5 Non-Dietary Factors That Influence Your Microbiome

Inline_5_Non-Dietary_Factors_MicrobiomeThe microorganisms that reside in, on, and around our bodies influence almost every facet of our well-being. Part of maintaining microbiome health is maintaining homeostasis. Another is supporting diversity.

Our goal, then, is to improve our microbiological real estate in the many areas of the body that commensal and symbiotic bacterial like to put down roots—the gut, mouth, lungs, skin, reproductive organs, and so on. The average Primal enthusiast is well-versed with the role of food choices and smart supplementation (although research is always uncovering new wrinkles—more on this to come). 

I thought I’d give a little attention to some of the other basic practices that can influence microbial diversity and homeostasis. There are more answers and nuances than I can cover today, but let’s start with some of the fundamentals.


Over the past decade, there’s been the odd study examining the link between exercise frequency, duration, and type and the microbial response to such in the body.

Studies in mice have shown considerable responses to exercise in the lab. A 2016 study placed mice on an “obesity-causing” diet and 6 weeks of high-intensity interval training (HIIT). The mice placed on the HIIT program had markedly increased microbial diversity within the distal gut, along with an increased Bacteroidetes/Firmicutes ratio. Perhaps even more importantly, the microbiome of the HIIT mice appeared to resist the typical adverse changes to the gut microbiota that occur with onset of obesity. In short, exercise stopped the poorer diet from degrading their gut microbiome.

An older 2013 paper showed that mice with free access to exercise experienced a significant increase in the number of Lactobacillus, Bifidobacterium and B. coccoides-E. rectale. Other studies have demonstrated the microbiological effects of exercise on diabetic mice and mice subjected to PCBs. But that’s just in mice.

As far as the human microbiome goes, there’s a lot more research needed regarding exercise. Much of what we have to go on ties back to experiments on the Irish international rugby team, 40 of whom were investigated in the days leading up to the last Rugby World Cup. Somehow, researchers managed to get their hands on 46 other healthy men of similar brutish size, analyzing both groups regarding their dietary and exercise habits.

They found that the rugby players all had significantly more diverse microbiomes than men in the comparison group, with notably higher proportions of Akkermansiaceae—a bacterial family commonly linked to lower rates of obesity and metabolic disorders. Interestingly, despite the rugby players having significantly higher levels of creatine kinase, an enzyme associated with muscle damage, they all had lower levels of inflammatory markers than the control group, along with a much better metabolic profile. Correlation or causation? It’s hard to tell.

The waters are muddied further when we examine the role of diet in hardcore athletes. The Irish rugby team unsurprisingly ate considerably more protein (22% versus 15-16% in the control group) but also ate a lot more fruit and vegetables and had fewer snacks than their non-athletic peers. A follow-up study last year reinforced these findings, but there’s a lot more to be revealed.

Was it the increased exercise (or type of exercise) that brought about the improved microbial diversity, or their improved diet? My thoughts are that it was both, but watch this space for more scientific discussion of the diet-exercise-microbiome paradigm.

Managing Your Stress (or Not) 

Of course you knew that stress would play a part in the health of your microbiome, but it certainly helps to have some research to back up the assumption. Currently, there’s an abundance of animal lab testing and a notable shortage of human studies. (Probably mostly on account of people not being keen to have their feet zapped or injected with carcinogenic compounds.)

An impressive study from January last year, however, took things one step further and examined the stress-induced changes to the microbiome of North American red squirrels in the wild. Using faecal glucocorticoid metabolites, an accurate marker of stress, researchers were able to confirm that increased stress in wild squirrels significantly lowered microbiological diversity.

This negative response, they postulated, was caused by a stress-induced activation of the immune system, increasing cytokine circulation, which in turn has a strong antimicrobial effect. The result, unfortunately, is an increase in host vulnerability to pathogenic invasion. Good one, stress.

