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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Journal ArticleDOI
Characterization and recognition of Brachyspira hampsonii sp. Nov., a novel intestinal spirochete that is pathogenic to pigs
TL;DR: B. hampsonii is classified as a unique species with genetically diverse yet phenotypically similar genomovars (I, II, and III) and the type strain NSH-16 (= ATCC BAA-2463 = NCTC 13792).
Journal ArticleDOI
Accurate reconstruction of bacterial pan- and core genomes with PEPPAN.
TL;DR: PEPPAN is introduced, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus and is more accurate and more specific than any of the other pipelines and was almost as fast as any of them.
Journal ArticleDOI
Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children
Guojun Wu,Chenhong Zhang,Jing Wang,Feng Zhang,R.Z. Wang,Jian Shen,Linghua Wang,Xiaoyan Pang,Xiaojun Zhang,Liping Zhao,Menghui Zhang +10 more
TL;DR: It is shown that a gut microbiota-targeted dietary intervention, which shifts the dominant fermentation of gut bacteria from protein to carbohydrate, significantly diminished the gut resistome and alleviated metabolic syndrome in obese children.
Journal ArticleDOI
Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics
Mamoona Mushtaq,Saima Zubair,Therese Råsbäck,Erik Bongcam-Rudloff,Désirée S. Jansson,Désirée S. Jansson +5 more
TL;DR: It is proposed that strains AN4859/03, AN1681:1/04, AN2384/04 and Dk12570-2 from pigs in Sweden and Denmark, and strains AN3949:2/02 and AN1418: 2/01 isolated from mallards in Sweden, represent a unique species within genus Brachyspira.
Journal ArticleDOI
Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium.
Nunzia Picone,Arjan Pol,Rob Mesman,Maartje A. H. J. van Kessel,Geert Cremers,Antonie H. van Gelder,Theo A. van Alen,Mike S. M. Jetten,Sebastian Lücker,Huub J. M. Op den Camp +9 more
TL;DR: This work reports on the discovery, cultivation, and physiological, genomic, and transcriptomic characterization of a novel gammaproteobacterial ammonia-oxidizing bacterium enriched via continuous bioreactor cultivation from an acidic air biofilter that was able to grow and oxidize ammonia at pH 2.5.
References
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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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