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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Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Drives Ecological Patterns
TL;DR: The Marine Group II Euryarchaea (MGII) have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter as discussed by the authors.
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Gut microbiota in colorectal cancer development and therapy
Chi Chun Wong,Jun Yu +1 more
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Metagenomic data reveals type I polyketide synthase distributions across biomes
Hans W. Singh,Kaitlin E. Creamer,Alexander B. Chase,Leesa J. Klau,Sheila Podell,Paul R. Jensen +5 more
TL;DR: In this paper , the authors used the web tool NaPDoS2 to detect and classify over 35,000 type I polyketide synthase (T1PKS) domains from 137 metagenomic data sets reported from eight diverse, globally distributed biomes.
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Evolution and function analysis of glycerol kinase GlpK in Pseudomonasaeruginosa.
TL;DR: Zhang et al. as discussed by the authors explored the molecular evolution and function of glycerol kinase GlpK in Pseudomonas aeruginosa and identified the prevalence of two glpK copies.
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Genome-centric portrait of the microbes’ cellulolytic competency
TL;DR: This is the first time that a pipeline was developed for an automatic recognition of the synergy among the carbohydrate active units annotated and this pipeline should be a good add to the bioinformatic tools for the genome-centric interpretations on the specific function niche of cellulose hydrolysis.
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