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Do Gut Microbes Control Your Food Cravings?


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Do you experience cravings for particular foods? Recent research on the gut-brain axis suggests that the microbes in your gut could strongly influence your food choices. Read on to learn how your gut microbes can manipulate your behavior and, in turn, how you might manipulate your gut microbes to curb food cravings.

gut bacteria food cravings
If you are dealing with a particular type of craving, your gut microbes could be to blame. istock.com/gerenme

A whopping 97 percent of women and 68 percent of men report experiencing cravings for certain foods (1). Cravings are thought to be a combination of social, cultural, psychological, and physiological factors and are a major barrier to weight loss and optimal health for many individuals (2).

A recent body of evidence suggests that gut microbes might play a significant role in influencing cravings. Given that microbes co-evolved with us and constantly depend on the incoming dietary substrates that we provide for their own sustenance, it’s really no surprise that they are able to preferentially shape our eating preferences to improve their own chances of survival. In this article, I’ll discuss our current understanding of how microbes shape eating behavior and how you might use this information to combat cravings.

The Gut-Microbiota-Brain Axis

Most of us are well aware of the billions of neurons that make up the fatty, three-pound organ in our skull. But did you know that your gut also contains a dense network of neurons? This network, called the enteric nervous system, governs the physiological function of the gastrointestinal tract. In fact, this network is so robust that it is commonly referred to as the “second brain.”

The enteric nervous system is connected to the central nervous system (the brain and spinal cord) via the gut-brain axis. This is not a physical axis, but rather a term to collectively describe the interrelationship of the intestines and the brain.

There are two ways in which they are connected. The first is the circulatory system. We have known for many years that hundreds of different hormonal, neuronal, and inflammation-related signals are constantly relayed between the gut and the brain via the bloodstream (3). Only recently, with the discovery of lymphatic vessels in the brain (4), have we come to understand that these gut-derived signals can likely enter the brain directly from the lymph as well.

The enteric nervous system is also connected directly to the brainstem via the vagus nerve. The vagus nerve acts as a superhighway for communication between the gut and the brain and is the longest nerve cell in the autonomic (unconsciously controlled) nervous system. Studies on the vagus nerve found that vagal blockade can lead to marked weight loss (5), while vagal stimulation triggers excessive eating in rats (6). In the next few sections, I’ll discuss the many other ways that microbes can influence eating behavior.

Craving a certain food? It could be your gut microbes are to blame.

Microbes Have Food Preferences, Too

Different microbes prefer different dietary substrates. While many microbes are “generalists” and can grow on a variety of substrates, they typically prefer one substrate over another, based on the amount of energy they can conserve during the process of breaking it down. Individual genera of bacteria have been shown to have these preferences. For example, Bacteroidetes has been shown to have a preference for particular fats; Prevotella grows best on a carbohydrate source; Bifidobacteria are able to outcompete others in the presence of dietary fiber (7, 8).  Other microbes are “specialists” and can only grow on a single nutrient source. Some microbes, such as Akkermansia muciniphila, do not depend on dietary substrates at all and instead thrive on the carbohydrate of the mucus layer secreted by host gut epithelial cells (9).

All of these microbes require a steady stream of substrates to grow and reproduce. Studies have shown that a low concentration of nutrients triggers increased virulence in many microbes as a survival mechanism. Virulence is the ability of a particular microbe to cause damage to the host. For many human-associated microbes, the production of virulence toxins is altered by the detection of simple sugars and other nutrients (10, 11).

Microbial Neuroactives

When microbes break down (metabolize) dietary substrates, they produce by-products called metabolites. Microbial metabolites include many neuroactive agents (12, 13) that are small enough to penetrate the selectively permeable blood-brain barrier. Studies on chocolate cravings have found that even when eating identical diets, people who are “chocolate desiring” have different microbial breakdown products in their urine than people who are “chocolate indifferent” (14, 15).

