16 Things That Affect Your Gut Bacteria


A couple months ago, we explored many of the ways our gut bacteria affect us, focusing on the lesser known effects like anti-nutrient nullification, vitamin manufacture, and neurotransmitter production. Today, we’re going to discuss all of the ways (that we know) we can affect our gut bacteria. It turns out that the food we eat, the amount of sun we get, whether we eat organic or not, the supplements we take, and even the kind of nuts or chocolate we decide to eat – just to name a few factors – can change the composition and function of our gut microbiota for the good or for the bad. We may still have a lot to learn about this gut stuff, but the bulk of the evidence says that we do have the power (and responsibility if you care to be healthy) to affect the health of our gut microbiota.

Here are 16 things to do, eat, avoid, and/or heed:

Fermentable fibers

I’ve discussed this variable to death, but it may be the single most important pro-gut biome dietary modification we can enact. Without fermentable fibers, our gut bacteria just aren’t getting the food they need to maintain the population – let alone grow it.

Fermented foods

From sauerkraut to pickles to kimchi to kefir to condiments to “high meat,” fermented foods have been a consistent part of the human diet for many thousands of years. And while it’s unlikely previous generations had detailed knowledge of the gut biome, today we know that fermented food plays an important role in shaping the health of our guts. Yogurt, one of my favorites, often changes the composition of the gut biome for the better. But even when it has no effect on the population or composition of a microbiome, fermented food can change the way the existing population works. In one study, for example, bacterial strains isolated from fermented milk didn’t colonize the gut but led to increased microbial expression of carbohydrate metabolizing enzymes. In another study, yogurt and probiotic supplementation allowed lactose-intolerant subjects to tolerate a greater amount of dietary lactose by changing their colonic bacteria.

Fermented foods aren’t a “one and done” deal. You have to maintain an ongoing relationship with them in order to enjoy the full benefits and sustain the colonization. It’s more accurate to consider them necessary foods we need to eat regularly rather than supplements or medicines.


Even though we usually think of the polyphenols found in blueberries, red wine, green tea, and other fruits and vegetables as plant pharmaceuticals that we absorb and utilize instantly, their bioavailability in humans is controversial. Emerging evidence suggests we derive many of the benefits through interaction between phenolic compounds and our gut bacteria, which consume the glycan bonds holding the polyphenols together and render them available for absorption. The glycans are prebiotics for the bacteria, and the liberated phenols are more bioavailable to us. Even red wine polyphenols may have prebiotic effects on the gut flora (though keep in mind that some of us have different reactions to it).

Dark chocolate

Dark chocolate falls under the “Polyphenols” and “Fermentable fiber” categories, so this section was probably unnecessary. But c’mon: it’s dark chocolate, a combination of gut-supportive polyphenols and prebiotic fiber so delicious that we should welcome any and all justifications for its consumption, however redundant they may be.


Pistachios are another special package of fiber and polyphenols with potent prebiotic power. Other nuts like almonds aren’t too shabby, but pistachios beat them soundly in a head-to-head matchup, producing a biome richer in butyrate-secreting bacteria. And since they usually come in shells, overconsumption is hard if you’re worried about self-control.

Resistant starch

Resistant starch, or RS, is a unique kind of starch that humans by and large cannot digest. It’s not a fermentable fiber, but it acts like it. Upon its consumption, RS travels mostly unperturbed through the digestive tract into the colon where the colonic bacteria – who can digest the stuff – feast on it, get frisky, and reproduce. Multiple studies indicate that RS consumption generally leads to an increase in beneficial colonic bacteria and a reduction in pathogenic colonic bacteria, including a boost to bifidobacteria and a decrease in firmicutes.

Animal “fiber”

Carnivorous animals like cheetahs treat otherwise indigestible animal parts like prebiotics, displaying evidence of healthier gut bacteria when eating whole rabbits than when eating beef muscle meat. As animals with a long (pre)history of consuming other animals, it’s a good bet that humans retain this ability as well. The gristly bits at the end of a drumstick, the snapping tendons that floss your teeth as you eat a turkey leg, the crunchy cartilage you have to scrape off the oxtails with your front teeth, the skin on a pork belly – these are examples of animal tissue with the potential to affect our gut bacteria.

Vitamin D status

Vitamin D helps regulate the immune system, as we know. Low vitamin D status (or low exposure to UV radiation) is consistently linked to increased autoimmune disease, allergies, infections, and other immune conditions. Meanwhile, our gut bacteria comprise a huge chunk of our immune system, modulating the allergenicity of food fragments, crowding out pathogens, and regulating the development and maintenance of our immune cells. Could one affect the other? Absolutely. A recent paper in rodents shows that vitamin D status regulates the microbiome, with a deficiency causing dysbiosis and inducing colitis.


In last week’s Dear Mark, I discussed a new study showing that professional rugby players participating in an intense training camp had a more diverse (and healthier) gut microbiome than age and BMI-matched controls, despite experiencing a ton of acute stress (all the exercise). While the rugby players also ate more gut-modulating foods like fruits, vegetables, and protein and snacked less than the control groups, and this may have improved their gut diversity, this study is the first to shows that lots of exercise is compatible with and even supportive of healthy gut flora. The flipside is that lots of exercise without adequate support (recovery, rest, good food, sleep) will probably be enough of a stressor to negatively impact gut flora. Don’t overtrain and don’t undertrain.

