Marks Daily Apple
Serving up health and fitness insights (daily, of course) with a side of irreverence.
25 Jun

16 Things That Affect Your Gut Bacteria

PistachiosA 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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You want comments? We got comments:

Imagine you’re George Clooney. Take a moment to admire your grooming and wit. Okay, now imagine someone walks up to you and asks, “What’s your name?” You say, “I’m George Clooney.” Or maybe you say, “I’m the Clooninator!” You don’t say “I’m George of George Clooney Sells Movies Blog” and you certainly don’t say, “I’m Clooney Weight Loss Plan”. So while spam is technically meat, it ain’t anywhere near Primal. Please nickname yourself something your friends would call you.

  1. I am so very confused about the (never garden without gloves!) comment. What is wrong with that? My assumption is he meant because of cross contamination between plants and their bacteria and not because its unsafe for humans. I assumed this because he said to eat a carrot with dirt on it or a dirt smoothie but made no mention of just kidding about those things. That being said, my confusion comes from being able to eat a dirty carrot but not being able to pull that carrot up with bare hands. Someone please clarify! Thanks!

    Mel wrote on June 25th, 2014
    • I’m not sure as well regarding gloves but I do have a lot of Black Widows in my back yard.

      victor wrote on June 26th, 2014
    • He think he was actually kidding about never gardening without gloves. I’m pretty sure it was the dirt smoothie that you really shouldn’t do and he might have thought that that was clearer than it was. You can definitely garden without gloves, I do it all the time!

      Caitlin wrote on June 30th, 2014
  2. Dear Mark, I won’t be the 1st to comment that you have a talent for reading our minds!

    My 1st comment/question has to do with fermented cabbage and the like to those with thyroid issues. As someone who’s thyroid markers suddenly went off line (hypothyroid), I scoured the internet (and MDA) for answers and finally arrived at Chris Kresser web site. In a 3 part series with Chris Masterjohn, they discuss the effect of goitgenic foods in general and fermented cabbage in particular on the thyroid gland.

    “Chris Masterjohn: Now, a lot of people think that cooking or fermenting cruciferous vegetables is going to get rid of the goitrogens, but that is not true. Fermenting actually activates them. It actually does the conversion to the thiocyanate right in the jar of sauerkraut. So, if you’re eating sauerkraut and kimchi, you are not getting rid of the goitrogens.”

    As of last week I sadly cut back on my fermented cabbage consumption and started to supplement with 380 mcg of iodine (kelp) and selenium (2 Brazilian nuts) to counter balance, to be followed with blood test in 6 weeks. In fairness, I also upped my carb again (sweet potatoes mostly). Due to elusive food energies (point of suffocation) and food restrictions, I thought that I mind as well switch to a Ketogenic diet. I now think that my symptoms are a failure of that attempt.

    I would love to get you take on an issue that plague many. And if not asking much what’s your opinion on “iodoral”? Readers out there – please report if you used it.

    My other comment/experience has to do with dirt and gut bacteria. After acclimating my feet with self-made 4m”m leather Huaraches (10K walks etc. over 3 months) – I spontaneously took them while walking in the park and managed to run barefoot (4K-2.48Mile) over grass (uphill sprints) and mostly hard sidewalk and asphalt without the slightest pain or a blister to show for. By the time I reached home (would have gone longer but there it was), I felt euphoric like never before (I’ve been running for nearly 40 years…. now if my abs were nearly as defined as yours… I’m tall and skinny and at 57 I am fit & toned then most of my peers). The part of my soles that touched the ground on the other hand was black as tar. Does this in any way have a positive effect on our gut bacteria; or does washing it away kill it, like in the NY time’s story (

    Thanks in advance and may I recommend that you try fresh pistachios? They are my 2nd best after macadamia nuts and so much tastier the dry ones, and, unlike macadamias they trick you to believe that you can eat more of them due to lower fat content. And addictive they are! Just get ready to end up with green fingers due to the dye they contain (harmless). Should be easy to get in California; no?

    P.S. You are welcome to address my thyroid question via your weekly “Dear Mark”. Also, my legs are still pain free two days later.

