Gut microbiomecourses.

Gut microbiome taxonomy, compositional data analysis, and the statistics behind 16S rRNA sequencing — replicate a published cross-population study, hand-build diversity metrics, and survey the pipelines (QIIME2, DADA2, GMWI2) used to generate this kind of data in practice.

The computational pipeline behind gut-health tools like GMWI2 — parse real sequence data with Biopython, hand-build a presence/absence matrix, and train your own cross-validated classifier with scikit-learn before seeing how a real, published 2024 tool does the same thing at scale.

A phylum-by-phylum tour of roughly twenty gut bacterial genera — naming and taxonomy, the diet-driven Bacteroides/Prevotella split, butyrate producers, opportunists, and a closing look at exactly where genus-level resolution stops being enough. Pulls real data directly from the other two courses.

What a bacterial species actually is — the ANI convention that defines one, real ongoing reclassification inside genera already covered on this site, and exactly where species-level data stops being enough. Reuses the bioinformatics course's species-level dataset throughout.

The resolution level below species — where commensal E. coli and dangerous E. coli finally split apart. Real virulence and resistance genes, plasmids and mobile genetic elements, why probiotic strains aren't interchangeable, and a real cross-validated strain classifier. Closes out the full genus → species → strain resolution ladder across all five courses on this site.