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
Metagenomic sequencing reveals altered gut microbiota of sojourners at high altitude: a longitudinal study
Brij Bhushan,Malleswara Rao Eslavath,Angad Yadav,A. K. Srivastava,M. P. K. Reddy,Tsering Norboo,Bhuvnesh Kumar,Shashi Bala Singh,Lilly Ganju +8 more
TL;DR: Under the stressful and hypoxic environment of extreme altitudes, associated microbial variation with altered metabolic pathways, reveals the influence of extreme environment on human gut microbiota with the predominance of Prevotella.
Journal ArticleDOI
High-Quality Draft Genome Sequence of Bacillus subtilis Strain WAUSV36
Jennifer Town,Jennifer Town,Patrice Audy,Susan M. Boyetchko,Tim J. Dumonceaux,Tim J. Dumonceaux +5 more
TL;DR: Bacterial strain WAUSV36 inhibits the growth of and decreases disease symptoms caused by the potato pathogen Phytophthora infestans and shared very high nucleotide sequence identity with previously sequenced strains of B. subtilis.
Journal ArticleDOI
Draft Genome Sequences of Two Paenibacillus Isolates from Goose and Chicken Gastrointestinal Material.
Jitendra Keshri,Rocio Ramirez,Molly Svendsen,Haley R. Keillor,Madeline L. Moss,Haley J. Jordan,Kristina M. Smith,Patrick N. Ball,Bruce S. Seal,Mark E. Berrang,Brian B. Oakley +10 more
TL;DR: The draft genome sequences of two Paenibacillus strains, An7 and USDA918EY, isolated from goose feces (Bend, OR, USA) and chicken ceca (Pomona, CA, USA), respectively, are presented to assist with analyses of microorganisms associated with free-ranging and commercial avian species.
Journal ArticleDOI
Community structure and metabolic potentials of the traditional rice beer starter ‘emao’
Diganta Narzary,Diganta Narzary,Nitesh Boro,Ashis Borah,Takashi Okubo,Hideto Takami,Hideto Takami +6 more
TL;DR: In this paper, a shot-gun whole-metagenome sequencing technology was used to detect enzymes that are known to catalyze saccharification, lignocellulose degradation, and biofuel production indicating the presence of metabolic functionome in the emao.
Posted ContentDOI
A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture
Rachel Gilroy,Anuradha Ravi,María Getino,Isabella Pursley,Daniel L. Horton,Nabil-Fareed Alikhan,David Baker,Karim Gharbi,Neil Hall,Mick Watson,Evelien M. Adriaenssens,Ebenezer Foster-Nyarko,Sheikh Jarju,Arss Secka,Martin Antonio,Aharon Oren,Roy R. Chaudhuri,Roberto M. La Ragione,Falk Hildebrand,Mark J. Pallen +19 more
TL;DR: This work exploits culture-independent and culture-dependent approaches to deliver a genomic blueprint of the chicken gut associated microbiome, encompassing dozens of novel candidate bacterial genera and hundreds of novel species.
References
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