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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Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread Sumerlaeota.
Yun Fang,Yun Fang,Yang Yuan,Jun Liu,Geng Wu,Jian Yang,Zheng-Shuang Hua,Jibin Han,Xiying Zhang,Wen-Jun Li,Wen-Jun Li,Hongchen Jiang,Hongchen Jiang +12 more
TL;DR: Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported, and their physiology, ecology, and evolutionary history remain unknown as mentioned in this paper.
Journal ArticleDOI
Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics.
TL;DR: In this paper, metagenomic binning was used to recover 2,809 microbial genomes from cattle, sheep, moose, deer, and bison, and demonstrated approximately one third of the metagenome-assembled genomes (MAGs) to represent species not present in current reference databases and rumen microbial genome collections.
Journal ArticleDOI
A rather dry subject; investigating the study of arid-associated microbial communities.
Peter Osborne,Lindsay J. Hall,Lindsay J. Hall,Noga Kronfeld-Schor,David Thybert,Wilfried Haerty +5 more
TL;DR: The interactions between arid environments and the microbial communities which inhabit them are reviewed, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field are reviewed.
Journal ArticleDOI
Mechanisms driving genome reduction of a novel Roseobacter lineage.
Xiaoyuan Feng,Xiao Chu,Yang Qian,Michael W. Henson,Michael W. Henson,V. Celeste Lanclos,Fang Qin,Shelby J. Barnes,Yanlin Zhao,J. Cameron Thrash,Haiwei Luo +10 more
TL;DR: In this paper, a marine roseobacter lineage, called CHUG, was found to possess the smallest genomes (2.6 Mb) among all known roseobacters, but they do not exhibit canonical features of typical bacterioplankton lineages theorized to have undergone genome streamlining processes.
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Contributions of single-cell genomics to our understanding of planktonic marine archaea.
TL;DR: Future progress in the application of single- cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening.
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.