Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TLDR
The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.Abstract:
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.read more
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"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments.
Smruthi Karthikeyan,Luis M. Rodriguez-R,Patrick Heritier-Robbins,Minjae Kim,Will A. Overholt,John Christian Gaby,John Christian Gaby,Janet K. Hatt,Jim C. Spain,Jim C. Spain,Ramon Rosselló-Móra,Markus Huettel,Joel E. Kostka,Konstantinos T. Konstantinidis +13 more
TL;DR: The metagenome-guided isolation of a novel organism that represents a phylogenetically narrow group of previously uncharacterized, crude-oil degraders that appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses toOil spills.
Journal ArticleDOI
Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must.
Kimmo Sirén,Sarah S.T. Mak,Chrats Melkonian,Christian Carøe,Jan Hendrik Swiegers,Douwe Molenaar,Ulrich Fischer,M. Thomas P. Gilbert,M. Thomas P. Gilbert +8 more
TL;DR: Community variation relating to three points is explored: how microbial communities vary by vineyard; how community biodiversity changes during alcoholic fermentation; and how microbial community varies between musts that successfully complete alcoholic fermentation and those that become ‘stuck’ in the process.
Journal ArticleDOI
Unravelling the diversity of magnetotactic bacteria through analysis of open genomic databases.
Maria Uzun,Maria Uzun,Lolita M. Alekseeva,Lolita M. Alekseeva,Maria S. Krutkina,Veronika V. Koziaeva,Denis S. Grouzdev +6 more
TL;DR: A large-scale search of magnetosome biomineralization genes is presented and reveals 38 new MTB genomes, several of which were detected in the phyla Elusimicrobia, Candidatus Hydrogenedentes, and Nitrospinae, where magnetotactic representatives have not previously been reported.
Posted ContentDOI
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
Alexandre Almeida,Alexandre Almeida,Stephen Nayfach,Stephen Nayfach,Miguel Boland,Francesco Strozzi,Martin Beracochea,Zhou Jason Shi,Katherine S. Pollard,Donovan H. Parks,Philip Hugenholtz,Nicola Segata,Nikos C. Kyrpides,Nikos C. Kyrpides,Robert D. Finn +14 more
TL;DR: The Unified Human Gastrointestinal Genome (UHGG) collection, a resource combining 286,997 genomes representing 4,644 prokaryotic species from the human gut, is presented, a collection that more than doubles the number of gut protein clusters over the Integrated Gene Catalogue.
Journal ArticleDOI
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat.
Jessica K. Jarett,Jessica K. Jarett,Mária Džunková,Mária Džunková,Frederik Schulz,Frederik Schulz,Simon Roux,Simon Roux,David Paez-Espino,David Paez-Espino,Emiley A. Eloe-Fadrosh,Emiley A. Eloe-Fadrosh,Sean P. Jungbluth,Sean P. Jungbluth,Natalia Ivanova,Natalia Ivanova,John R. Spear,Stephanie A. Carr,Christopher B. Trivedi,Frank A. Corsetti,Hope A. Johnson,Eric D. Becraft,Eric D. Becraft,Nikos C. Kyrpides,Nikos C. Kyrpides,Ramunas Stepanauskas,Tanja Woyke,Tanja Woyke,Tanja Woyke +28 more
TL;DR: Observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.
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