Alright nerds, this one's for you. I'm a microbiome researcher at a mid-tier R1 and I've been running 16S rRNA sequencing on my own stool samples since before I started semaglutide (n=1, I know, I know). But the data is genuinely interesting.
Background: 16S ribosomal RNA gene sequencing lets you profile which bacterial taxa are present in a fecal sample and in what relative abundance. I used the V3-V4 hypervariable region, Illumina MiSeq, QIIME2 pipeline, Silva 138 database.
I collected baseline samples (3 samples over 2 weeks pre-sema), then monthly samples for 6 months on Ozempic (titrated 0.25 → 0.5 → 1.0 → 2.0mg).
Key findings:
| Metric | Baseline | Month 3 | Month 6 |
|---|
| Shannon Diversity | 3.82 | 3.41 | 3.67 |
| Firmicutes:Bacteroidetes ratio | 2.8:1 | 1.9:1 | 1.6:1 |
| Akkermansia muciniphila (%) | 0.3% | 1.8% | 4.2% |
| Prevotella copri (%) | 8.1% | 3.4% | 2.1% |
| Bifidobacterium spp. (%) | 2.4% | 5.7% | 6.1% |
The Akkermansia bloom is the standout. A. muciniphila is consistently associated with improved metabolic health, better glucose tolerance, and reduced inflammation in the literature.[1] A 14x increase in 6 months is substantial.
The F:B ratio decrease tracks with weight loss — higher F:B ratios are associated with obesity in most (though not all) studies.[2]
Important caveats: my diet changed significantly (less processed food, more fiber, smaller portions). So I CANNOT attribute this to semaglutide directly vs. dietary changes. This is a confounder I can't resolve with n=1.
Anyone else tracking their microbiome on GLP-1 agonists? Has anyone seen published data on this?
[1] Depommier C, Everard A, Druart C, et al. "Supplementation with Akkermansia muciniphila in overweight and obese human volunteers." Nat Med. 2019;25(7):1096-1103.
[2] Ley RE, Turnbaugh PJ, Klein S, Gordon JI. "Human gut microbes associated with obesity." Nature. 2006;444(7122):1022-1023.