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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AMBER: Assessment of Metagenome BinnERs
Fernando Meyer,Peter Hofmann,Peter Belmann,Ruben Garrido-Oter,Adrian Fritz,Alexander Sczyrba,Alice C. McHardy +6 more
TL;DR: AMBER, an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark data sets, is presented, which calculates the performance metrics and comparative visualizations used in the first benchmarking challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI).
Journal ArticleDOI
Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome
TL;DR: This strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level and revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements.
Posted ContentDOI
The anaerobic digestion microbiome: a collection of 1600 metagenome-assembled genomes shows high species diversity related to methane production
Stefano Campanaro,Laura Treu,Laura Treu,Luis M. Rodriguez-R,Adam Kovalovszki,Ryan M. Ziels,Irena Maus,Xinyu Zhu,Panagiotis Kougias,Arianna Basile,Gang Luo,Andreas Schlüter,Konstantinos T. Konstantinidis,Irini Angelidaki +13 more
TL;DR: The recovery of many MAGs belonging to Candidate Phyla Radiation and other underexplored taxa suggests their specific involvement in the anaerobic degradation of organic matter, highlighting a high flexibility of the biogas microbiome.
Journal ArticleDOI
Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats.
TL;DR: It was found that more than 80% of all known ARGs are not carried by any plasmid or integron sequences, and both total ARGs and intI1 genes show little correlation to the degree of anthropogenicity, highlighting the needs to differentiate ARGs of high clinical relevance.
Journal ArticleDOI
“ Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system
Adrian E. Naas,Lindsey M. Solden,Angela D. Norbeck,Heather M. Brewer,Live Heldal Hagen,I. M. Heggenes,Alice C. McHardy,Roderick I. Mackie,Ljiljana Paša-Tolić,Magnus Ø. Arntzen,V.G.H. Eijsink,Nicole M. Koropatkin,Matthias Hess,Kelly C. Wrighton,Phillip B. Pope +14 more
TL;DR: The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria and anaerobic fungi, suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.
References
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