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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Journal ArticleDOI
Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes
Jintao Yang,Cuihong Tong,Danyu Xiao,Longfei Xie,Ruonan Zhao,Zhipeng Huo,Ziyun Tang,Jie Hao,Zhenling Zeng,Wenguang Xiong +9 more
TL;DR: This study established the largest chicken gut resistance gene catalogue to date through metagenomic analysis of 629 chicken gut samples and established a reference genome of gut antibiotic resistance genes in chickens, which will help to rationalize the use of drugs in poultry farming.
Dissertation
Taxonomic and functional exploration of the biosphere of serpentinizing hydrothermal systems by metagenomics
TL;DR: In this article, les communautes microbiennes ont ete etudiees en se focalisant sur Prony, un ecosysteme serpentinise cotier de Nouvelle-Caledonie, en comparant differents ecosystemes serpentinises, pour faire emerger des similarites taxonomiques and fonctionnelles.
Posted ContentDOI
ganon: continuously up-to-date with database growth for precise short read classification in metagenomics
Vitor C. Piro,Vitor C. Piro,Temesgen Hailemariam Dadi,Enrico Seiler,Knut Reinert,Bernhard Y. Renard +5 more
TL;DR: Ganon is a k-mer based short read classification tool which uses Interleaved Bloom Filters in conjunction with a taxonomic clustering and a k -mer counting-filtering scheme and shows strongly improved precision while having equal or better sensitivity compared to state-of-the-art tools.
Journal ArticleDOI
Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits
TL;DR: In this article , the authors explored the genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deepsea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles.
Journal ArticleDOI
Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities.
Yunyan Zhou,Min Liu,Jiawen Yang +2 more
TL;DR: Genome binning is a culture-independent approach that can recover a vast number of microbial genomes from short-read high throughput shotgun metagenomic sequencing data as discussed by the authors , which is essential for analyzing the metabolic and functional potentials of microbiomes.
References
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Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
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