Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.

ABSTRACT:

Background

The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.

Results

Of the workflows examined, those using the V4-V4 primer se

SUBMITTER: De Wolfe TJ 

PROVIDER: S-EPMC10114302 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature