ArticleiScience2020
Environmental Atlas of Prokaryotes Enables Powerful and Intuitive Habitat-Based Analysis of Community Structures.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Molecular evolution and diversity of isomerase-reductase clusters involved in the bacterial metabolism of glycosaminoglycans.mSphere · 2026Article
- Genomic and Functional Characterization ofFrontiers in microbiology · 2026Article
- Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats.ISME communications · 2026Article
- Gut microbiome shifts during frog development parallel host-association patterns across vertebrate lineages.Frontiers in microbiology · 2026Article
- Culture-independent discovery of a novel thermotolerant lipase and its producer from mesophilic anaerobic digestion sludge.Applied microbiology and biotechnology · 2025Article
- Experimental mapping of bacterial fitness landscapes reveals eco-evolutionary fingerprints.Scientific reports · 2025Article
- Repeatability of protein structural evolution following convergent gene fusions.Nature communications · 2025Article
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- Bacterial lifestyle shapes pangenomes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The recent prevalence of high-throughput sequencing has been producing numerous prokaryotic community structure datasets. Although the trait-based approach is useful to interpret those datasets from ecological perspectives, available trait information is biased toward culturable prokaryotes, especially those of clinical and public health relevance, and thus may not represent the breadth of microbiota found across many of Earth's environments. To facilitate habitat-based analysis free of such bias, here we report a ready-to-use prokaryotic habitat database, ProkAtlas. ProkAtlas comprehensively links 16S rRNA gene sequences to prokaryotic habitats, using public shotgun metagenome datasets. We also developed a computational pipeline for habitat-based analysis of given prokaryotic community structures. After confirmation of the method effectiveness using 16S rRNA gene sequence datasets from individual genomes and the Earth Microbiome Project, we showed its validness and effectiveness in drawing ecological insights by applying it to six empirical prokaryotic community datasets from soil, aquatic, and human gut samples.
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