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ARS Home » Plains Area » Fort Collins, Colorado » Center for Agricultural Resources Research » Soil Management and Sugarbeet Research » Research » Publications at this Location » Publication #393514

Research Project: Agricultural Management for Long-Term Sustainability and Soil Health

Location: Soil Management and Sugarbeet Research

Title: Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

item Stevens, Bo
item Creed, Timothy
item Reardon, Catherine - Kate
item Manter, Daniel

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/30/2023
Publication Date: 6/8/2023
Citation: Stevens, B.M., Creed, T.B., Reardon, C.L., Manter, D.K. 2023. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Scientific Reports. 13. Article e9323.

Interpretive Summary: New gene sequencing platforms hold the promise of reducing costs while producing comparable results to established technologies. ARS scientists in Fort Collins tested the potential for adopting these new platforms in research on soil and plant health. While small, site-specific differences were found between technologies, their research supports expanded use of new gene sequencing platforms in agricultural research.

Technical Abstract: Illumina MiSeq is the current standard for characterizing microbial communities in soil. The Oxford Nanopore Technologies MinION sequencer is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (90% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the output of short MiSeq to short and full-length MinION 16S rRNA amplicons using similar bioinformatic methods with a mock community and agricultural soil samples. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9-90.5%; species: >70.9-85.2% Bray-Curtis similarity). Beta diversity of each method produced unique communities and clustered by method. Communities characterized with short reads were more similar to each other than to the MinION long read community. We compare various filtering thresholds to accurately estimate alpha diversity, which was overestimated by all methods. Estimates of alpha diversity and differential abundance were improved with a species filtering threshold of 0.07% of sample abundance for MiSeq and MinION data, respectively.