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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Genomic analysis of family UBA6911 (Group 18 Acidobacteria) expands the metabolic capacities of the phylum and highlights adaptations to terrestrial habitats.
TL;DR: In this article, the metabolic capabilities and ecological role of members of the family UBA6911 (group 18) acidobacteria were analyzed from Zodletone Spring, an anaerobic sulfide and sulfur-rich spring in southwestern Oklahoma.
Journal ArticleDOI
Quantitative stable isotope probing with H218O to measure taxon-specific microbial growth
Alicia M. Purcell,Paul Dijkstra,B. K. Finley,Michaela Hayer,Benjamin J. Koch,Rebecca L. Mau,Ember M. Morrissey,Katerina Papp,Katerina Papp,Egbert Schwartz,Bram W. G. Stone,Bruce A. Hungate +11 more
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Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database
TL;DR: This article exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within the Genome Taxonomy Database (GTDB).
Posted ContentDOI
An integrated metagenome catalog reveals novel insights into the murine gut microbiome
Till Robin Lesker,Abilash Chakravarthy,Eric J. C. Gálvez,Ilias Lagkouvardos,John F. Baines,John F. Baines,Thomas Clavel,Thomas Clavel,Alexander Sczyrba,Alice C. McHardy,Till Strowig +10 more
TL;DR: This work generated a comprehensive resource, the integrated mouse gut metagenome catalog (iMGMC), comprising 4.6 million unique genes and 660 high-quality meetagenome-assembled genomes linked to reconstructed full-length 16S rRNA gene sequences, which enables unprecedented coverage and taxonomic resolution.
Journal ArticleDOI
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere
TL;DR: An overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses is provided and a variety of complementary techniques are discussed that are considered crucial for making further progress in the understanding of the TOL and its interconnection with the virosphere.
References
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