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
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OUP accepted manuscript
TL;DR: In this paper , the authors developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation.
Posted ContentDOI
Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles
Antoni Luque,Cynthia B. Silveira +1 more
TL;DR: Lysogeny was found to be more frequent in high-productive environments like the gut, due to higher phage and bacterial densities and faster phage adsorption rates, and a biophysical model that incorporated a meta-analysis of the properties of marine and gut microbiomes.
Journal ArticleDOI
Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)
TL;DR: The constrained Double Principal Coordinates Analysis (cDPCoA) is able to enforce a priori classifications to retrieve subtle differences and (or) remove the effect of confounding factors.
Journal ArticleDOI
Evaluation of plant-growth promoting properties of Gluconacetobacter diazotrophicus and Gluconacetobacter sacchari isolated from sugarcane and tomato in West Central region of Colombia
TL;DR: The results constitute the first report confirming the presence of G. diazotrophicus and G. sacchari associated with sugarcane in Colombia under natural conditions and are potential candidates for the development of novel biotechnological processes for production of new alternative biofertilizers considering the significant plant-growth promotion properties determined in this work.
Journal ArticleDOI
Draft Genome Sequence of Rhodomicrobium udaipurense JA643T with Special Reference to Hopanoid Biosynthesis
TL;DR: In this article, the whole genome of Rhodomicrobium udaipurense JA643T was sequenced from a fresh water stream of Udaipur in Himachal Pradesh, India, by using the Illumina HiSeq pair end chemistry of 2 × 100 bp platform.
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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