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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Unified rational protein engineering with sequence-only deep representation learning
Ethan C. Alley,Grigory Khimulya,Surojit Biswas,Mohammed AlQuraishi,George M. Church,George M. Church +5 more
TL;DR: This work applies deep learning to unlabelled amino acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily, and biophysically grounded.
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Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
TL;DR: A genome-resolved metagenomics workflow that enabled assembly of bacterial and archaeal genomes that were at least 80% complete and predicted and annotated a large set of rumen proteins will enable a better understanding of the structure and functions of the rumen microbiota.
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An evolving view of methane metabolism in the Archaea.
Paul N. Evans,Joel A. Boyd,Andy O. Leu,Ben J. Woodcroft,Donovan H. Parks,Philip Hugenholtz,Gene W. Tyson +6 more
TL;DR: This Review examines the diversity, metabolism and evolutionary history of mcr-containing archaea in new euryarchaeotal lineages and novel archaeal phyla and highlights the evolutionary relationships of key enzymes with recently discovered alkane-oxidizing archaea.
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IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
TL;DR: IDTAXA is introduced, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors in reference taxonomies, and it is demonstrated that it has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier.
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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.
Francesco Asnicar,Andrew Maltez Thomas,Francesco Beghini,Claudia Mengoni,Serena Manara,Paolo Manghi,Qiyun Zhu,Mattia Bolzan,Fabio Cumbo,Uyen May,Jon G. Sanders,Jon G. Sanders,Moreno Zolfo,Evguenia Kopylova,Edoardo Pasolli,Edoardo Pasolli,Rob Knight,Siavash Mirarab,Curtis Huttenhower,Nicola Segata +19 more
TL;DR: PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences, and reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers.
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