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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Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater
Yohei Nishikawa,Masato Kogawa,Masahito Hosokawa,Ryota Wagatsuma,Katsuhiko Mineta,Kai Takahashi,Keigo Ide,Kei Yura,Hayedeh Behzad,Takashi Gojobori,Haruko Takeyama +10 more
TL;DR: Wang et al. as mentioned in this paper developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for singlecell isolation, lysis, and whole genome amplification.
Journal ArticleDOI
Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems.
TL;DR: In this paper, an intracellular bacterium inhabiting the flagellated protist Bodo saltans (Kinetoplastida) was characterized, and a complete bacterial genome comprising a 1.39mb circular chromosome with 40.6% GC content was presented.
Journal ArticleDOI
Genomic Insights of "Candidatus Nitrosocaldaceae" Based on Nine New Metagenome-Assembled Genomes, Including "Candidatus Nitrosothermus" Gen Nov. and Two New Species of "Candidatus Nitrosocaldus".
Zhen-Hao Luo,Manik Prabhu Narsing Rao,Hao Chen,Zheng-Shuang Hua,Zheng-Shuang Hua,Qi Li,Brian P. Hedlund,Zhou-Yan Dong,Bing-Bing Liu,Shu-Xian Guo,Wen-Sheng Shu,Wen-Jun Li +11 more
TL;DR: In this paper, a metagenomics approach was employed to obtain "Ca. Nitrosocaldaceae" metagenomic-assembled genomes (MAGs) from hot spring samples collected from India and China.
Journal ArticleDOI
The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut
Erin Wong,Emma Brownlie,Katharine M. Ng,Sornnujah Kathirgamanathan,Feiqiao Brian Yu,Bryan D. Merrill,Kerwyn Casey Huang,Alberto Martin,Carolina Tropini,William Wiley Navarre +9 more
TL;DR: A large-scale isolation of bacteria from the intestines of laboratory mice either prone to or suffering from gut inflammation is reported, providing the first metabolic analysis of species within the genus Adlercreutzia, revealing these representatives to be nitrate-reducing and severely restricted in their ability to grow on carbohydrates.
Journal ArticleDOI
Compositionally Biased Dark Matter in the Protein Universe.
TL;DR: The UniProt protein database has been surveyed for evidence of compositionally ‘‘dark matter’’ protein types that have not been characterized experimentally and it is estimated that how many DBRs there might be for the high bias levels examined, deriving a reasonable range of 0.7–7.2% of proteins having such D BRs.
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