Back in the lab, stress-induced microbial alterations continue to be the center of study. A 2011 study exposed mice to a social stressor called social disruption, designed to prime the innate immune system and increase circulating cytokines—much the same as the high-strung wild squirrels. The findings were textbook: “stressor exposure significantly changed the community structure of the microbiota, particularly when the microbiota were assessed immediately after stressor exposure.”

As far as species composition goes, the stressed mice showed a decreased abundance of bacteria in the genus Bacteroides and an increase in Clostridium. In simple terms, commensal-type bacteria were suppressed by stress and pathogenic-type bacteria were promoted.

Another mice vs. stress study elicited much the same results, with restraint stress causing a decline in microbial species richness and an overgrowth of anaerobic bacteria. Researchers then tested whether this decline in microbial diversity had set the stressed mice up for increased risk of pathogen colonization by orally introducing the murine pathogen Citrobacter rodentium. Funnily enough, those mice subjected to stress were far more likely to come down with a bad case of the C. rodentium than their more chilled out peers.

Using Medications

Regardless of their often necessary role in your life, many medications can exert a considerable influence over the health and diversity of your microbiome.

In a 2016 study, the influence of several NSAIDs over the gut microbiome was determined during the course of 30 days in 155 adults. Interestingly, it was the type of medication, rather than the amount of medication, that influenced the gut microbiome the most. Aspirin users have markedly different numbers of Prevotella, Bacteroides, Ruminococcaceae, and Barnesiella species, while both celecoxib and ibuprofen users had larger numbers of Acidaminococcaceae and Enterobacteriaceae. The list goes on. Suffice it to say that the bacterial diversity in the gut microbiome strongly reflected the combinations of medications that people ingested.

A year earlier, researchers were examining the same relationship between proton pump inhibitors (PPIs) and the human microbiome. PPIs reduce the production of acid in the stomach in a bid to prevent formation of ulcers, and are among the top 10 most popular drugs in the world. Incidentally, they’ve also been associated with an increased risk of intestinal infection.

Using a cohort of 1815 individuals (211 of which were PPI users), researchers were able to demonstrate a significant decrease in microbial diversity in PPI users, along with changes in 20% of the bacterial taxa. Curiously, there was an increase in bacteria associated with the oral microbiome, and a big step up in potentially problematic bacteria like Enterococcus, Streptococcus, Staphylococcus and E. coli. Based on their findings, the study proponents didn’t have too much trouble explaining why PPI users were more prone to enteric infection.

The implications of these studies, and many more like them, reach far beyond mere infections and bacterial dysbiosis. When we consider that microbiomes like the gut play a critical role in the metabolism of most medications, the very way in which these drugs alter microbial compositions and lower diversity may reduce their efficacy or even render themselves toxic. It’s fair to say that plenty more work is needed on the interactions between medications and the microbiome.

Having Sex

I’ve actually already written about the considerable transfer of germs that takes place in just one bout of kissing, but science has since taken it one step further and suggested that our individual microbiomes may play an important role in that ever-elusive “chemistry” that draws people together.

How’s that? Well in this case, opposites very much attract. Studies show that we’re instinctually attracted to sexual partners whose microbiome is complementary to our own. And knowing what we know about the importance of microbial diversity, complementary means different. Thus, when two people with very different microbiomes engage in intimate relations, they diversify their respective microbiome.

This ties in to the concept that odor (a.k.a. pheromones) plays a role in sexual attraction, as our microbiome very much influences our smell. Neat, huh?

Getting down to business, there’s some serious microbiological changes taking place every time we have sex. A 2015 study published in Research in Microbiology found that there was a significant decrease in the abundance of Lactobacillus crispatus after sex, along with a certain bacterial homogeneity between seminal and vaginal samples.

The microbial picture isn’t just more is better. Another study of 52 women found that those who partook in unprotected sex had a temporary increase in bacterial species associated with bacterial vaginosis. Over time, it appeared that their vaginal microbiome retained a remarkably similar composition, but those temporary post-sex increases in G. vaginalis and L. iners have led some to believe that unprotected sex is “bad” for the health of the vaginal microbiome.

