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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The next million names for Archaea and Bacteria
TL;DR: This work proposes an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed, and document over a million new names for Bacteria and Archaea.
Posted ContentDOI
Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity
Nicholas D. Youngblut,Jacobo de la Cuesta-Zuluaga,Georg H. Reischer,Silke Dauser,Nathalie Schuster,Chris Walzer,Gabrielle Stalder,Andreas H. Farnleitner,Ruth E. Ley +8 more
TL;DR: The gut microbiome of a large set of mostly wild animal species consisting of mammals, birds, reptiles, amphibians, and fish is studied to find that existing reference databases commonly used for metagenomic analyses failed to capture the microbiome diversity among vertebrates.
Journal ArticleDOI
High-throughput sequencing for algal systematics
Mariana Cabral de Oliveira,Sonja I. Repetti,Cintia Iha,Cintia Iha,Christopher J. Jackson,Pilar Díaz-Tapia,Pilar Díaz-Tapia,Karoline Magalhães Ferreira Lubiana,Valéria Cassano,Joana Costa,Ma. Chiela M. Cremen,Vanessa R. Marcelino,Vanessa R. Marcelino,Heroen Verbruggen +13 more
TL;DR: How HTS technologies can advance algal systematics is described, including how HTS data such as organellar genomes and transcriptomes can be used to construct well-resolved phylogenies, leading to a stable and natural classification of algal groups.
Journal ArticleDOI
Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces
TL;DR: It is shown that long reads are essential to gain biological insights that are otherwise missed in short-read MAGs catalogs, as shown by the mobilome functions detected in the long-read HQ MAGs.
Journal ArticleDOI
Omics and the metabolic function of insect-microbial symbioses.
TL;DR: Omic studies of metabolic interactions between insects and their microbial symbionts enable us to construct precise hypotheses, especially regarding the metabolic services provided by microbial partners and the identity of metabolites exchanged between microorganisms and the insect host.
References
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