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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 “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.
Polyphenols
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
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.Exercise
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.
Antibiotics
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.Probiotics
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).
Roundup
“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.
Smoking
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.Time
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.Dirt
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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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.Read more: http://www.marksdailyapple.com/16-things-that-affect-your-gut-bacteria/#ixzz3inWsNtYZ
Other times when I was less zonked I’ve eaten small amounts of soil, like a spoonful, to get some bacteria.
I didn’t notice any ill effects from any of this dirt consumption other than a taste that was not terrible but not good and a texture that was a little unpleasant.
Why not give it a try, sample a tiny amount, it probably won’t hurt.
50g coconut oil
10g dark chocolate
both melted over (not in) hot water
then add to
100g yogurt
25g chia seeds
1/4 teaspoon cinnamon
Stir and eat. Yummo!
Better than dirt or compost.
HALF OF THEM ARE ROTTEN.
I wonder if those rugby players had better gut bacteria because they face-plant into the grass regularly, while the controls merely on their fire-retardant-infused couches all day.
Green bananas, powdered potato starch (personally I think the bananas are probably the better option).
http://www.marksdailyapple.com/resistant-starch-your-questions-answered/
I’m disappointed that there was no mention of sucralose of other artificial sweeteners, however. Don’t they destroy friendly bacteria as well? So many paleo eaters rely on splenda for their occasional or not-so-occasional cheats. I used to pound sugar-free monster, thinking it was a safe indulgence. Then I learned the sucralose was harming my gut biome. Can anyone give me more info about this?
http://www.sott.net/article/280386-Is-there-evidence-that-xylitol-sorbitol-and-other-sugar-alcohols-are-safe-replacements-for-sugar-It-looks-like-it
Regarding your story, it doesn’t sound to me like sorbitol wiped out your gut biome–if it’s a prebiotic then it should be food for the friendly bacteria. Sounds like it was other things that upset your system, or perhaps the sorbitol caused you a kind of distress, but didn’t actually harm your gut bacteria.
However, here’s a list of a few other potential stressors / culprits that probably played a part, and it’s probably not a complete list:
– I didn’t chew my food as thoroughly back then (I also ate nuts all the time and swallowing them in big jagged pieces probably made them scrape against my intestinal lining)
– I was consuming lots of artificial sweeteners, including plenty of aspartame, via gum, energy drinks (many of which were probably too acidic and full of BPA), and various other products.
– I was consuming a lot of sugar.
– I ate grains regularly (which I seem to be able to digest well enough these days when I eat them, which is rare except beer, and since that’s liquid it probably goes through easier). My breakfast (or snack) was often a bowl of sugary cereal with milk. Normally I can handle sane amounts of dairy but with the problems I already had and with the grains, sugar, and whatever other crud in the cereal mixed in it probably did some damage back then. I also ate a lot of bagels (often grilled cheese, and with a big glass of milk or Nestle chocolate milk) and Kraft Dinner.
– I was also mixing other foods indiscriminately. I’ve found that one of the most effective things to do for better digestion is to only eat certain food combinations or one food or type of food at a time. If you have gut issues, I recommend trying this if you haven’t already. In general, fruit is best alone, but ok with vegetables, and not too bad with nuts. Never mix it with dairy. (That means saying no to all those fruity yogurt cups). Vegetables pair decent with meat and just about anything that isn’t dairy. Nuts are best by themselves or with other plant foods, favouring vegetables a little over fruit, though they also seem to go alright with a bit of dairy and sometimes I mix nut butter with a natural sweetener without any apparent problems. I think legumes (maybe not peanuts) would be best with vegetables if you mix them with anything.
The simplest advice is get most of your calories from animals and most of your food volume from vegetables, and spend lots of time outside.
What I would like to know is why, whenever my digestive system gets “off,” what always puts it right is eating beef or pork! There must be some beneficial effect of red meat on my gut microbes.
How’s the dirt in Washington? I live in TN and my county is notorious statewide for some of the worst dirt in the state….lots of clay and you’re doing good if you dig 2 inches before you hit a rock the size of your head. If anyone can guess which county in TN, you’ve earned a pat on the back!
For GA, it’s not rocks below the “topsoil” (which is just slightly looser red clay) — it’s hardpan. ROCK-hard clay! When I garden, I have to use a pickaxe!
