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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Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes
TL;DR: How improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events is discussed.
Journal ArticleDOI
Heterotrophic Thaumarchaea with Small Genomes Are Widespread in the Dark Ocean.
TL;DR: HMT is a group of putatively heterotrophic marine thaumarchaeota with small genome sizes that is globally abundant in the mesopelagic, apparently lacking the ability to oxidize ammonia.
Journal ArticleDOI
Evolution of photosynthesis and aerobic respiration in the cyanobacteria
TL;DR: Recent findings on the evolution of aerobic respiration in the non-photosynthetic cyanobacterial classes are described, and how this has been interpreted by researchers interested in the Evolution of oxygenic photosynthesis is described.
METABOLIC: High-Throughput Profiling of Microbial Genomes for Functional Traits, Metabolism, Biogeochemistry, and Community-scale Functional Networks
Zhichao Zhou,Patricia Q. Tran,Adam M. Breister,Yang Liu,Kristopher Kieft,Elise S. Cowley,Ulas Karaoz,Karthik Anantharaman +7 more
TL;DR: METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities is presented.
Posted ContentDOI
Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy
Donovan H. Parks,Maria Chuvochina,Pierre-Alain Chaumeil,Christian Rinke,Aaron J. Mussig,Philip Hugenholtz +5 more
TL;DR: This work proposes 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species, and provides the first complete domain to species taxonomic framework which will improve communication of scientific results.
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