Fixing Digestion, Pt. 4

The final stage of our digestion (for the purposes of this series) is the passage of foodstuffs through our large intestine, or colon. This organ is like a highway compared to the backroads of our small intestine; wider, more direct, built for volume. For reference, it is about five feet long compared to our small intestine’s 20, and about 50% wider.

Digestively-speaking, the colon itself does little. In a healthy body, all the nutrient absorption from our meals happens in our small intestine, as does hormone production, enzyme activity, and most of the active motion. At first glance, in fact, the colon seems like a snoozy place. It’s mainly credited with absorbing water and electrolytes from our foods (yawn), and moving indigestible foodstuffs -fibers- out of our body.

But to leave it at that would be like describing planet earth as a sphere with land and water, and neglecting to mention the crazy humans that inhabit it.

(Which might sound a little like utopia these days...)

The Microbiome

Please take a seat.

Please take a seat.

When we read about the microbiome -or gut flora, or gut bugs- we’re usually talking about the inhabitants of our colon (although our skin and a few other anatomical parts also have their own “microbiomes”). The relatively calm, warm interior of our colon, regular supply of fermentable fibers, and friendly pH levels make this an ideal piece of real estate from a bacterium’s perspective.

A healthy microbiome is like a balanced ecosystem; life is abundant, biodiversity is high, and there’s a constant turnover of old to new. The less desirable species are kept in check by the good, and any imbalances caused by contaminated food, inflammation, or other triggers self-correct quickly.

This biodiversity and balance is important because bacteria play a large role in our health- much larger, we’re learning, than was ever thought possible. They modulate our immune system, making us more or less reactive to things we should be more or less reactive to. They influence our mood, with the better bugs contributing towards calm feels and the worse tending us towards anxiety and sugar cravings. And they regulate inflammation, linking them to the development of obesity, type 2 diabetes, and autoimmune disease.

A balanced microbiome also contributes towards our health by extracting an extra boost of nutrition from our food. As fibers make their way through the large intestine, friendly gut bugs ferment them, creating nutrient byproducts -notably the vitamins K2, folate, B12, and biotin, which are absorbed into the bloodstream and put to work in our bodies. Bacterial fermentation also produces compounds called short chain fatty acids (SCFAs) which are exactly what they sound like: short chains of carbon molecules with hydrogen atoms attached to them (duh) (kidding about the duh).

These compounds, primarily three musketeers known as butyrate, propionate, and acetate, are particularly helpful at fighting inflammation. Researchers have found strong links between levels of SCFAs and the development of autoimmune flares, especially in IBD. SCFAs are also involved in maintaining cardiovascular health through reducing blood pressure, boosting our overall metabolic health, and keeping the walls of our colon healthy and strong.

Wait… is that fiber?

Wait… is that fiber?


To get more of the good bugs into our guts, we have all sorts of options these days. The probiotic market is literally flooded with products, and you find them conscientiously added to everything from popcorn to nut butters. You can choose between bacterial blends, yeast blends, soil organisms, or spores. You can pick your potency- a gajillion colony-forming-units (CFUs) or a bajillion? You can shop from a refrigerator or a shelf, choose for women, men, or children, or pick out a function (improved mood, sharper memory, better vaginal health, etc.).

Some of these products are wonderful. Others are worthless. But I’m not going to take you down the rabbit-hole of probiotic reviews here (although for my gut health go-to, you can check out this blog post). Instead, I want to make the case for prioritizing a diet that creates a flourishing microbiome without reliance on capsulated probiotics.

why you shouldn’t just take the darn pill

Studies of traditional cultures and modern day folk living in traditional, isolated societies show the same thing: a bacterial blend MUCH more diverse than what we see in western societies. In fact, researchers have warned that certain beneficial bacterial species are actually going extinct, thanks to an industrialized diet high in processed snacks and low in diverse fibers. Unfortunately, this extinction seems to only apply to the good species, of course.

