ARPHA Conference Abstracts : Conference Abstract
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Conference Abstract
Comparing total RNA sequencing and metagenomics pipelines for multi-domain taxonomic profiling: implications for ecological assessments
expand article infoChristopher A. Hempel‡, Julia Harvie‡, Jose S. Hleap Lozano§, Natalie Wright‡, Sarah J. Adamowicz‡, Dirk Steinke‡
‡ Department of Integrative Biology, University of Guelph, Guelph, Canada
§ SHARCNET, University of Guelph, Guelph, Canada
Corresponding author: Christopher A. Hempel (hempelc@uoguelph.ca)
Received: 24 Feb 2021 | Published: 04 Mar 2021
© 2021 Christopher Hempel, Julia Harvie, Jose Hleap Lozano, Natalie Wright, Sarah Adamowicz, Dirk Steinke
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Hempel CA, Harvie J, Hleap Lozano JS, Wright N, Adamowicz SJ, Steinke D (2021) Comparing total RNA sequencing and metagenomics pipelines for multi-domain taxonomic profiling: implications for ecological assessments. ARPHA Conference Abstracts 4: e64996. https://doi.org/10.3897/aca.4.e64996
 Open Access

Abstract

Ecological assessments are necessary to evaluate the status of our deteriorating ecosystems, however, assessment methods traditionally omit most microbes because unicellular organisms are challenging to identify. This omission is not ideal, as microbes might be better indicators for changes in environmental conditions than taxa traditionally used. DNA- and RNA-based techniques are increasingly applied for ecological assessments to overcome this challenge but require more testing and optimization. In this study, we compare metagenomics and total RNA sequencing (total RNA-Seq) for their taxonomic profiling performance for microbial communities. We applied both techniques on two sample sets, 1) a commercially available microbial mock community consisting of eight bacterial and two eukaryotic species, and 2) a display tank water sample. We processed the data using 1,532 bioinformatics pipelines and evaluated each workflow, i.e., the combination of sample type (metagenomics or total RNA-Seq) and pipeline, in terms of their accuracy and precision. This talk will showcase preliminary results and highlight differences in workflow performances. A recommended workflow to maximize taxonomic profiling accuracy of microbial communities will also be presented.

Keywords

Metagenomics, metatranscriptomics, bioinformatics pipelines, taxonomic profiling, multi-domain, mock community

Presenting author

Christopher A. Hempel

Presented at

1st DNAQUA International Conference (March 9-11, 2021)

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