But the issue may be more novelty related. Each new partner means a new microbial influence—for both men and women. That likely involves a period of microbial imbalance. Aside from serious infection (e.g. STDs), adaptations to a partner’s profile over time, one would imagine, would confer the benefits of microbial diversity and allow a shift back toward relative homeostasis in most cases. It’s a complicated but fascinating topic—maybe worthy of its own post sometime.

Living with Animals

Moving on to lighter matters, there’s plenty of research that points towards pets as a positive influence on our microbiome…particularly the furry kinds. A study published late last year investigated the effects of early-life exposure to household pets on 746 infants from 2009 to 2012. Along with participating mothers being asked to fill out questionnaires regarding their pet situation during and after pregnancy, infant gut microbiota was sampled at around 3 months of age.

Those infants that had been exposed to at least one furry pet (more than half the group) were found to be more than twice as likely to have a high abundance of Oscillospira and/or Ruminococcus bacterial species—regardless of whether they had received prenatal or postnatal exposure to fur-bearing pets. These species, incidentally, have been associated with a lower risk of childhood atopy and obesity. What’s more, pet-exposed vaginally-birthed infants with maternal intrapartum antibiotic prophylaxis exposure (say that ten times) had considerably lower abundances of Streptococcaceae than infants who hadn’t been exposed to furry pets.

These findings, and plenty more besides, tie in nicely with what we know about Strachan’s hygiene hypothesis, which implies that children growing up in overly hygienic environments are more likely to develop allergic disease. Interestingly, there appears to be a curious tendency for older siblings to dampen that microbial abundance effect. Equally of note, breastfeeding may work synergistically with that positive pet-effect.

For those of us not exposed to pets during our developmental years, I strongly suspect that there’s still hope for your microbiome. Exposing ourselves on a daily basis to potential sources of microorganisms, furry pets included, should help to encourage microbial diversity and help your body stay truly Primal.

That’s it for me, folks. The research keeps coming, so look for more on this topic soon. In the meantime, share your questions and thoughts on the topic below. Thanks for stopping by.


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 three decades researching and 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 Primal/paleo, keto, and Whole30-friendly kitchen staples.

If you'd like to add an avatar to all of your comments click here!

30 thoughts on “5 Non-Dietary Factors That Influence Your Microbiome”

Leave a Reply

Your email address will not be published. Required fields are marked *

    1. The best way to assess this is to take a tour at your local hospital through the lung cancer/emphysema ward – this will answer all your questions – the role of smoking is to speed up your chances of being one of those poor souls being carted out in a body bag.

  1. Well, looks like it’s time to start playing rugby again. Good way to follow rule number six, but makes rule number eight harder to follow.

  2. Excellent article Mark. This are really interesting and unique factors which many of us haven’t considered before. I subscribed. Thank you

  3. Our tribe loves the live probiotic product AO+ Mist by Mother Dirt (no affiliation). Since using, our family hasn’t had the need for deodorant… considering that we live in Houston and we do crossfit (multiple workouts a day), I’d say that there’s something pretty interesting here.

    “Formulated with a patented, live “peacekeeper” bacteria to restore essential bacteria that’s been removed by modern hygiene and lifestyles.” — MOTHERDIRT

  4. I know that painkillers are bad for me so I try to limit them but I would really like to know the elusive question of weather painkillers are worst for my health or pain is worst for my health. The amount of pain I have to deal with is really stressing me out and I imagine it’s somehow not good for my gut diversity and causing my leaky gut to worsen. Maybe I just want someone to give me permission to gobble all the painkiller I need, but the problem is that I remember being sicker than I am now and I highly suspect that’s because my leaky gut has heal some. I don’t want to wreck it now so I’m scared to take too much painkiller.

