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
Preliminary view of the global distribution and spread of the tet(X) family of tigecycline resistance genes.
TL;DR: The results provide the first view of the global distribution of tet (X) genes, demonstrate the features of tet(X)-carrying fragments and highlight the possible evolution of tigecycline-inactivation enzymes in diverse bacterial species and habitats.
Journal ArticleDOI
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Supriya Khedkar,Georgy Smyshlyaev,Ivica Letunic,Oleksandr M. Maistrenko,Luís Coelho,Askarbek N Orakov,Sofia K. Forslund,Falk Hildebrand,Mechthild Luetge,Thomas Schmidt,Orsolya Barabas,Peer Bork +11 more
TL;DR: A computational framework is developed that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation, and established TEs as dominant carriers of antibiotic resistance genes.
Journal ArticleDOI
The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities.
Kevin D. Ricks,Roger T. Koide +1 more
TL;DR: Endophytic fungal communities in leaves of Bromus tectorum and Elymus elymoides, Chrysothamnus depressus and Artemisia tridentata, Alyssum alyssoides, and Atriplex canescens are analyzed to learn how to efficiently colonize revegetation plants using endophyticFungal inoculum.
Posted ContentDOI
A robust statistical framework for reconstructing genomes from metagenomic data
TL;DR: MetaBAT is developed, a robust statistical framework that integrates probabilistic distances of genome abundance with sequence composition for automatic binning that permits the identification of OTUs in large complex communities where many species are unknown.
Journal ArticleDOI
Complete genome sequence of Bacillus oceanisediminis 2691, a reservoir of heavy-metal resistance genes.
TL;DR: It is demonstrated that each cadC gene located in the chromosome or plasmid of 2691 cells are similar to those of various near or distant microbes, which might shed light on evolutionary trajectories of redundant heavy metal resistance genes.
References
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