling of rumen and hindgut microbiota revealed enterotypes affecting the microbial interactions and assembly in the gut of dairy cows.ISME communications · 2025Article
- Networks as tools for defining emergent properties of microbiomes and their stability.Microbiome · 2024Review
- From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Assembling bacterial puzzles: piecing together functions into microbial pathways.NAR genomics and bioinformatics · 2024Article
- Article
- A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data.BMC bioinformatics · 2024Article
- Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities.Nature communications · 2024Article
151 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.