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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Exploring neighborhoods in large metagenome assembly graphs reveals hidden sequence diversity
TL;DR: An information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome is introduced.
Journal ArticleDOI
The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes
Fergus W. J. Collins,Fergus W. J. Collins,Calum J. Walsh,Calum J. Walsh,Beatriz Gómez-Sala,Elena Guijarro-García,D. Stokes,Klara B. Jakobsdóttir,Kristján Kristjánsson,Finlay Burns,Paul D. Cotter,Paul D. Cotter,Mary C. Rea,Mary C. Rea,Colin Hill,R. Paul Ross,R. Paul Ross +16 more
TL;DR: In this article, the extent of which adaptations may have been found in the deep-sea can be investigated, with fish displaying behaviors and appearances unlike those seen in any other aquatic habitat.
Journal ArticleDOI
Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation.
TL;DR: In this article, a microfluidic single-cell dispenser was used for label-free isolation of individual bacteria from a complex sample retrieved from a wastewater treatment plant, demonstrating the potential of this technique for single cell genomics and other alternative downstream applications.
Journal ArticleDOI
A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome
Shuqin Zeng,Dhrati V. Patangia,Alexandre Almeida,Zhemin Zhou,Dezhi Mu,R. Paul Ross,Catherine Stanton,Shaopu Wang +7 more
TL;DR: The Early-Life Gut Genomes (ELGG) catalog as mentioned in this paper contains 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography.
Posted ContentDOI
New insights from 33,813 publicly available metagenome-assembled-genomes (MAGs) assembled from the rumen microbiome
TL;DR: For the first time, all available resources are combined, catalogued and de-replicated to define putative species-level bins as discussed by the authors, providing new insights into the constitution of the rumen microbiome.
References
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