Research Scientist USDA ARS Fort Collins, Colorado, United States
Background/Question/Methods
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 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 reads of MiSeq to short and long reads of MinION using similar bioinformatic methods with a mock community and agricultural soil samples.
Results/Conclusions
For all three methods, we found that taxonomic assignments of the mock community at genus and species level matched expectations with minimal deviation from our mock community (74% to 85% Bray-Curtis similarity). Beta diversity of each method produced unique communities, clustered by method. Communities characterized with short reads were more similar to each other than to the MinION long read community. Results were not always consistent across methods when comparing differences between sites. We compare various OTU filtering thresholds to accurately estimate alpha diversity, which was overestimated by all methods. Estimates of alpha diversity and differential abundance were improved with an OTU filtering threshold of 0.07% of sample abundance for MiSeq and MinION data. Compared to established methods, MinION produces output similar to that of MiSeq, suggesting that these techniques are interchangable.
