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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Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms.
Spencer Diamond,Peter F. Andeer,Zhou Li,Alexander Crits-Christoph,David Burstein,David Burstein,Karthik Anantharaman,Karthik Anantharaman,Katherine R Lane,Brian C. Thomas,Chongle Pan,Chongle Pan,Trent R. Northen,Jillian F. Banfield +13 more
TL;DR: Using metagenomics and proteomics on Mediterranean grassland soil samples resulted in the recovery of 793 metagenome-assembled genomes and provided insights into microbial activity in this environment, and how this changes with soil depth and exposure to extended rainfall.
Journal ArticleDOI
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing.
Caitlin M. Singleton,Francesca Petriglieri,Jannie Munk Kristensen,Rasmus Hansen Kirkegaard,Thomas Yssing Michaelsen,Martin Hjorth Andersen,Zivile Kondrotaite,Søren Michael Karst,Morten Simonsen Dueholm,Per Halkjær Nielsen,Mads Albertsen +10 more
TL;DR: In this paper, the authors used long-read and short-read sequencing to recover 1083 high-quality metagenome-assembled genomes (MAGs) from 23 Danish full-scale wastewater treatment plants.
Journal ArticleDOI
Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.
Michael A. Skinnider,Chad W. Johnston,Mathusan Gunabalasingam,Nishanth J. Merwin,Agata M. Kieliszek,Robyn J. MacLellan,Haoxin Li,Michael R. M. Ranieri,Andrew L. H. Webster,My P. T. Cao,Annabelle Pfeifle,Norman Spencer,Q. Huy To,Dan Peter Wallace,Chris A. Dejong,Nathan A. Magarvey +15 more
TL;DR: The accuracy of chemical structure prediction enables the development of machine-learning methods to predict the likely biological activity of encoded molecules, and PRISM 4 is presented, a comprehensive platform for prediction of the chemical structures of genomically encoded antibiotics, including all classes of bacterial antibiotics currently in clinical use.
Journal ArticleDOI
A census-based estimate of Earth's bacterial and archaeal diversity.
TL;DR: These estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.
Journal ArticleDOI
Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments.
Xiyang Dong,Chris Greening,Jayne E. Rattray,Anirban Chakraborty,Maria Chuvochina,Daisuke Mayumi,Daisuke Mayumi,Jan Dolfing,Carmen Li,James M. Brooks,Bernie B. Bernard,Ryan A. Groves,Ian A. Lewis,Casey R. J. Hubert +13 more
TL;DR: Overall, it is inferred that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.
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