OTUer

An OTUer is a person who analyzes microbial sequence data by grouping sequences into operational taxonomic units (OTUs). OTUers typically work in microbial ecology, environmental sequencing, or metagenomics, using OTUs as a practical stand-in for species in diversity analyses. The term OTUer is informal and used primarily among practitioners rather than as a formal designation.

Core activities include quality filtering of reads, clustering sequences into OTUs according to similarity thresholds (commonly 97%), annotating OTUs by comparing representative sequences to reference databases, and generating downstream summaries such as alpha and beta diversity, rarefaction curves, and taxonomic profiles. OTUers often run pipelines with software packages such as QIIME, mothur, USEARCH, or VSEARCH, and may use scripts to produce OTU tables and phylogenetic trees. The field also involves decisions about thresholds, alignment methods, and reference databases, which can affect results.

History and evolution: OTU concept arose in the late 1990s as a pragmatic solution to species-level identification in short marker-gene sequences. Although widely used for two decades, OTU-based analyses have faced criticism for arbitrary thresholds and reproducibility issues. In recent years many researchers have shifted toward amplicon sequence variants (ASVs), which aim for single-nucleotide resolution, while still using OTU-based methods in some contexts.

OTUer community and impact: The work of OTUers supports studies of microbial diversity in soils, oceans, human-associated microbiomes, and extreme environments. Challenges include standardization of methods and proper interpretation of ecological signals.