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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #419789
Research Project: Genomes to Phenomes in Beef Cattle Research

Location: Genetics and Animal Breeding

Title: Missing mate pairs reported as poly-G reads can confound analyses of rare members of microbial assemblages

Author
item DHILLON, AMRIT - North Carolina State University
item Workman, Aspen
item Kuehn, Larry
item EARLEY, BERNADETTE - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY)
item COSBY, SARA - Agri-Food And Biosciences Institute
item POWELL, AMY - Sandia National Laboratory
item McDaneld, Tara
item CONANT, GAVIN - North Carolina State University

Submitted to: Ecological Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2025
Publication Date: 12/1/2025
Citation: Dhillon, A.K., Workman, A.M., Kuehn, L.A., Earley, B., Cosby, S.L., Powell, A.J., McDaneld, T.G., Conant, G.C. 2025. Missing mate pairs reported as poly-G reads can confound analyses of rare members of microbial assemblages. Ecological Genetics and Genomics. 37. Article 100399. https://doi.org/10.1016/j.egg.2025.100399.
DOI: https://doi.org/10.1016/j.egg.2025.100399

Interpretive Summary: Sampling and sequencing DNA from the environmental samples allows researchers to understand microbial ecosystems. For this experiment, we used sequence from environmental samples collected from both cattle and sheep. From these data we describe how failures in pairing of the forward and reverse sequence reads can interact with bioinformatics pipelines to give spurious results. We found several sequence datasets where the paired sequence matched a viral database at very different frequencies. We found a source of error that can be controlled by quality filtering sequence data in the future.

Technical Abstract: Using sequence reads from shotgun metagenomic analyses in both cattle and sheep, we describe how failures in mate pairing on Illumina sequencing can interact with bioinformatics pipelines to give spurious patterns among rare components of a metagenomic sample. We identified several different shotgun metagenomic datasets from different animals and different laboratories where the two members of the read pair matched a viral database at very different frequencies. We traced this bias to a set of poly-G reads of high quality that resulted from failures in generating read pairs during library preparation. These results reinforce the need to remove poly-G-rich reads when quality filtering shotgun metagenomic data.