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Title: Towards a balanced view of the bacterial tree of life

Abstract

The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1544021
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Microbiome
Additional Journal Information:
Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2049-2618
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bacteria; Bacterial diversity; Tree of life; Small subunit (SSU) rRNA; Candidate Phyla Radiation (CPR); Microbial dark matter (MDM); Metagenomics; Novel bacterial lineages

Citation Formats

Schulz, Frederik, Eloe-Fadrosh, Emiley A., Bowers, Robert M., Jarett, Jessica, Nielsen, Torben, Ivanova, Natalia N., Kyrpides, Nikos C., and Woyke, Tanja. Towards a balanced view of the bacterial tree of life. United States: N. p., 2017. Web. doi:10.1186/s40168-017-0360-9.
Schulz, Frederik, Eloe-Fadrosh, Emiley A., Bowers, Robert M., Jarett, Jessica, Nielsen, Torben, Ivanova, Natalia N., Kyrpides, Nikos C., & Woyke, Tanja. Towards a balanced view of the bacterial tree of life. United States. doi:10.1186/s40168-017-0360-9.
Schulz, Frederik, Eloe-Fadrosh, Emiley A., Bowers, Robert M., Jarett, Jessica, Nielsen, Torben, Ivanova, Natalia N., Kyrpides, Nikos C., and Woyke, Tanja. Tue . "Towards a balanced view of the bacterial tree of life". United States. doi:10.1186/s40168-017-0360-9. https://www.osti.gov/servlets/purl/1544021.
@article{osti_1544021,
title = {Towards a balanced view of the bacterial tree of life},
author = {Schulz, Frederik and Eloe-Fadrosh, Emiley A. and Bowers, Robert M. and Jarett, Jessica and Nielsen, Torben and Ivanova, Natalia N. and Kyrpides, Nikos C. and Woyke, Tanja},
abstractNote = {The bacterial tree of life has recently undergone significant expansion, chiefly from candidate phyla retrieved through genome-resolved metagenomics. Bypassing the need for genome availability, we present a snapshot of bacterial phylogenetic diversity based on the recovery of high-quality SSU rRNA gene sequences extracted from nearly 7000 metagenomes and all available reference genomes. We illuminate taxonomic richness within established bacterial phyla together with environmental distribution patterns, providing a revised framework for future phylogeny-driven sequencing efforts.},
doi = {10.1186/s40168-017-0360-9},
journal = {Microbiome},
number = 1,
volume = 5,
place = {United States},
year = {2017},
month = {10}
}

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Works referenced in this record:

Search and clustering orders of magnitude faster than BLAST
journal, August 2010