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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Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Joan Mas-Lloret,Mireia Obón-Santacana,Gemma Ibáñez-Sanz,Elisabet Guinó,Miguel L. Pato,Francisco Rodríguez-Moranta,Alfredo Mata,Ana García-Rodríguez,Victor Moreno,Ville Pimenoff +9 more
TL;DR: Cross-sectional colon biopsies and faecal samples from nine participants in the COLSCREEN study are obtained and sequenced in high coverage using Illumina pair-end shotgun and IonTorrent 16S technologies to provide informed insights into designing comprehensive microbiome analysis.
Journal ArticleDOI
Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater.
Patricia Geesink,Carl-Eric Wegner,Alexander J. Probst,Martina Herrmann,Hang T. Dam,Anne-Kristin Kaster,Kirsten Küsel +6 more
TL;DR: Investigation of a member of the superphylum Microgenomates from oligotrophic groundwater using mini-metagenomics and 16S rRNA gene analyses suggested that Cand.
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Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants.
TL;DR: In this paper, the authors applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China.
Journal ArticleDOI
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
TL;DR: MAGpy as discussed by the authors is a scalable and reproducible pipeline that takes multiple genome assemblies as FASTA and compares them to several public databases, checks quality, suggests a taxonomy and draws a phylogenetic tree.
Journal ArticleDOI
Dialogue on the nomenclature and classification of prokaryotes.
TL;DR: This discussion explores some major disagreements but also considers the opportunities associated with the nomenclature of the uncultured taxa, the use of genome sequences as type material, the plurality of thenomenclatural code, and the roles of an official or computer-assisted taxonomy.
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