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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Tenuifilum thalassicum gen. nov., sp. nov., a novel moderate thermophilic anaerobic bacterium from a Kunashir Island shallow hot spring representing a new family Tenuifilaceae fam. nov. in the class Bacteroidia.
Olga A. Podosokorskaya,Tatiana V. Kochetkova,Andrei A. Novikov,Stepan V. Toshchakov,Alexander G. Elcheninov,Ilya V. Kublanov +5 more
TL;DR: A novel anaerobic moderately thermophilic bacterium, designated strain 38H-strT, was isolated from a 12m deep hot spring of the Kunashir Island shore and represents the first genus and species Tenuifilum thalassicum gen. nov.
Journal ArticleDOI
Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions.
Lucas Palma Perez Braga,Roberta Verciano Pereira,Layla Farage Martins,Livia Maria Silva Moura,Fabio Beltrame Sanchez,José S. L. Patané,Aline Maria Da Silva,João C. Setubal +7 more
TL;DR: In this article, 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level.
Journal ArticleDOI
Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities.
Chelsea L. Murphy,Andriy Sheremet,Peter F. Dunfield,John R. Spear,Ramunas Stepanauskas,Tanja Woyke,Mostafa S. Elshahed,Noha H. Youssef +7 more
TL;DR: A global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum, highlights the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.
Journal ArticleDOI
DiTing: A pipeline to infer and compare biogeochemical pathways from metagenomic and metatranscriptomic data
Chun-Xu Xue,Heyu Lin,Xiao-Yu Zhu,Jiwen Liu,Yunhui Zhang,Gary Rowley,Jonathan D. Todd,Meng Li,Xiao-Hua Zhang +8 more
TL;DR: DiTing as discussed by the authors is a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database.
Journal ArticleDOI
Evolutionary Ecology of Natural Comammox Nitrospira Populations
TL;DR: The microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process, are identified and it is revealed that evolutionary processes are more affected by habitat type than by species identity.
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