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
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Draft Genome Sequences of Pseudomonas putida UV4 and UV4/95, Toluene Dioxygenase-Expressing Producers of cis-1,2-Dihydrodiols.
Timofey Skvortsov,Patrick Hoering,Ksenia Arkhipova,Roger C. Whitehead,Derek R. Boyd,Christopher C. R. Allen +5 more
TL;DR: Draft genome sequences of Pseudomonas putida strains UV4 and UV4/95 demonstrate an ability to conduct a wide range of industrially important biotransformations of arenes, alkenes, and phenols.
Journal ArticleDOI
Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean
Corentin Hochart,Lucas Paoli,Hans-Joachim Ruscheweyh,Guillem Salazar,Emilie Boissin,Sarah Romac,Julie Poulain,Guillaume Bourdin,Guillaume Iwankow,Clémentine Moulin,Maren Ziegler,Barbara Porro,Eric J. Armstrong,Benjamin C. C. Hume,Jean-Marc Aury,Claudia Pogoreutz,David A. Paz-García,Maggy M. Nugues,Sylvain Agostini,Bernard Banaigs,Emmanuel Boss,Chris Bowler,Colomban de Vargas,Eric Douville,Michel Flores,Didier Forcioli,Paola Furla,Eric Gilson,Fabien Lombard,Stephane Pesant,Stéphanie Reynaud,Olivier P. Thomas,Romain Troublé,Patrick Wincker,Didier Zoccola,Denis Allemand,Serge Planes,Rebecca Vega Thurber,Christian R. Voolstra,Shinichi Sunagawa,Pierre E. Galand +40 more
TL;DR: In this paper , the authors studied the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean.
Posted ContentDOI
Identifying Clostridioides difficile-inhibiting gut commensals using culturomics, phenotyping, and combinatorial community assembly
Sudeep Ghimire,Chayan Roy,Supapit Wongkuna,Linto Antony,Gavin J. Fenske,Abhijit Maji,Mitchell Chan Keena,Andrew Foley,Joy Scaria +8 more
TL;DR: The results show that the interaction of bacteria with each other in a mix and with other members of gut commensals must be investigated for designing defined bacterial mixes for inhibiting C. difficile in vivo.
Posted ContentDOI
Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation
Thomas Schmidt,Shanshan Li,Shanshan Li,Oleksandr M. Maistrenko,Akkani W,Luis Pedro Coelho,Dolai S,Anthony Fullam,Glazek A,Rajna Hercog,Hilde Herrema,Jung F,Stefanie Kandels,Askarbek Nurlanuly Orakov,Van Rossum T,Benes,Thomas J. Borody,de Vos Wm,de Vos Wm,Ponsioen Cy,Max Nieuwdorp,Peer Bork +21 more
TL;DR: In this paper, the authors quantified strain-level dynamics of 1,089 microbial species based on their pangenome, complemented with 47,548 newly constructed metagenome-assembled genomes.
References
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Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Book
Bergey's Manual of Systematic Bacteriology
TL;DR: BCL3 and Sheehy cite Bergey's manual of determinative bacteriology of which systematic bacteriology, first edition, is an expansion.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
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