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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Platforms to accelerate biomanufacturing of enzyme and probiotic animal feed supplements: discovery considerations and manufacturing implications
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pH-Dependent Hydrogenotrophic Denitratation Based on Self-Alkalization.
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Improved Assembly of Metagenome-Assembled Genomes and Viruses in Tibetan Saline Lake Sediment by HiFi Metagenomic Sequencing
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Book ChapterDOI
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes.
Davide Albanese,Claudio Donati +1 more
TL;DR: In this paper, the authors review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.
Posted ContentDOI
Sulfur-fueled chemolithoautotrophs replenish organic carbon inventory in groundwater
Martin Taubert,B. M. Heinze,Will A. Overholt,G. Azemtsop,Rola Houhou,Nico Jehmlich,M. von Bergen,M. von Bergen,Petra Roesch,Juergen Popp,Juergen Popp,K. Kuesel +11 more
TL;DR: In this paper, stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA) is presented.
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