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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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Jean Sébastien Gounot,Chia Minghao,Denis Bertrand,Woei-Yuh Saw,Aarthi Ravikrishnan,A. Low,Yichen Ding,Ng Hui Qi Amanda,Linda Wei Lin Tan,T. Yik-Ying,Henning Seedorf,Niranjan Nagarajan +11 more
TL;DR: In this paper , a cross-sectional survey of 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement.
Posted ContentDOI
Oligotyping and Genome-Resolved Metagenomics Reveal Distinct Candidatus Accumulibacter Communities in Full-Scale Side-Stream versus Conventional Enhanced Biological Phosphorus Removal (EBPR) Configurations
Varun Srinivasan,Guangyu Li,Dongqi Wang,Nicholas B. Tooker,Nicholas B. Tooker,Zihan Dai,Annalisa Onnis-Hayden,Ameet J. Pinto,April Z. Gu,April Z. Gu +9 more
TL;DR: This study demonstrates and validates the use of a high-throughput approach of oligotyping analysis of 16S rRNA gene sequences to elucidate CAP clade-level diversity and shows the existence of a previously uncharacterized diversity of CAP clades in full-scale EBPR communities through extraction of MAGs, for the first time from full- scale facilities.
Journal ArticleDOI
Supercarriers of antibiotic resistome in a world’s large river
Jiawen Wang,Rui Pan,Peiyan Dong,Shufeng Liu,Qin Chen,Alistair G.L. Borthwick,Liyu Sun,Nan Xu,Jinren Ni +8 more
TL;DR: Wang et al. as mentioned in this paper found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively.
Journal ArticleDOI
Shedding light on the functional role of the Ignavibacteria in Italian rice field soil: A meta-genomic/transcriptomic analysis
TL;DR: Functional annotation revealed that the Ignavibacteria in Italian paddy soil are facultative anaerobes, represent a novel lineage in the Ignvibacteriae phylum, and have the ability for aerobic-hybrid phenylacetate degradation.
Journal ArticleDOI
Type IV pili trigger episymbiotic association of Saccharibacteria with its bacterial host
Bingliang Xie,Jian Wang,Yong Nie,Jing-Yun Tian,Ze Wang,Dongwei Chen,Beiyu Hu,Xiao-Lei Wu,Wenbin Du +8 more
TL;DR: A gene-targeted method that brought about the cultivation of a candidate phyla radiation (CPR) bacterium, designated Saccharibacteria TM7i, with its basibiont from an enriched sample of an insect was developed as mentioned in this paper .
References
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