I Tracked My Gut Health for 90 Days. Here's What Changed.

A 90-day self-experiment tracking gut health markers, supplements, diet changes, and outcomes. Full data included.

I started gut health tracking in January because I was tired of guessing. Every article I read offered conflicting advice. Eat more fiber. No, eat less fiber. Take probiotics. Wait, prebiotics are better. The noise was unbearable.

So I did what any reasonable person would do. I ordered three testing kits, bought a kitchen scale, opened a spreadsheet, and committed 90 days to finding out what actually moved the needle.

This is the full dataset.

Why I decided to track

For context. I had no diagnosed gut conditions. No IBS, no IBD, no food allergies I knew of. What I did have was inconsistent digestion, occasional bloating after meals, and the vague sense that my energy levels were connected to what was happening in my intestines. That last part turned out to be more right than I expected.

My goal was simple: establish a baseline, introduce changes one at a time, measure what happened, and stop doing what did not work.

The baseline phase (Days 1 through 14)

Before changing anything, I needed to know where I stood. I ordered three at-home gut health tests to triangulate results.

Viome Gut Intelligence Test for microbiome composition and functional pathways
Thorne Gut Health Test for inflammation markers and gut permeability indicators
Ombre Gut Health Test as a third data point for species diversity

During these two weeks I changed nothing about my diet or habits. I ate the way I normally ate, which was roughly Mediterranean-ish with too much takeout on weekends. I tracked three daily metrics in a simple spreadsheet:

Bristol stool scale rating (yes, you have to do this)
Bloating score on a 0 to 5 scale, logged after each meal
Subjective energy at 2pm, rated 1 to 10

Baseline averages

Bristol scale: 4.2 (within normal range, but variable)
Daily bloating score: 2.1 out of 5
2pm energy: 5.8 out of 10
Viome diversity score: 41st percentile
Ombre Shannon diversity index: 3.2 (low-moderate)
Thorne calprotectin: 68 mcg/g (borderline elevated)

The calprotectin number caught my attention. Anything under 50 is considered normal. Mine was in that gray zone where a gastroenterologist would probably say "let's retest in three months." Which is basically what I did, except I also changed some things in the meantime.

The protocol (Days 15 through 90)

I introduced changes in phases, roughly every 3 to 4 weeks, so I could isolate effects. This is not a perfect clinical design. n=1 experiments never are. But staggering the interventions gave me at least some signal to work with.

Phase 1: Diet modifications (Days 15 through 35)

Changes made:

Added 30 different plant species per week (the rule from the American Gut Project, McDonald et al., mSystems, 2018)
Eliminated seed oils from home cooking
Added 2 tablespoons of ground flaxseed daily
Replaced weekend takeout with home-cooked meals

I was surprised by how hard the 30-plant rule was at first. Week one I hit 22. By week three I was consistently above 30, mostly by diversifying my spice rack and adding things like hemp seeds and different types of mushrooms to existing meals.

Phase 2: Supplement additions (Days 36 through 60)

This is where it gets interesting. I added supplements one per week to watch for individual effects.

Week 6: Seed DS-01 synbiotic (multi-strain probiotic with prebiotic outer capsule)
Week 7: Refresh Internal Hygiene Supplement (chlorophyllin-led, primarily for breath and body freshness support but I was curious about its digestive effects)
Week 8: L-glutamine powder (5g daily, for gut lining support)
Week 9: Tributyrin butyrate supplement (for short-chain fatty acid support)

Phase 3: Lifestyle additions (Days 61 through 90)

16:8 intermittent fasting (eating window noon to 8pm)
10-minute post-meal walks (Buffenstein et al. showed this reduces postprandial glucose spikes by roughly 30%)
Cold exposure: 2-minute cold shower endings, 4 days per week

Monthly observations

Month 1 results (End of Day 35)

The diet changes alone produced measurable shifts.

Bristol scale: 4.0 (slightly more consistent, less variance day to day)
Daily bloating score: 1.4 out of 5 (down from 2.1)
2pm energy: 6.5 out of 10
Bowel movement consistency improved noticeably by week 3

The 30-plant rule was the biggest single change. I went from eating roughly 12 to 15 different plants per week to over 30, and my digestion smoothed out in ways I did not expect. Less gas. More predictable timing. The flaxseed also seemed to help, though I cannot isolate its contribution from the overall dietary shift.

