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
More filters
Posted ContentDOI
Metapopulation Structure of Diatom-associated Marine Bacteria
Liping Qu,Liping Qu,Xiaoyuan Feng,Yuerong Chen,Lingyu Li,Xiaojun Wang,Zhong Hu,Hui Wang,Haiwei Luo +8 more
TL;DR: In this paper, the authors sequenced genomes of 294 bacterial isolates associated with 19 coexisting diatom cells and found that these bacteria constitute eight genetically monomorphic populations of the globally abundant Roseobacter group.
Journal ArticleDOI
Was the Last Bacterial Common Ancestor a Monoderm after All?
Raphaël R. Léonard,Eric Sauvage,Valeria Lupo,Amandine Perrin,Damien Sirjacobs,Paulette Charlier,Frédéric Kerff,Denis Baurain +7 more
TL;DR: It is suggested that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture, which would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture.
Journal ArticleDOI
Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions.
Ana Moya-Beltrán,Ana Moya-Beltrán,Simon Beard,Simon Beard,Camila Rojas-Villalobos,Francisco Issotta,Yasna Gallardo,Ricardo Ulloa,Alejandra Giaveno,Mauro Degli Esposti,D. Barrie Johnson,Raquel Quatrini,Raquel Quatrini +12 more
TL;DR: The most comprehensive classification and pangenomic analysis of this deep-branching class of Proteobacteria to date is presented in this paper, where nearly 100 genomes from the class sampled from a wide range of habitats are analyzed.
Journal ArticleDOI
Genomic Characteristics of Desulfonema ishimotonii Tokyo 01T Implying Horizontal Gene Transfer Among Phylogenetically Dispersed Filamentous Gliding Bacteria.
TL;DR: Insight is provided into the genomic evolution of filamentous bacteria belonging to diverse lineages, characterized by various physiological functions and different ecological roles, and significant genetic transfer among filamentous gliding bacteria in phylogenetically dispersed lineages including filamentous sulfate reducers.
Posted ContentDOI
Diverse arctic lake sediment microbiota shape methane emission temperature sensitivity
Ben J. Woodcroft,Joanne B. Emerson,Ruth K. Varner,Martin Wik,Donovan H. Parks,Rebecca B. Neumann,Joel E. Johnson,Caitlin M. Singleton,Rodney Tollerson,Akosua Owusu-Dommey,Morgan Binder,Nancy L. Freitas,Patrick M. Crill,Scott R. Saleska,Gene W. Tyson,Virginia I. Rich +15 more
TL;DR: The results suggest that deeper lake regions, which currently emit less CH4 than shallower edges, could add substantially to overall CH4 emissions in a warmer Arctic with longer ice-free seasons and that future CH4 emission predictions from northern lakes may be improved by accounting for spatial variations in sediment microbiota.
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.