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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
TLDR
This work used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence.
Insights into the phylogeny and coding potential of microbial dark matter
TLDR
This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet.
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
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.
A complete domain-to-species taxonomy for Bacteria and Archaea
TLDR
This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
TLDR
Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor
TLDR
State-of-the-art omics tools are employed to generate draft genomes and transcriptomes for uncultivated organisms spanning 15 phyla and the first genomic insight into candidate phyla Atribacteria, Hydrogenedentes and Marinimicrobia in methanogenic environments is reported.
Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics
TLDR
C cultivation-independent genomic approaches were used to provide a first comprehensive view of the phylogeny, conserved genomic features and metabolic potential of members of this ubiquitous candidate phylum, and confirmed the monophyly of the ‘Atribacteria’ inclusive of OP9 and JS1.
Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics
TLDR
The protocol encompasses the preservation and pretreatment of differing environmental samples, followed by the physical separation, lysis, whole-genome amplification and 16S rRNA–based identification of individual bacterial and archaeal cells.
An environmental bacterial taxon with a large and distinct metabolic repertoire
TLDR
Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei.
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
TLDR
Prokaryotic diversity from the perspective of the GTDB is explored and the importance of metagenome-assembled genomes in expanding available genomic representation is highlighted and the use of average nucleotide identities as a pragmatic approach for delineating proKaryotic species is discussed.
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