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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Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities
David W. Waite,David W. Waite,Maria Chuvochina,Claus Pelikan,Donovan H. Parks,Pelin Yilmaz,Michael Wagner,Alexander Loy,Takeshi Naganuma,Ryosuke Nakai,William B. Whitman,Martin W. Hahn,Jan Kuever,Philip Hugenholtz +13 more
TL;DR: This work systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes and indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrio, which is consistent with their distinct modes of action.
Journal ArticleDOI
Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences.
Franziska Wemheuer,Jessica A. Taylor,Rolf Daniel,Emma L. Johnston,Peter Meinicke,Torsten Thomas,Bernd Wemheuer,Bernd Wemheuer +7 more
TL;DR: Tax4Fun2 is an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences that is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles.
Journal ArticleDOI
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
F. A. Bastiaan von Meijenfeldt,Ksenia Arkhipova,Diego D. Cambuy,Felipe H. Coutinho,Felipe H. Coutinho,Felipe H. Coutinho,Bas E. Dutilh,Bas E. Dutilh +7 more
TL;DR: It is shown that the conventional best-hit approach often leads to classifications that are too specific, especially when the sequences represent novel deep lineages, and a classification method is presented that integrates multiple signals to classify sequences and metagenome-assembled genomes.
Journal ArticleDOI
Functional effects of the microbiota in chronic respiratory disease.
Kurtis F. Budden,Shakti D. Shukla,Saima Firdous Rehman,Kate L Bowerman,Simon Keely,Philip Hugenholtz,Darius Armstrong-James,Ian M. Adcock,Sanjay H. Chotirmall,Kian Fan Chung,Philip M. Hansbro,Philip M. Hansbro +11 more
TL;DR: Recent advances in the understanding of the composition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these microbes interact with host immunity, and their functional effects on the pathogenesis, exacerbations, and comorbidities of chronic respiratory diseases are reviewed.
Journal ArticleDOI
Diversity, ecology and evolution of Archaea
Brett J. Baker,Valerie De Anda,Kiley W. Seitz,Nina Dombrowski,Alyson E. Santoro,Karen G. Lloyd +5 more
TL;DR: How genomes belonging to uncultured groups from the environment elucidate the metabolic capabilities of the Archaea and their ecological roles are discussed, while also expanding the view of the tree of life and of eukaryogenesis.
References
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