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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The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review.
TL;DR: Detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential is provided.
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Metagenomic Data Assembly – The Way of Decoding Unknown Microorganisms
Alla Lapidus,Anton Korobeynikov +1 more
TL;DR: In this paper, the authors describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenome assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers.
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Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil
Rubén López-Mondéjar,Vojtěch Tláskal,Tomáš Větrovský,Martina Štursová,Rodolfo Brizola Toscan,Ulisses Nunes da Rocha,Petr Baldrian +6 more
TL;DR: The results confirm the importance of bacteria, in addition to fungi, as decomposers of complex organic matter in forest soils, and indicate the key role of some bacterial genera in the degradation of plant biomass and microbial biomass.
Journal ArticleDOI
Anaerobic hydrocarbon degradation in candidate phylum 'Atribacteria' (JS1) inferred from genomics
TL;DR: Genes involved in anaerobic hydrocarbon degradation were found in seven MAGs associated with hydrocarbon-enriched environments, and suggest that some Atribacteria could ferment short-chain n-alkanes into fatty acid while conserving energy.
Journal ArticleDOI
Novel prosthecate bacteria from the candidate phylum Acetothermia.
Liping Hao,Simon Jon McIlroy,Rasmus Hansen Kirkegaard,Søren Michael Karst,Warnakulasuriya Eustace Yrosh Fernando,Hüsnü Aslan,Rikke Louise Meyer,Mads Albertsen,Per Halkjær Nielsen,Morten Simonsen Dueholm +9 more
TL;DR: It is hypothesized that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
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.
Journal ArticleDOI
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Journal ArticleDOI
BLAST+: architecture and applications.
Christiam Camacho,George Coulouris,Vahram Avagyan,Ning Ma,Jason S. Papadopoulos,Kevin Bealer,Thomas L. Madden +6 more
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.
Journal ArticleDOI
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Todd M. Lowe,Sean R. Eddy +1 more
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
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
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.