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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A Viral Ecogenomics Framework To Uncover the Secrets of Nature's "Microbe Whisperers".
TL;DR: This work outlines how a comprehensive host-resolved mapping of viral sequence space will enable a thorough characterization of virus-encoded mechanisms for microbial manipulation, before multi-omics approaches can be leveraged to fully decipher virus-host dynamics in nature.
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Strain identification and quantitative analysis in microbial communities.
TL;DR: A discussion of recently available computational tools that can be applied for this task, as well as statistical models and gaps in performing and interpreting any of these three main types of studies using strain-resolved shotgun metagenomic profiling of microbial communities can be found in this article .
Journal ArticleDOI
Increasing the power of interpretation for soil metaproteomics data.
Virginie Jouffret,Virginie Jouffret,Guylaine Miotello,Karen Culotta,Sophie Ayrault,Olivier Pible,Jean Armengaud +6 more
TL;DR: In this paper, a two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog was proposed to maximize the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information.
Journal ArticleDOI
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data.
Sinje Neukirchen,Filipa L. Sousa +1 more
TL;DR: DiSCo as mentioned in this paper is a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data and lists the identified proteins and their classification in terms of protein family and predicted type.
Journal ArticleDOI
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
Edmund R. R. Moody,Tara Mahendrarajah,Nina Dombrowski,James W. Clark,Celine Petitjean,Pierre Offre,Gergely J. Szöllősi,Anja Spang,Tom A. Williams +8 more
TL;DR: It is shown that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set, and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable.
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