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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Journal ArticleDOI
A Protocol for Species Delineation of Public DNA Databases, Applied to the Insecta.
Douglas Chesters,Chao-Dong Zhu +1 more
TL;DR: The L × S matrix represents a post-taxonomic framework that can be used for species-level organization of metagenomic data, and incorporation of these methods into phylogenetic pipelines will yield matrices more representative of species diversity.
Journal ArticleDOI
Labedella phragmitis sp. nov. and Labedella populi sp. nov., two endophytic actinobacteria isolated from plants in the Taklamakan Desert and emended description of the genus Labedella.
TL;DR: Two novel strains, isolated from surface-sterilized plant tissues collected from the Taklamakan Desert in the Xinjiang Uygur Autonomous Region, China, showed chemotaxonomic characteristics and phenotypic properties in agreement with the description of the genus Labedella and also confirmed the differentiation from the closest species.
Journal ArticleDOI
Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation
Daniel Podlesny,Cesar Arze,Elisabeth Dörner,Sandeep Verma,Sudhir Dutta,J. Walter,W. Florian Fricke +6 more
TL;DR: SameStr as mentioned in this paper identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity.
Posted ContentDOI
Extensive Transmission of Microbes along the Gastrointestinal Tract
Thomas Schmidt,Matthew R. Hayward,Luis Pedro Coelho,Simone S. Li,Paul I. Costea,Anita Y. Voigt,Jakob Wirbel,Oleksandr M. Maistrenko,Renato J. Alves,Emma Bergsten,Carine de Beaufort,Iradj Sobhani,Anna Heintz-Buschart,Shinichi Sunagawa,Georg Zeller,Paul Wilmes,Peer Bork +16 more
TL;DR: Evidence is found for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens.
Journal ArticleDOI
High-Quality Draft Genome Sequence of Pseudomonas sp. BRG100, a Strain with Bioherbicidal Properties against Setaria viridis (Green Foxtail) and Other Pests of Agricultural Significance
Tim J. Dumonceaux,Tim J. Dumonceaux,Jennifer Town,Jennifer Town,Matthew G. Links,Matthew G. Links,Sue Boyetchko +6 more
TL;DR: Genome sequence comparisons revealed that this strain may represent a novel species of Pseudomonas, and is a potentially useful biopesticide for weeds and plant diseases.
References
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