So what creates a biodiverse bacterial homestead? Diet variety. This applies to food in general, and especially fiber-rich foods like nuts, seeds, vegetables, tubers, and fruits. More roughage, different roughage, all the roughage seems to be the message for the healthy adult.

Fermented foods are a huge boon as well- cultured vegetables, lacto-fermented condiments, and bacterial dairy powerhouses like kefir. If you think you can’t stomach your veggies in fermented form, remember that up until relatively recently, humankind didn’t have the benefits of refrigeration and almost all vegetable matter enjoyed in the off season was preserved through fermentation. From an evolutionary perspective, fermented food is literally in our DNA.

Pickle feels.

Pickle feels.

What about PREBIOTICS?

You can barely consider probiotics these days without prebiotics flashing across the radar. And you’re not alone if you’ve been wondering what the eff these are.

“Prebiotic” refers to a particular world of food fibers shown to provide an especially beneficial source of food for good gut bugs. They’re fibers that good gut bugs LOVE to ferment, providing nourishment to them and an abundance of beneficial byproducts to us- like the vitamins and SCFAs mentioned above. Prebiotics are found naturally in many foods, with the highest concentrations in garlic, leeks, onions, jerusalem artichokes, dandelion greens, and chicory root. (And -best news yet if you can trust a Nestle study- possibly coffee!)

It wouldn’t be a thing worth having if we weren’t also extracting, isolating, bottling, and marketing to the public -of course- and prebiotics have stepped into this space nicely. Not only are they often added to probiotics, but you can also shop them as acacia fiber, inulin, glucomannan, psyllium, fructooligosaccharides (FOS) and a variety of blends.

So should you?

As with probiotics, I recommend obtaining prebiotics primarily from whole foods. But unlike probiotic supplements, which can be extremely beneficial in some cases, I almost never recommend adding isolated prebiotics. This is because studies have shown that single-source prebiotics can preferentially feed certain bacterial strains over others, leading to less biodiversity and more dysbiosis. So while you might be pooping like a rockstar, you could still be compromising your overall health.

Another downside of prebiotic supplements is that they can be extremely stimulating to the bad gut bugs as well as the good. And because people often turn to these in times of gut distress -gas, bloating, diarrhea, or constipation- they might be setting themselves up for an even worse time down the road.



in conclusion

I often describe our gut microbiome as the wild, wild west. It’s the latest frontier in modern medicine but still largely uncharted territory. We’re learning in leaps and bounds, manufacturing new products as quickly as each study hits the ground, but still a little uncertain of the outcomes.

So eat whole foods. Increase your variety tenfold. Note some easy prebiotic foods that you like and include them when you can. Learn to ferment, or at least buy a traditionally fermented foods (you can find these in the refrigerated section) and eat them with your meals every day (yes, every day). If you tolerate dairy, include a high quality yogurt or kefir from cow or goat milk. If you don’t, make this amazing two ingredient coconut milk yogurt. And if things go awry, don’t be afraid to take a course of probiotics to help get things back on track. Do your shopping homework, follow the dosage intructions, and note if you feel differently in 2-4 weeks. If not, try a different product until you find one that works.

There are, of course, other things besides probiotics, prebiotics, and food choices that can help or hurt our large intestine health. Like:

  • Hydration is extremely important to this chunk of anatomy.

  • Enemas and colonics can be surprisingly healing for constipation resulting from impacted feces.

  • Supplementing with collagen powder or a daily cup of bone broth will help keep the intestine walls at their healthiest.

  • Imbalanced mucus production along these walls can be too high or too low and can effect the absorption of important minerals.

Health is complex; you get it. But focusing on microbial health is an excellent starting place for fixing up your large intestine health. If you continue struggling to sort things out, consider reaching out to a functional medicine practitioner or a nutritionist (::waves::).

want more microbes?

And if you want to nerd out more on all-things gut health, check out the blog of Jeff Leach. He’s one of my favorites for open-minded, n-of-one, deep microbial experimentation.