“Farming My Microbiome: Turning My Gut Into a Living Ecosystem

Quantified Self Diet, Nutrition, and Weight
, ,
1

Hi everyone — I’m “Farmer”, and for the past several months I’ve been running a personal experiment that sits somewhere between nutrition, ecology, and DIY bio. The short version: I’m actively farming my microbiome. Not just “eating healthy” or “taking random probiotics,” but treating my gut as an actual garden, a managed ecosystem with inputs, rotations, inoculants, and measurable outputs.

My working model is that the gut behaves like a living farm:

  • Microbial guilds instead of crops

  • Ferments as inoculants

  • Fibers and polyphenols as soil amendments

  • Meal timing and substrate sequencing as irrigation and nutrient pulses

  • Telemetry (glucose, ketones, BP, weight, subjective markers) as the feedback loop

What I’m doing right now

I’m running a daily rotation of DIY Home-made ferments and purchased substrates, including:

  • Kefir

  • Yogurt, Bulgarian style

  • Natto

  • Mixed vegetable ferments (6–8 tbsp/day), multiple varieites

  • Fermented Hot Sauce

  • Ginger/turmeric ferments

  • Lacto-fermented ginger drink

  • A structured prebiotic blend (psyllium, inulin, acacia, resistant starch, flax)

  • Polyphenol inputs like pomegranate peel and black cumin and matcha tea

  • A high‑diversity plant intake, with a garden and an orchard in the startup phase now

The goal is a stable, high‑diversity ecosystem that can handle metabolic stress, dietary shifts, and aging without collapsing into inflammation or dysbiosis.

What I’m tracking

I’m logging:

  • Waking glucose

  • Post‑coffee glucose

  • Meal‑timed glucose curves

  • Weight, waist, BP, Heat rate

  • Subjective markers (energy, digestion, sleep)

  • Ferment batches and substrate timing

  • Fasting windows and feeding pulses

  • I’m also following a keto IF style diet and losing weight (30lbs down so far)

I’m especially curious about how different ferments behave as inoculants — which ones “take,” which ones seem transient, and which ones shift metabolic markers in a measurable way, which ones I haven’t tried but should…

Why I’m posting

I have heard that others here are experimenting with ferments, fibers, microbiome tests, or metabolic tracking. I’d like to compare notes with anyone who’s:

  • Trying to cultivate specific microbial guilds

  • Using ferments as targeted inoculants

  • Sequencing fibers or substrates intentionally

  • Tracking metabolic responses to different ferments

  • Or just contemplating a more ecological approach to gut health

What’s working for you? What surprised you? What didn’t behave the way you expected?

Looking forward to hearing from others who are cultivating their own internal ecosystems.

2

I’m going to add something you did not ask about and make a recommendation to read The Way To Quiet Inflammation. Her book discusses in detail what happens chemically in our body from the moment food enters through digestion. This is critical IMHO in any gut investigation, and perhaps you were alluding to this when you mention meal timing so excuse me if I’m not sharing anything you don’t already know, because modern society talks about snacking and all sorts of cues when in reality our system as designed has an innate process and by working with that process we can achieve better results. Upon reading the book and following its recommendations I understood why there were so many people who experienced vast improvements in their health conditions and desire, for some, for weight loss. For me not being able to drink warm drinks when I want throughout the day was annoying but in times I wanted to truly lower inflammation I did so without adding any kind of “milk” (so plain tea or coffee). Most studies I’ve read on the gut indicate that a predictable eating pattern helps the gut settle in and that it can take several months to a year for a disordered gut to fully benefit from changes (and behave more ideally). I’m a fan of eating foods that work but if you were to want to develop something to help others then it also becomes important to recognize that there are mild/moderate to severe sugar digestion issues that I’ve learned are more common, as well as mast cells and other phenomena that make farming a particular gut difficult.

I do love your analogy and enjoy knowing what’s working for you. I recently discovered by accident that although ground flaxseed would formerly cause my gut to bleed, I can now ingest 32 g/day (more of a medical level of ingestion) and it immediately changed how my GI tract works (when every other soluble and insoluble food did not). So, I suggest taking a look at the research. I’m more than 12 years into a serious gut journey and was pleasantly surprised. Being open minded (forever) seems to be an advantage.

Best of luck to you!

3

Good points, I’ll look that book up! Who is the author?

I am 100% added sugar free, the only sugars I get are the ones naturally in the foods I eat, and mostly right now I don’t eat those anyway - being on keto/IF pretty much eliminates those for now.

And the only milk I get is after it has been fermented, which changes its nature pretty radically.

What was going on that ground flax caused your gut to bleed? That sounds intensely interesting.