ArticlePloS one2007
Predicting prokaryotic ecological niches using genome sequence analysis.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A bacterial sensor taxonomy across earth ecosystems for machine learning applications.mSystems · 2024Article
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- Vitamin A Deficiency Exacerbates Gut Microbiota Dysbiosis and Cognitive Deficits in Amyloid Precursor Protein/Presenilin 1 Transgenic Mice.Frontiers in aging neuroscience · 2021Article
- Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.Communications biology · 2020Article
- Genomics of the Pathogenic Clostridia.Microbiology spectrum · 2019Review
- Niche and fitness differences determine invasion success and impact in laboratory bacterial communities.The ISME journal · 2019Article
- Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling.PloS one · 2015Article
- Niches, population structure and genome reduction in Ochrobactrum intermedium: clues to technology-driven emergence of pathogens.PloS one · 2014Article
- Article
- Presence and diversity of Streptomyces in Dendroctonus and sympatric bark beetle galleries across North America.Microbial ecology · 2011Article
- The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes.PloS one · 2011Article
- Article
- A flood of microbial genomes-do we need more?PloS one · 2009Article
- Massive comparative genomic analysis reveals convergent evolution of specialized bacteria.Biology direct · 2009Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as 'mountains' on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.
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