That said, if I’m just pulling out a weed here or there, or harvesting some greens, I don’t worry about occasionally getting dirty!
http://www.mudglove.com/
loved the 16 things on gut bacteria; it’s everything i’m already doing. thank you!
http://www.marksdailyapple.com/eating-earth-exploring-the-mysterious-world-of-geophagy/#axzz35i0SZaDM
They were only about a foot high each when I got booked and didn’t get released until, I don’t remember exactly because I spent half of the last year in and out of the local prison basically every month or two… at least a month later. I was anxious to see if they were still there. They were, and they’d grown to about six feet tall. The fertilizer I put around them when I planted them might have had something to do with that. There were a few fairly big weeds growing among them but they seemed not to be disrupting my plants, and there were little vines growing around some of them, and actually holding some of them up. It looked like symbiosis to me. I think the plants might have communicated to each other so they could all live in harmony. I talked to my plants sometimes because that’s supposed to be scientifically proven to make them grow better. I picked and enjoyed small amounts of buds from them frequently. I loved it.
So, definitely, I want to do some more gardening: herbs and food, and some mushrooms if I ever get the chance.
I have a new batch of pickles to make so I’ll photograph the process. Culturing pickles is a recipe in itself. It’s based on the one in Sandor Katz’ Wild Fermentation book. There is some good information on the web like http://www.culturesforhealth.com they sell basic fermentation supplies. The yogurt is http://www.bellwetherfarms.com It’s the best for savory applications like tzatziki and cold potato salad of course.
Often I eat some when I eat other plant foods for better digestion and sometimes I have some with protein rich foods for smoother bowel movements.
And of course the number one reason I eat it is better gut flora in general.
Careful though, because I’ve found when I eat a whole lot of sauerkraut I sometimes get minor pains, presumably due to its acidity irritating my stomach or intestines.
Lactobacillus creates an acidic environment that kills yeast so pickles, sauerkraut and acetobacter in cider vinegar are fungal antagonists.
Sounds too good to be true, but it works most of the time. I find that when eating a food that hasn’t been in the mix for awhile (e.g. had cooked pak choi after not eating it for ages), a smelly fart or two may emerge.
Around the same age at another big family meal I ate a bunch of broccoli and then had to unload, and though my digestion was pretty sound as a kid, chunks of broccoli came out that time. I don’t think I’d eaten any prior for at least a couple days, so naturally my suspicion is that somehow, though most of my recently eaten food did what it was supposed to, that broccoli found its way out in what couldn’t have been any more than a couple hours.
To me both of these events seem impossible.
Apparently, that broccoli was in a hurry to reach The Outer Limits.
I did take measurements recently and noticed a small increase in size but it’s small enough it could be attributed to bloating. Hopefully those extra gut bugs will help balance that out
Another great post! I’ve been palying around with Kombucha recipes and created my Raspberry Kombucha, which I’ll post on my site soon…
http://freetheanimal.com/2013/12/resistant-primer-newbies.html
Richard, Tatertot Tim and Dr. Grace, along with many regular commenters, have posted many hundreds of links to research already done, what they have done to fix their gut biomes (Dr. Grace a couple of times), and the testimonials of many people who have had success and failures along the way.
I personally have been doing resistant starch since January, and added in the soil based organisims (SBO’s) in April. I’ve noticed things like my body temp has gone up from 95.5 to normal 98.6 degrees, I don’t crave carbs, I sleep like a log, all sorts of good things. I’ve had my setbacks, in that RS didn’t work until I filled the ’empty cages’ with the SBO’s.
Go read the posts that started the RS and gut microbiome revolution.
Lynamevan@gmail.com
I’m beginning to see that approaching the primal (or ANY health) journey from an all-or-nothing attitude, getting stressed about the nitty gritty, and forgetting to let go and just live, can do more harm than good. THIS IS ALL ABOUT BALANCE. About being playful, as you so often mention – and we forget that.
(This does not mean I believe in only doing this halfway, either. I strongly believe that if you want the full benefit of the primal lifestyle, you have to commit to it fully.)
I have to admit that at first blush it DOES seem overwhelming to take gut flora into account on top of primal life, (and for me, following Sarah Ballantyne’s Autoimmune Protocol). But an important part of this journey is to take the knowledge we gain and be empowered, strengthened by it, and NOT turn it into overwhelm and a long list of dos and don’ts.
