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
Citations
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Journal ArticleDOI
Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria.
Christian Zenner,Christian Zenner,Thomas C. A. Hitch,Thomas Riedel,Esther Wortmann,Stefan Tiede,Eva Miriam Buhl,Birte Abt,Klaus Neuhaus,Philippe Velge,Jörg Overmann,Jörg Overmann,Bernd Kaspers,Thomas Clavel +13 more
TL;DR: In this article, the authors investigated the effect of microbiome-based interventions on host mucosal immune responses and found that increased levels of IgA and IgY were observed in chickens exposed to maternal feces after hatching compared with strict hygienic conditions.
Posted ContentDOI
Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes
TL;DR: This study provides the first evidence to support a transcriptionally active mixotrophic lifestyle of Asgard archaea, shedding light on the potential roles of these microorganisms in the global biogeochemical cycling.
Journal ArticleDOI
Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations.
Mukan Ji,Mukan Ji,Timothy J. Williams,Kate Montgomery,Hon Lun Wong,Julian Zaugg,Jonathan F. Berengut,Andrew Bissett,Maria Chuvochina,Philip Hugenholtz,Belinda C. Ferrari +10 more
TL;DR: In this paper, the authors analyzed 63 public metagenome-assembled genomes (MAGs) and nine new MAGs generated from Antarctic soil metagenomes and concluded Ca. Eremiobacteria to be an ecologically versatile phylum with the potential to thrive under an array of extreme environmental conditions.
Book ChapterDOI
Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics
TL;DR: This chapter describes how performing population genomic analyses using metagenomic data allows resolution of ecologically and genetically cohesive populations in the environment, tracking of evolutionary processes within them, and application of metatranscriptomic and metaproteomic analyses to determine the in situ physiology of distinct populations.
Journal ArticleDOI
Ten Years of Collaborative Progress in the Quest for Orthologs.
Benjamin Linard,Ingo Ebersberger,Shawn E. McGlynn,Natasha Glover,Natasha Glover,Tomohiro Mochizuki,Mateus Patricio,Odile Lecompte,Yannis Nevers,Yannis Nevers,Paul Thomas,Toni Gabaldón,Erik L. L. Sonnhammer,Christophe Dessimoz,Ikuo Uchiyama +14 more
TL;DR: The 6th Quest for Orthologs (QFO) meeting as discussed by the authors was held in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology (NIBB) conference.
References
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