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Open AccessJournal ArticleDOI

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

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.

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A genomic perspective on genome size distribution across Earth's microbiomes reveals a tendency to gene loss

TL;DR: It is suggested that the known phylogenetic diversity of environmental microorganisms possess significantly smaller genomes than the collection of laboratory isolated microorganisms, and the variation in genome sizes across different types of environments reflects the different ecological and evolutionary strategies used by microorganisms to thrive in their native environment.
Journal ArticleDOI

Vulcanimicrobium alpinus gen. nov. sp. nov., the first cultivated representative of the candidate phylum “Eremiobacterota”, is a metabolically versatile aerobic anoxygenic phototroph

TL;DR: Vulcanimicrobium alpinus gen. nov. as discussed by the authors is the first successful isolation of a Ca Eremiobacterota strain from a fumarolic ice cave on Mt. Erebus volcano (Antarctica).
Posted ContentDOI

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

TL;DR: It is inferred that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.
Journal ArticleDOI

Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota.

TL;DR: The results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination, and the genes responsible for synthesizing the pigments of the Brown form are subject to active horizontal transfer.
Journal ArticleDOI

Molecular hydrogen in seawater supports growth of diverse marine bacteria

TL;DR: In this article , the authors used a suite of approaches to show that marine bacteria consume hydrogen to support growth and showed that H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
References
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Journal ArticleDOI

Fast and accurate short read alignment with Burrows–Wheeler transform

TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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BLAST+: architecture and applications.

TL;DR: The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences.
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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
Journal ArticleDOI

Database resources of the National Center for Biotechnology Information

TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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