Journal ArticleDOI
Accurate and universal delineation of prokaryotic species
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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HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Patrick W. Laffy,Elisha M. Wood-Charlson,Dmitrij Turaev,Karen D. Weynberg,Emmanuelle S. Botté,Madeleine J. H. van Oppen,Madeleine J. H. van Oppen,Nicole S. Webster,Thomas Rattei +8 more
TL;DR: Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVIR provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.
Journal ArticleDOI
Whole Genome Characterization of Bacillus cereus Associated with Specific Disease Manifestations
Ti-Cheng Chang,Jason W. Rosch,Zhengming Gu,Hana Hakim,C. Hewitt,Aditya H. Gaur,G. Wu,Randall T. Hayden +7 more
TL;DR: A whole-genome analysis of B. cereus isolates from patients with a range of disease manifestations, including noninvasive colonizing disease, superficial skin infections, and invasive bacteremia, was performed in this paper.
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.
Journal ArticleDOI
Aerococcus urinae Isolated from Women with Lower Urinary Tract Symptoms: In Vitro Aggregation and Genome Analysis
Evann E. Hilt,Catherine Putonti,Krystal Thomas-White,Amanda L. Lewis,Karen L. Visick,Nicole M. Gilbert,Alan J. Wolfe +6 more
TL;DR: The ability of 24 strains of A. urinae isolated from women with lower urinary tract symptoms to display aggregation phenotypes in vitro is explored and a potential association between phylogeny and flocking is suggested.
Journal ArticleDOI
A null model for microbial diversification.
TL;DR: It is shown that simple cell death and division over time could also explain the observed clustering, and recommended that the presented birth−death model as a null hypothesis in prokaryotic speciation studies is recommended.
References
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Journal ArticleDOI
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Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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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.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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