    1. Painkillers of any kind, including OTC, can have a nasty rebound effect if you suddenly cut back or stop taking them. It can make you think you’re in much worse shape than you really are. Taking them on a regular basis can lead to a need for increasingly stronger, more frequent doses. Also, they tend to suppress your body’s own natural pain-relieving mechanisms.

      Try tapering off whatever you are taking, then, if you can, try to go without them as much as possible while still remaining reasonably comfortable. (You’re right; being in pain isn’t good either.) Try other things instead, such as a heating pad, ice pack, topical pain relievers, herbal muscle relaxers, etc. There are various tinctures and teas that might help, such as white willow bark tea and ginger tea. As you undoubtedly already know, all painkillers are bad for the liver and kidneys. Ibuprofen has also been linked to hearing loss. There’s a very dark side to all that stuff, regardless of what you’re taking.

      1. I don’t take painkillers every day, I only take some when I have my period or a bad headache or migraine. I tried every natural product I ever heard of but they don’t work, I’m not really surprised though because Tylenol barely work at all. I even tried one that made my pain go three times worse than normal, haha! I’ve never heard of willow bark though, is it better for the digestive system than Aspirin? I’m wary of it.

    2. I’ve suffered from painful injuries and operations that eventually get much better, to suffer from ongoing daily chronic pain had got to be exhausting. Of course there are pain management clinics that specialize in that area and there are some holistic pain management folks out there. Trying to find the right balance of traditional and holistic approaches and eating a low inflammation diet is challenging for sure. Curcumin, boswellia, fish oil, chondroitin and glucosamine, MSM and wobenzym are some nutritional supplements you may want to research Coccinelle. Also consider l-glutamine, aloe vera and ACV for your leaky gut. If you suspect h-pylori is causing you gut problems a two month cycle of taking mastic gum will often keep h-pylori at bay. All the best to you. – George

      1. Thanks! You made many suggestions I had never heard of. I’m especially tented by the MSM. Boswellia is out because I have GERD and won’t take any chance of getting a flare of those symptoms at all.

        I didn’t know about wobenzym but I already take papain and bromelain. It seems to help me feel better on days that I’m already feeling low level of pain but hey, I will take anything!

        I’m also considering taking a fish oil for the vitamin A, but I’m bummed that they don’t say how much omega 3 they got.

        Anyway, thanks a lot!

    3. So sorry to hear of your chronic pain, Coccinelle. I understand from personal experience how frustrating and stressful it can be dealing with pain day in and day out.

      I agree with the what Shary said here about gradually tapering the pain meds and working to replace them with more natural remedies. HealthyHombre listed some excellent ideas here too.

      In addition, I would add a turmeric curcumin supplement, magnesium supplement (both internal and topical). Taking hot baths in epsom salts can help with achy muscles. And essential oils like peppermint, lavender, ginger and frankincense can also help.

      I hope this helps and you start seeing some improvements and getting some relief.

      1. Like I said, I don’t take pain meds daily and so far, nothing natural I’ve tried ever worked. I’m not saying I have stopped trying though! I would love to found something that works!

        I already take magnesium daily but maybe I should dig out my magnesium oil that I completely stop taking for some reason. I also tried many essential oils and I found out that it doesn’t really do anything for me unfortunately.


  5. Water sourcing is huge. All my life I more or less drank some sort of filtered water, though I wasn’t aware of this. In summer of 2016, I started an internship away from home, and ended up drinking tap water on a regular basis. I figured tap water is potable so should be good to drink. This continued for the rest of the year when I started the school year living in a new apartment, intaking water through my refrigerator’s ice machine. Little did I know the refrigerator lacked a water filter, meaning I was ingesting straight Houston tap water. Yikes!

    Over this period my health slowly declined. My sleep got worse. My muscle mass decreased. I couldn’t focus and found myself more and more anxious. At times my belly would be terribly bloated despite being an overall skinny guy. My cold tolerance was absolutely in the tank – even 50 degrees with sunlight seemed frigid.