    Time Travler wrote on June 26th, 2014
  3. My prayers were heard; Thanks Mark! (-:

    Time traveler wrote on June 26th, 2014
    • And by that I mean that my reply was finally posted; I will wait silently for feedback from Mark.

      Time traveler wrote on June 26th, 2014
  4. I’ve never heard of a soil smoothie. Can someone write down how to make one?


    Frank wrote on June 26th, 2014
  5. Good info. I’ve been a tree trimmer most of my working life. Not a lot of places to wash up out in the field. My hard boiled eggs would look like dirt in my hands when I would eat them. Never bought into the over cleaning anti bacterial stuff.

    dave wrote on June 26th, 2014
  6. Important mention for FODMAP sensitive readers.
    Pistachios are High FODMAP & can trigger IBS like symptoms.
    Low FODMAP nuts are walnut, pecan, macadamia, pine.

    LISA wrote on June 27th, 2014
  7. Question. Can OTC probiotics cause problems? I have started suffering from esophageal spasms which have landed me in the ER thinking I was having a heart attack. I love taking probiotics because it boosts my immune system, but the pain I have started getting from spasms is not worth it. Doc said spasms are a result of Gerd. I don’t get heartburn though, just spasms and a pain like someone put a dagger in the middle of my gut and is twisting it. I am a Celiac, but keep a constant gf diet. Can you “over do” probiotics? I take Ultimate Flora 30 Billion.

    Carol wrote on June 27th, 2014
  8. I get dirty every day in the garden, but I stopped having dirt smoothies b/c I found out that soil has giardias in it sometimes. I don’t know how common this is, but giardias are not just in lakes and streams.

    Also, sometimes I have to spray poison ivy or other weeds that are impossible to get rid of any other way, and I use Roundup, as the least toxic herbicide available for perennial weeds anyway. (Annual weeds can simply be dug up or sprayed with vinegar.) I wear a mask and gloves and an impermeable suit. I think that’s pretty safe. Then I take a shower.

    shannon wrote on June 27th, 2014
  9. Thanks Mark, I’ve had a feeling for a while now that probiotics are the answer to just about everything. They say they can even help Autism.. :)

    Rhonda wrote on June 27th, 2014
  10. Interesting. I feel like I never eat the same thing twice (prepared in the same way) consistenly. Whatever I make for dinner and other meals is always different. I don’t have a meal rotation like other people do. Very interesting

    Meagan wrote on June 27th, 2014
  11. If you believe Roundup can affect gut bacteria, you need to cite studies to support it. Wouldn’t that be part of the very low LD50?

    James Cooper wrote on June 28th, 2014
    • He did cite studies. Click on the links in the paragraph.

      Sheri wrote on June 29th, 2014
  12. I wonder if alcohol should be on this list.

    Does alcohol negatively affect your gut bacteria?

    Or, are beer and wine considered fermented foods and thus, good for your gut?

    Sheri wrote on June 29th, 2014
  13. I was told not to eat pistachios as most have mould. I eat macadamias, almonds and walnuts mostly and the odd brazil nut but dislike hazelnuts (unless in dark chocolate). Should I stop throwing away the activated pistachios?

    Cathie wrote on June 30th, 2014
  14. Nice post, though very long. I had to take 2 breaks to complete it fully. Being indian fermented foods are part of our everyday diet. There are many cases wherein, old grannies will suggest home remedies based diets for many illness.

    Rups wrote on June 30th, 2014
  15. Dirt smoothies, love it! Have you checked out the book An Epidemic of Absence? It’s a great look into how our obsession with getting rid of germs and sterilizing everything my be adversely effecting our health.

    Caitlin wrote on June 30th, 2014
  16. umm, I’m not sure if he was kidding about eating the dirt covered carrot or not. I’m a bacteria lover but think I might be afraid that the animals had crapped in my garden a few too many times to risk e coli contamination.

    Bob Werner wrote on July 10th, 2014
  17. I really enjoyed reading this thread…..I have just finished an antibiotic protocol for H.Pylori. I’ve decided to take a probiotic…will this also help kill the H.Pylori bacteria? Thanks!

    Lynlee wrote on August 2nd, 2014
  18. The number one deterrent to having healthy gut bacteria is consuming meat and maybe even any animal protein…

    Richard wrote on December 14th, 2015

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