Journal ArticleDOI
Accurate and universal delineation of prokaryotic species
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TLDR
The specI (species identification tool) as mentioned in this paper ) is a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes, applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters.Abstract:
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.read more
Citations
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Polarization of microbial communities between competitive and cooperative metabolism.
Daniel Machado,Daniel Machado,Oleksandr M. Maistrenko,Sergej Andrejev,Yongkyu Kim,Peer Bork,Kaustubh R. Patil,Kiran Raosaheb Patil,Kiran Raosaheb Patil +8 more
TL;DR: In this paper, the authors use genome-scale metabolic modeling to assess the potential for resource competition and metabolic cooperation in large co-occurring groups (up to 40 members) across thousands of habitats.
Journal ArticleDOI
metaSNV: A tool for metagenomic strain level analysis.
TL;DR: MetaSNV as mentioned in this paper is a tool for single nucleotide variant (SNV) analysis in metagenomic samples, capable of comparing populations of thousands of bacterial and archaeal species.
Journal ArticleDOI
TIPP: taxonomic identification and phylogenetic profiling.
TL;DR: TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn.
Journal ArticleDOI
The microbiomes of blowflies and houseflies as bacterial transmission reservoirs
Ana Carolina M. Junqueira,Ana Carolina M. Junqueira,Aakrosh Ratan,Enzo Acerbi,Daniela I. Drautz-Moses,Balakrishnan N. V. Premkrishnan,Paul I. Costea,Bodo Linz,Rikky W. Purbojati,Daniel F. Paulo,Nicolas E. Gaultier,Poorani Subramanian,Nur A. Hasan,Rita R. Colwell,Rita R. Colwell,Peer Bork,Ana Maria Lima de Azeredo-Espin,Donald A. Bryant,Donald A. Bryant,Stephan C. Schuster +19 more
TL;DR: The environmental sequencing approach presented here detected a stochastic distribution of human pathogens, such as Helicobacter pylori, thereby demonstrating the potential of flies as proxies for environmental and public health surveillance.
Journal ArticleDOI
A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations
TL;DR: A metric of recent gene flow is introduced, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin, to facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals.
References
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