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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Dissertation
Analysis of the sinonasal microbiome during health and chronic rhinosinusitis
TL;DR: This thesis is for research or private study purposes only, and the author's right to be identified as the author of this thesis is recognized.
Journal ArticleDOI
Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities.
Noha H. Youssef,Ibrahim F. Farag,C. Ryan Hahn,Jessica K. Jarett,Eric D. Becraft,Emiley A. Eloe-Fadrosh,Jorge Lightfoot,Austin Bourgeois,Tanner Cole,Stephanie Ferrante,Mandy Truelock,William S. Marsh,Michael Jamaleddine,Samantha Ricketts,Ronald Simpson,Allyson McFadden,Wouter D. Hoff,Nikolai V. Ravin,Stefan M. Sievert,Ramunas Stepanauskas,Tanja Woyke,Mostafa S. Elshahed +21 more
TL;DR: This study reports on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences, within the broader FCB.
Posted ContentDOI
Distributed representations of protein domains and genomes and their compositionality
TL;DR: The proposed novel representation of function called nanotext is applied to data from the Tara ocean expedition to predict plausible culture media and growth temperatures for microorganisms from their metagenome assembled genomes (MAGs) alone.
Journal ArticleDOI
Changes in microbial community composition, activity, and greenhouse gas production upon inundation of drained iron-rich peat soils
Anniek E. E. de Jong,Anniek E. E. de Jong,Simon Guererro-Cruz,Josepha M. H. van Diggelen,Annika Vaksmaa,Leon P. M. Lamers,Mike S. M. Jetten,Mike S. M. Jetten,Alfons J. P. Smolders,Olivia Rasigraf +9 more
TL;DR: In this article, the effects of inundation of drained iron (Fe)-rich peat topsoils on nutrient release, surface water quality, GHG production and consumption, and on the composition and activity of the microbial community were investigated in incubation experiments.
Journal ArticleDOI
Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability.
Jose M. Haro-Moreno,Felipe H. Coutinho,Asier Zaragoza-Solas,Antonio Picazo,Salvador Almagro-Moreno,Mario López-Pérez +5 more
TL;DR: Investigation of perturbations in samples from marine farms of gilthead seabream cultures revealed dysbiosis and functional imbalance within the net cage with a unique structure with little interference with samples from the fish microbiota or those collected far away from the coast.
References
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