When you are trying everything possible to build health out of perplexing physical challenges, you run the risk of running into overwhelm quite easily, especially when your lifestyle changes don’t seem to deliver results and you keep searching for the holy grail of that perfect combination of changes that will make you better.
Thank you for that conclusion to remind us to keep looking at the big picture. Stress, after all, affects gut flora, too. For me the bottom line is that our microbiome needs to BALANCED. And that means a BALANCED mindset, too, otherwise we might be missing the point.
Keep up the good work!
Also, I’ve stopped eating nuts because I can’t stand rancid oil and I stopped trusting my really sensible taste buds because even when I only eat the nuts that taste good to me, I end up feeling bad afterward. But I love nuts! They are tasty and filling. Any tips to buy FRESH nuts??
Are you eating wheat and other grains? Those are a common cause of leaky gut. Also carbonated sodas, which is not generally known.
To get fresh nuts, one idea is to buy them when the new crop appears in the store in the fall and freeze them. This is valid for temperate zone nuts such as pecans and walnuts. Also, buy whole nuts (not sliced almonds, for example) and store them in the fridge.
Also, try different (for you) varieties such as macadamia nuts. Or, take a break from eating nuts if your gut can’t tolerate them at this time. My hubby couldn’t eat nuts until he stopped drinking sodas and let his gut calm down.
Fresh almonds are here now at the store but I don’t see how it will affect the stuck of dried almonds. Also, I have no idea when any other nuts “appear”.
I eat rice and organic corn but the last time I drank soda must be 15 years ago. The problem with nuts is not my gut but that they cause headaches.
Fermented vegetables – Mark’s made posts about this topic along with recipes. His recipe for fermented dill pickles are delicious…and I don’t even like pickles!
Kombucha – I just recently discovered my local Kroger’s sells a ton of varieties. The ones I drink typically have extra healthy things added into it like chia seeds, blue-green algae, acetic acid, etc.
Greek Yogurt full fat – not much beats this. If you don’t have any negative reactions to yogurt, then knock yourself out.
Despite all the hype over almonds, I’m not nuts about them, and much prefer some hazelnuts and occasionally pumpkin seeds, pistachios as a treat (because vendors seem to think that they are made of silver, gold, and platinum), or some pecans.
I just googled kombucha and I found a maker down town! I will go check them when I will go to buy soap soon enough.
And no, I cannot eat yogourt, it’s actually yogourt with added lactase that made me notice my intolerance. Before that, it’s only milk that I was not eating.
One of the reasons given is that’s it’s omega 3s are bad for you.
(just pretend instead of this line, there’s the most epic facepalm .gif that exists)
At the moment I post this my argument is at the top of the comments section. I think I did a decent job with it but I’m sure many of you have more knowledge on the subject than me and could probably give an answer more based on science, while mine relies mostly on what should be common sense.
http://www.mindbodygreen.com/0-14180/5-reasons-you-should-stop-eating-salmon.html?utm_campaign=recommendation&utm_medium=popular&utm_source=feature
The ecology of the gut is emerging as a vital ingredient for good mental and emotional as well as physical health.
I’ve also personally had some issues with probiotics and fermented foods, although I may just have not found the right balance for myself. Or time. Giving it time after a lifetime of issues is important, as well as moderating stress, which is a huge thing for me.
The last line of the Exercise section is “don’t overtrain and don’t undertrain.” This is my biggest struggle right now…how do we know what our exercise sweet spot is?? Thanks in advance
isomalto-oligosaccharides (Quest Bars) and
inulin/chicory root used as an alternative sweetener?
That aside, being non-GMO won’t necessarily protect you from glyphosate (RoundUp) in your food. Farmers use it off-label on non-resistant crops to terminate growth for harvest, a practice euphemistically called “dessication”.
Dessication is common with wheat (which is not GMO [yet], but which readers of this blog aren’t apt to be eating anyway). Dessication is a potential issue with other crops that must stop growing before being harvested.
My stomach is the happiest it’s ever been since I’ve started downing my daily dose of RS plus soil based probiotics in a nice tall glass of raw milk.
I’ve gone from terrible gut health to decent gut health without ever in my life taking a single probiotic pill. I have eaten a lot of fermented food though.