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
Citations
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Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.
TL;DR: Pangenome analysis suggests that Dia microorganisms have evolved cluster-specific enzymes and biosynthesis capabilities and are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration in marine Dia.
Journal ArticleDOI
New technologies for developing phage-based tools to manipulate the human microbiome.
Mohammadali Khan Mirzaei,Li Deng +1 more
TL;DR: In this paper, the authors discuss recent advances in cultivation-independent technologies and argue their relevance to different key steps, that is, identifying the modulation targets and developing phage-based tools to precisely modulate gut bacteria and restore a sustainable microbiome in humans.
Journal ArticleDOI
Advancing Genome-Resolved Metagenomics beyond the Shotgun
TL;DR: Three main avenues for promising future developments are highlighted, including coupling stable isotope probing and genome-resolved metagenomics, applying fluorescence-activated cell sorting approaches to target mini-metagenomes within a larger community, and utilizing single-molecule long-read and synthetic long- read technology to link mobile elements to host microbial cells.
Journal ArticleDOI
Machine learning meets genome assembly.
Kleber Padovani de Souza,João C. Setubal,André C. P. L. F. de Carvalho,Guilherme Oliveira,Annie Chateau,Ronnie Alves,Ronnie Alves +6 more
TL;DR: A broad review of pioneering literature comprising artificial intelligence-based DNA assemblers-particularly the ones that use machine learning-is presented to provide an overview of state-of-the-art approaches and to serve as a starting point for further study in this field.
Book ChapterDOI
Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems.
TL;DR: The current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function is reviewed, comparing the authors' knowledge in this area to that obtained by macroecologists who use more traditional techniques.
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