Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment

Beaudry, Megan S.; Wang, Jincheng; Kieran, Troy J.; Thomas, Jesse; Bayona-Vásquez, Natalia J.; Gao, Bei; Devault, Alison; Brunelle, Brian; Lu, Kun; Wang, Jia-Sheng; Rhodes, Olin E.; Glenn, Travis C.

doi:10.3389/fmicb.2021.644662

Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment

Journal Article · Tue Apr 27 00:00:00 EDT 2021 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2021.644662· OSTI ID:1849075

Beaudry, Megan S. ^[1]; Wang, Jincheng ^[2]; Kieran, Troy J. ^[3]; Thomas, Jesse ^[4]; Bayona-Vásquez, Natalia J. ^[5]; Gao, Bei ^[3]; Devault, Alison ^[6]; Brunelle, Brian ^[6]; Lu, Kun ^[3]; Wang, Jia-Sheng ^[7]; Rhodes, Olin E. ^[8]; Glenn, Travis C. ^[9]

Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science; Univ. of Georgia, Athens, GA (United States)
Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science; Univ. of Georgia, Athens, GA (United States). Interdisciplinary Toxicology Program
Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science
Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science; Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL)
Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science; Univ. of Georgia, Athens, GA (United States). Institute of Bioinformatics
Daicel Arbor Biosciences, Ann Arbor, MI (United States)
Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science; Univ. of Georgia, Athens, GA (United States). Interdisciplinary Toxicology Program
Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL)
Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science; Univ. of Georgia, Athens, GA (United States). Interdisciplinary Toxicology Program; Univ. of Georgia, Athens, GA (United States). Inst. of Bioinformatics

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.

View Accepted Manuscript (DOE)

Research Organization:: University of Georgia, Athens, GA (United States)

Sponsoring Organization:: USDOE Office of Environmental Management (EM)

Grant/Contract Number:: FC09-07SR22506

OSTI ID:: 1849075

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 12; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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