Food variety

Much of the gut bacteria we get comes riding on the food we eat or our gut bacteria learn how to break down certain foods from the bacteria riding on the food. One example of this is that in most Japanese people, some of their gut bacteria have picked up the genes for seaweed digestion from the bacteria found on seaweed. The seaweed bacteria “taught” the resident gut flora how to handle the food. This gene transfer doesn’t happen with a single seaweed meal. They need sustained exposure to the seaweed and its bacteria. A recent study in fish even supports this idea: fish eating the most diverse diet had the least diverse gut microbiome.

So variety is good, just not too much. You want enough variety that you expose yourself (and your flora) to colorful fruits and veggies, fermentable fibers, and healthy fats, but not so much that you never eat the same thing twice. Eating some staple foods on a regular basis will allow you to develop the gut flora equipped to break them down. Be consistent.


Of course antibiotics affect the gut flora. Their stated purpose is to (negatively) affect microbial life. Use them if it’s medically necessary, but be advised that most antibiotics are indiscriminate killers WW2-era carpet bombing entire cities of bacteria. They get the pathogens (unless they’re resistant, of course) and the good guys, reducing microbial diversity and shifting the balance of the microbiome to favor unwanted strains. These changes may be lasting without serious and sustained prebiotic and probiotic interventions. Unfortunately, with even doctors prescribing them to patients with conditions for which antibiotics don’t help, medical necessity is difficult for the layperson to parse.


Like with fermented foods, we should think of probiotic supplements as friends. Not those friends you always tell “we should totally hang out more!” when you run into them but never do. Real friends. The ones you have over for dinner every week. The ones you include in group texts that go for months without breaking. That’s how you should treat probiotics – like real friends whose company you genuinely enjoy and who come in capsules and require refrigeration.

Take probiotics with food or 30 minutes before meals, as our bodies are “meant” to consume probiotics with food (i.e. fermented food); they seem to survive the transit through our gut when taken this way (as opposed to after a meal).


“Skeptic” science writers and corporatist apologists are quick to point out that glyphosate, the active herbicide used in Roundup, is non-toxic to humans. Roundup kills weeds by disrupting the shikimate pathway (PDF), a pathway involved in the biosynthesis of several crucial amino acids. Human cells are relatively unaffected by the herbicide because our cells don’t use the shikimate pathway. There’s nothing to disrupt. All good?

Unfortunately, no. Bacteria also employ the shikimate pathway, and we’ve got an awful lot of them living inside our bodies and handling some very important tasks, including immune function, digestion, production of neurotransmitters, mood regulation, and many more. This means our gut bacteria may be susceptible to Roundup residue on the foods we eat (and the air we breathe, the water we drink, and so on). This isn’t a big issue for people eating Primal because the biggest offenders are genetically modified soybeans and corn (and all the related food products) – two foods you likely aren’t eating. That said, your exposure may be elevated if the food you eat eats a lot of Roundup-laden soy and corn (PDF), like CAFO livestock, dairy, and battery-farmed poultry. All the more reason to favor pastured animal products.


Or rather, cessation of smoking. Smokers who give up smoking experience weight gain and more microbial diversity. The media reports focused mostly on the weight gain, but I think the shift in gut bacteria – toward the mostly beneficial Actinobacteria away from the Proteobacteria (home to “a lot of your bad guys”) – is the most significant news.


It takes time to build your gut flora. Initial changes happen rapidly, but sustaining them requires giving your bugs time to adapt and dig in. If you try resistant starch, don’t give up after a day. Give it a few weeks. If you try probiotics or sauerkraut, take them consistently for an extended period of time before throwing in the towel and assuming they don’t work. If you’re expecting your monthly gym foray to positively affect your gut, think again.


I almost forgot. Get dirty. Don’t be a clean freak if you can help it. I’m not saying you shouldn’t wash your hands after wiping, handling raw chicken, or dumpster diving, but be a bit more relaxed when it comes to getting your hands dirty. Garden, and don’t freak out if you misplace your gloves. Eat a fresh carrot pulled straight from the ground. Enjoy a soil smoothie twice a week. Pet a dog. Expose yourself to the outside world, soil and grime and dust and dirt and all, on a regular basis. I’m kidding about one of those (never garden without gloves!). Bacteria are everywhere – you really can’t avoid it – and most of it isn’t out to kill you.

Don’t be overwhelmed by this information. Don’t feel like anything and everything you do could have a drastic effect on your gut bacteria. For all the warnings and studies and focus, our gut flora are resilient buggers that have evolved – and are still evolving – to respond and react to the environment. If something affects them negatively, they can bounce back. And even in the case of major changes wrought by antibiotics or months of stress or medical procedures, you can help them bounce back.

Information like this should empower you. When I learn how the fate of my gut flora (or muscle mass, or bone density, or eyesight) ultimately rests in my hands, I’m excited and eager to assume the mantle of responsibility. That’s total freedom and it’s the most important thing in this life. It’s all we’ve got.

Thanks for reading, everyone. How do you feel about this information? Empowered, overwhelmed? A bit of both?

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About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending more than three decades educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates flavorful and delicious kitchen staples crafted with premium ingredients like avocado oil. With over 70 condiments, sauces, oils, and dressings in their lineup, Primal Kitchen makes it easy to prep mouthwatering meals that fit into your lifestyle.

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