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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Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches.
TL;DR: In this article, a review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the anaerobic digestion (AD) process.
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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea
Monique Aouad,Jean-Pierre Flandrois,Frédéric Jauffrit,Manolo Gouy,Simonetta Gribaldo,Céline Brochier-Armanet +5 more
TL;DR: In this article , a divide-and-conquer approach was used to resolve deep phylogenetic relationships in the tree of life, which can be applied to progressively resolve the entire Tree of Life.
Journal ArticleDOI
MGnify: the microbiome sequence data analysis resource in 2023
Lorna Richardson,B. Allen,Germana Baldi,Martín Beracochea,Maxwell L. Bileschi,Tony Burdett,Josephine Burgin,Juan Caballero-Pérez,Guy Cochrane,Lucy J. Colwell,Tom Curtis,Alejandra Escobar-Zepeda,Tatiana A Gurbich,Varsha Kale,Anton Korobeynikov,Shri K. Raman Raj,Alexander B Rogers,Ekaterina A. Sakharova,Santiago Sanchez,Darren J. Wilkinson,Robert D. Finn +20 more
TL;DR: The MGnify platform as mentioned in this paper provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets.
Journal ArticleDOI
Current understanding and perspectives in anaerobic digestion based on genome-resolved metagenomic approaches
TL;DR: In this paper , a review looks at how these up-to-date metagenomic analyses can be applied to promote our understanding and improved the development of the anaerobic digestion process.
Journal ArticleDOI
Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation.
Chelsea L. Murphy,R. Yang,T. Decker,C. Cavalliere,V. Andreev,N. Bircher,Jo Cornell,R. Dohmen,C. J. Pratt,A. Grinnell,J. Higgs,C. Jett,E. Gillett,R. Khadka,S. Mares,C. Meili,Jing Liu,H. Mukhtar,Mostafa S. Elshahed,Noha H. Youssef +19 more
TL;DR: In this paper, a set of 634 genes informative of social lifestyle predicted a nonsocial behavior for Zodletone Myxococcota from an anoxic freshwater spring in Oklahoma, USA.
References
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