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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Expanding the Verrucomicrobial Methanotrophic World: Description of Three Novel Species of Methylacidimicrobium gen. nov.
Muriel C. F. van Teeseling,Arjan Pol,Harry R. Harhangi,Sietse van der Zwart,Mike S. M. Jetten,Huub J. M. Op den Camp,Laura van Niftrik +6 more
TL;DR: The discovery of three new species of mesophilic acidophilic verrucomicrobial methanotrophs from a volcanic soil in Italy that are more acid tolerant than their thermophilic relatives and contain intracytoplasmic membrane stacks shows that they are present in many more ecosystems than previously assumed.
Journal ArticleDOI
Temporal and technical variability of human gut metagenomes
Anita Y. Voigt,Anita Y. Voigt,Paul I. Costea,Jens Roat Kultima,Simone S. Li,Georg Zeller,Shinichi Sunagawa,Peer Bork,Peer Bork +8 more
TL;DR: Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability, and short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of feces for metagenomic studies.
Journal ArticleDOI
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.
Tommi Vatanen,Damian R. Plichta,Juhi Somani,Philipp C. Münch,Timothy D. Arthur,Andrew Brantley Hall,Sabine Rudolf,Edward J. Oakeley,Xiaobo Ke,Xiaobo Ke,Rachel A. Young,Henry J. Haiser,Raivo Kolde,Moran Yassour,Moran Yassour,Kristiina Luopajärvi,Heli Siljander,Suvi M. Virtanen,Suvi M. Virtanen,Jorma Ilonen,Jorma Ilonen,Raivo Uibo,Vallo Tillmann,Sergei Mokurov,Natalya Dorshakova,Jeffrey A. Porter,Alice C. McHardy,Harri Lähdesmäki,Hera Vlamakis,Curtis Huttenhower,Curtis Huttenhower,Mikael Knip,Ramnik J. Xavier +32 more
TL;DR: Integration of longitudinal gut metagenomic datasets from children in Finland, Estonia and Russian Karelia reveals high strain-level diversity, which consequently impacts the functional capabilities of the early life microbiome.
Journal ArticleDOI
MOCAT2: a metagenomic assembly, annotation and profiling framework
Jens Roat Kultima,Luis Pedro Coelho,Kristoffer Forslund,Jaime Huerta-Cepas,Simone S. Li,Marja Driessen,Anita Y. Voigt,Georg Zeller,Shinichi Sunagawa,Peer Bork +9 more
TL;DR: The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes.
Journal ArticleDOI
Environmental drivers of a microbial genomic transition zone in the ocean's interior.
Daniel R. Mende,Jessica A. Bryant,Jessica A. Bryant,Frank O. Aylward,Frank O. Aylward,John M. Eppley,Torben Nielsen,Torben Nielsen,David M. Karl,Edward F. DeLong,Edward F. DeLong +10 more
TL;DR: Metagenomic analyses reveal that microbial genomes undergo a community-wide transition in size and GC content across a narrow depth range, indicating that nutrient limitation is a major driver in marine microbial genomic and proteomic evolution.
References
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