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Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches Open Access

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Author or creator
Li, Fuyong
Henderson, Gemma
Sun, Xu
Cox, Faith
Janssen, Peter H.
Guan, Leluo
Additional contributors
Subject/Keyword
Targeted Amplicon Sequencing
Archaea
Rumen Microbiota
Bacteria
Total RNA Sequencing
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.
Date created
2016
DOI
doi:10.7939/R39G5GT0X
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Attribution 4.0 International
Citation for previous publication
Li, F., Henderson, G., Sun, X., Cox, F., Janssen, P. H., & Guan, L. L. (2016). Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches. Frontiers in Microbiology, 7(987), [15 pages].  http://dx.doi.org/10.3389/fmicb.2016.00987

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File title: Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches
File author: Le Luo Guan
Page count: 15
File language: en
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