    Then one day while home on winter break I was maintaining my fish tank and made a connection. I use RO/DI water (with some minerals replenished) for my fish tank, because many of the substances in tap water (especially but not just limited to chlorine) are harmful to every living component of the tank, whether it be microbes, plants, invertebrates or fish. I realized I was giving my aquatic plants better water than I was giving myself! From then on I resolved to be much more picky about the sources of water I was consuming, and most of these symptoms spontaneously improved.

  6. Microbiome aside, do mice suffer from inflammation (the way chronic workouts effect humans), given their propensity to exercise for hours on end?

  7. Circumcision, the most common form of sexual assault, reduces not only his pleasure and sensitivity but his bacterial contribution (either for the good or bad.) 7/8 of the men on earth are in tact, the 1/8 that aren’t are constantly at war.

    1. Thank you for addressing this topic. Routine circumcision is brutal, and this early trauma for boys and men has psycho social consequences that perpetuate the cycle of anxiety, fear, aggression, and post traumatic stress syndrome most commonly manifested through machismo, violence and war. Our two sons (now adults) were not brutalized in this way and we need to protect all males from this culturally sanctioned assault.

  8. Grew up on a farm, kissed a lot animals, shoveled tons of manure, ate a lot of dirt and no doubt bacteria. Still kicking.

  9. “Additionally, there are thousands of informed Primal readers using the Mark’s Daily Apple forum at any given moment. Please, ask your question on the forum. Mark’s Daily Apple readers are smart; they will not do you wrong.”

    Dear Mark, if you are serious about the forum please give a number of legit members moderator qualities to get rid of the trolls, spammers & advertisers that are undermining the forum. It used to be such a great place and in some ways it still can be, provided those can be handled in a proper manner. If not sure if the new mod is a good one, have the admins create some sort of vault to put in the unapproved members that no longer deserve posting privileges because of acting against MDA rules, so they can see whether it was useful or not. There are and have been plenty of members that offered their time to do this, yet never even received an answer.

    Flagging is no use as no one acts upon this… it would be understandable if it took some time, but in the mean time these people are ruining the forum for those that do care about it.

    Hopeful that this message will be read and those members that left because of this will return once everything runs smoothly again, I ask you for your help in this.

    1. I agree. The forums here USED to be full of informed primal readers. Now it seems to be primarily dominated by a few people who argue endless and contribute almost nothing of value. It is a shame. Please fix the forums!

    2. I was unable to sign in/register, left my info as requested about a year ago on a thread here, and never heard from anyone. I’m sad.

    3. The forum is absolutely worthless since the format was changed a while back. A crying shame and a real comedown from what it used to be. Increased spam is only one reason.

    4. Alexandra, I understand people’s frustration with the forum. We’ve been going through several phases of fixes, all of which have brought up additional issues, including moderation difficulties. This week we’re preparing for a permanent move of the forum (users won’t notice a difference) that will essentially allow us to reboot some of the basic structures and even add features and sections I’ve long wanted to include. You should notice changes in the next two weeks, and I’ll be making formal announcements soon after that. Believe me, I haven’t given up on the forum.

      1. Thank you Mark, this is welcome news indeed. Please don’t take away older threads, which often contain much invaluable knowledge. I am thinking in particular of the 3-part series, “Intermittent Fasting—A Primer”, by member pklopp.

        I can hardly express my profound thanks for all that Mark’s Daily Apple and The Primal Blueprint have done for me. It is not too much to say they have literally saved my life. Thank you Mark!

  10. Would love to see a post on microbial transfer due to sexual behavior. It seems plausible that such behavior is not so much for the benefit of human DNA as it is for microbial reproductive fitness — both “good” and “bad” microbes — and therefore at least partially driven by the microbes themselves.

  11. The section about how sex affects the microbiome was fascinating…I’d love a more in-depth article on that sometime.