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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Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria
Thomas C. A. Hitch,Thomas Riedel,Aharon Oren,Jörg Overmann,Jörg Overmann,Trevor D. Lawley,Thomas Clavel +6 more
TL;DR: Protologger is developed, a bioinformatic tool that automatically generates all the necessary readouts for writing a detailed protologue, and highlights the need to utilise multiple taxonomic delineation methods, as while inconsistencies between each method occur, a combined approach provides robust placement.
Journal ArticleDOI
Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate
Pål Trosvik,Eric J. de Muinck,Eli Knispel Rueness,Peter J. Fashing,Evan C. Beierschmitt,Kadie R. Callingham,Jacob B. Kraus,Thomas H. Trew,Amera Moges,Addisu Mekonnen,Addisu Mekonnen,Vivek Venkataraman,Nga Nguyen +12 more
TL;DR: This study represents the first analysis of the gelada GI microbiota, providing insights into the adaptations underlying graminivory in a primate, and highlights the role of social organization in structuring the GI microbiota within a society of wild animals.
Journal ArticleDOI
Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.
TL;DR: An updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data is provided.
Journal ArticleDOI
Metagenomic tools in microbial ecology research.
TL;DR: In this article, the authors review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities.
Journal ArticleDOI
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria
Paula B. Matheus Carnevali,Frederik Schulz,Cindy J. Castelle,Rose S. Kantor,Patrick M. Shih,Patrick M. Shih,Patrick M. Shih,Itai Sharon,Itai Sharon,Joanne M. Santini,Matthew R. Olm,Yuki Amano,Brian C. Thomas,Karthik Anantharaman,Karthik Anantharaman,David Burstein,David Burstein,Eric D. Becraft,Eric D. Becraft,Ramunas Stepanauskas,Tanja Woyke,Jillian F. Banfield +21 more
TL;DR: It is predicted that sediment-associated Margulisbacteria have a fermentation-based metabolism featuring a variety of hydrogenases, a streamlined nitrogenase, and electron bifurcating complexes involved in cycling of reducing equivalents, and inferring their metabolic potential and supporting that their common ancestor was an anaerobe capable of fermentation and H2 metabolism.
References
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