A self-guided lab notebook · runs in your browser

Bacteria genusoverview.

A twelve-module tour of the gut microbiome's major bacterial genera, grouped by phylum — real biology, real research citations, and real numbers pulled directly from the datasets used in this site's other two courses. Covers naming and taxonomy, diet-driven genera, butyrate producers, opportunists, a mucin specialist, and a cross-dataset comparison, closing on exactly where genus-level resolution stops being enough. Runs natively in-browser; no local installation required.

Start the course →
Fig. 1 — Phyla covered in this course
Bacteroidetes
Bacteroides, Prevotella, Alistipes, Parabacteroides
№ 02–03
Firmicutes
Faecalibacterium, Roseburia, Eubacterium, Ruminococcus, Blautia, Dorea, Lachnospira, Oscillospira
№ 04–05
Actinobacteria
Bifidobacterium
№ 06
Proteobacteria
Escherichia, Klebsiella
№ 07
Verrucomicrobia
Akkermansia
№ 08
Fusobacteria & others
Fusobacterium, Veillonella, Dialister
№ 09
Six phyla, roughly twenty genera — most already sitting unexplained as data columns in this site's other two courses. Notebook 10 pulls all three datasets together; Notebook 11 covers what genus-level data can't tell you.

Specimen log — course order

№ 00 Welcome
How this course works, and why it reuses data from the other two
 → № 01 What Is a Genus, Anyway?
Taxonomic ranks, naming, and the mystery of the "[Ruminococcus]" bracket
 → № 02 Bacteroidetes I
Bacteroides & Prevotella — the diet-driven pair, plus enterotypes
 → № 03 Bacteroidetes II
Alistipes & Parabacteroides — not every genus splits by diet
 → № 04 Firmicutes I
The butyrate producers: Faecalibacterium, Roseburia, Eubacterium
 → № 05 Firmicutes II
Ruminococcus, Blautia, Dorea, Lachnospira, Oscillospira
 → № 06 Actinobacteria
Bifidobacterium — one of two genera in all three site datasets
 → № 07 Proteobacteria
Escherichia & Klebsiella — the opportunists
 → № 08 Verrucomicrobia
Akkermansia — a mucin specialist and a metabolic-health research darling
 → № 09 Fusobacteria & Friends
Fusobacterium, Veillonella, Dialister
 → № 10 Comparing Genus Profiles
All three site datasets, loaded and compared side by side
 → № 11 Genus Isn't the Whole Story
The limits of genus-level resolution, and what's next
 →
Nothing to install. Every notebook here uses only pandas and matplotlib, and reads CSVs directly from the other two courses on this site — no setup cells, no new datasets, no waiting on installs.