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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Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont.
TL;DR: The genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum is presented and it is hypothesized that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain.
Journal ArticleDOI
Evaluating techniques for metagenome annotation using simulated sequence data.
TL;DR: A simulated metagenome is used to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast and concludes that there is a trade-off between taxonomic resolution and annotation accuracy.
Journal ArticleDOI
Akkermansia muciniphila abundance is lower in severe obesity, but its increased level after bariatric surgery is not associated with metabolic health improvement
Maria Carlota Dao,Eugeni Belda,Edi Prifti,Amandine Everard,Brandon D. Kayser,Jean-Luc Bouillot,Jean-Marc Chevallier,Nicolas Pons,Stanislav Dusko Ehrlich,Joël Doré,Judith Aron-Wisnewsky,Jean-Daniel Zucker,Patrice D. Cani,Karine Clément +13 more
TL;DR: Although decreased in severe obesity, relative abundance of A. muciniphila was not associated with glucose homeostasis before or after BS, and this may partly explain the discrepancy with previous findings in less obese populations.
Journal ArticleDOI
Phylogeny of a relapsing fever Borrelia species transmitted by the hard tick Ixodes scapularis.
TL;DR: Comparisons of the several species of Borrelia, including those in the two major clades, showed that LB-2001 and related hard tick-associated organisms, likeborrelia lonestari, are deeply positioned within the RF group of species and that these organisms did not, as some earlier estimations had suggested, constitute a paraphyletic group.
Journal ArticleDOI
leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences.
TL;DR: leBIBIQBPP is a powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny using an approximate maximum likelihood approach and providing fully documented results to help the user in decision making.
References
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