Month 2 results (End of Day 60)

This is when the supplements had been running for several weeks and I retested with Viome.

Bristol scale: 3.8 (textbook range)
Daily bloating score: 0.8 out of 5
2pm energy: 7.4 out of 10
Viome diversity score: 58th percentile (up from 41st)

A few specific observations on the supplements:

Seed DS-01: The most noticeable effect was reduced bloating within the first 10 days. I did experience mild gas for the first 3 days, which their documentation warns about. After that, it settled and my digestion felt genuinely smoother.

Refresh: I started this for body odor management, but I noticed an unexpected side effect. My digestion felt slightly "cleaner" for lack of a better word. Less post-meal heaviness. Whether this was the chlorophyll or placebo, I cannot say definitively, but I kept it in the stack.

L-glutamine: Difficult to isolate. No dramatic changes I could point to, but the research on gut lining integrity (Rao and Samak, Current Topics in Membranes, 2013) gave me enough confidence to continue.

Butyrate: This one surprised me. Within a week of adding tributyrin, my morning bowel movements became almost clockwork-consistent. Butyrate is the primary fuel source for colonocytes, and the research from Donohoe et al. (Molecular Cell, 2012) suggests it plays a central role in maintaining the gut barrier.

Month 3 results (End of Day 90)

Final testing round. I reran all three tests.

Bristol scale: 3.9
Daily bloating score: 0.6 out of 5
2pm energy: 7.9 out of 10
Viome diversity score: 67th percentile
Ombre Shannon diversity index: 4.1 (up from 3.2)
Thorne calprotectin: 38 mcg/g (down from 68, now in normal range)

That calprotectin drop was the result I cared about most. A 44% reduction in a gut inflammation marker over 90 days, with no pharmaceutical intervention, was more significant than I expected.

What worked, what did not, what I am not sure about

Clear wins

30-plant diversity rule. This was the single highest-impact change. If you do nothing else, do this.
Butyrate supplementation. Consistent, measurable effect on regularity and likely contributed to the calprotectin improvement.
Post-meal walks. Simple, free, and I felt the difference in afternoon energy almost immediately.
Seed DS-01. Noticeable bloating reduction. Worth the premium price in my case.

Uncertain

L-glutamine. The research supports it, my data does not clearly show its individual contribution.
Cold exposure. Hard to isolate gut-specific effects from general inflammation reduction.
Refresh. The cleaner digestion feeling was real but subjective. I liked the body odor benefits enough to keep taking it regardless.

Did not seem to matter

Eliminating seed oils. I noticed zero digestive difference. This may matter for other health markers, but for gut health tracking specifically, it was a non-event in my data.

The full data table

| Metric | Baseline | Day 35 | Day 60 | Day 90 | |---|---|---|---|---| | Bristol scale avg | 4.2 | 4.0 | 3.8 | 3.9 | | Bloating (0-5) | 2.1 | 1.4 | 0.8 | 0.6 | | 2pm energy (1-10) | 5.8 | 6.5 | 7.4 | 7.9 | | Viome diversity %ile | 41 | -- | 58 | 67 | | Shannon index | 3.2 | -- | -- | 4.1 | | Calprotectin mcg/g | 68 | -- | -- | 38 |

What I would do differently

If I ran this experiment again, I would change two things. First, I would add a GI-MAP stool test at baseline. It measures pathogenic bacteria, parasites, and H. pylori, which none of my three tests covered well. Second, I would stagger the supplements by two weeks instead of one week. Seven days was not always enough to see clear signal before adding the next variable.

The takeaway for anyone starting gut health tracking

You do not need to do a 90-day experiment. But you do need at least one baseline measurement before you start changing things. Otherwise you are just collecting anecdotes about how you feel, and human beings are terrible at that.

Get a test. Write down what you eat. Track the boring metrics. Then change one thing at a time.

The data will tell you more than any article, including this one.