So what are some of these metabolites? Short-chain fatty acids (SCFAs), breakdown products produced from the fermentation of dietary fiber in the GI tract, are able to modify the expression of genes in cells throughout the body, including brain cells. In particular, the SCFA butyrate has been shown to dampen the inflammatory response of microglia, the immune cells of the brain (16), and has profound effects on behavior and mood in mice (17).

Other microbially derived molecules are able to mimic hunger or satiety hormones. Your body normally secretes hormones like ghrelin (to stimulate your appetite) and peptide YY (to signal that you are full). Many gut bacteria are able to manufacture small peptides that mimic these hormones.

Interestingly, humans produce antibodies against these microbial hormone mimics in an effort to maintain the integrity of host signaling mechanisms. These antibodies, however, while meant to target microbial hormones, can also bind to mammalian hormones, effectively making them “auto-antibodies” (antibodies that react against one’s own body) (18). Microbes therefore can interfere with human appetite by either directly mimicking satiety and hunger hormones or indirectly inducing this autoimmune response.

Microbes Produce Neurotransmitters and Influence Neuroplasticity

Microbes may not have a nervous system, but they do produce neurotransmitters! More than 50 percent of your body’s dopamine and 90 percent of your body’s serotonin are produced in your gut, along with about 30 other neurotransmitters (19, 20). These molecules are critical for signaling between cells of the nervous system. Dopamine in the striatum and serotonin in the hypothalamus have both been shown to be involved in the regulation of eating behavior (21).

Microbes may also influence neuroplasticity, the ability of the brain to reorganize and create new neural pathways. This is particularly important since the formation of new connections between neurons may be necessary to reshape emotional eating behavior (22). One potent stimulator of neuroplasticity is brain-derived neurotrophic factor (BDNF). Studies have shown that mice lacking a gut microbiota (germ-free mice) have decreased levels of BDNF in the hippocampus, the learning and memory center of the brain. Hippocampal BDNF is also decreased in normal mice following antibiotic administration (23).  

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Microbes Shape Host Stress Response, Mood, and Behavior

An increasing number of studies are showing connections between the gut microbiota, and stress, depression, and anxiety (24, 25).

Poor mental health has long been associated with an increased likelihood to eat unhealthy foods (26). In 2004, a seminal experiment showed that germ-free mice raised in sterile conditions with no gut microbes had an exaggerated hypothalamic–pituitary–adrenal (HPA) axis response to stress (27). The effect was reversed by colonization with a single Bifidobacterium species. A similar 2013 study showed that germ-free mice had increased anxiety-like behavior, which was ameliorated by short-term colonization in adulthood.

Furthermore, a study published in 2012 found that germ-free mice prefer sweets and have a greater number of sweet taste receptors (28). While germ-free mice can tell us a lot about the role of microbes in mammalian physiology, they are certainly not very translatable to our own lives. At the end of this article, I’ll discuss a few human studies that have shown improvements in mood through interventions that manipulate the gut microbiota.

Microbial Diversity May Determine How Susceptible You Are to Suggestions from Your Microbes

Microbial diversity may determine how easily host behavior can be manipulated.  Members of the microbiota constantly compete with one another over habitat and nutrients. A less diverse microbial population has fewer distinct microbial species and therefore likely has a few species with large population sizes. Researchers have hypothesized that species with large population sizes are able to use fewer resources for outcompeting other microbial species, leaving more resources available for manipulating the behavior of the host (29).

Interestingly, obese individuals tend to have lower microbial diversity than individuals of a healthy weight (30, 31). This may partially explain why people who are overweight tend to have more difficulty with food cravings. In other words, microbes could be a major barrier to weight loss.

Can Manipulating the Gut Microbiota Reduce Cravings?

In this article, we discussed the connection between gut microbes and food cravings. Research on the oral microbiota may yet provide more links between microbes and our eating behavior. Functional and structural brain imaging alongside microbiota and metabolite analysis will be essential to improving our understanding of the microbiota–brain connection and its impact on human health and disease (32).

If you’re feeling powerless to the will of your microbes right about now, you should know that there are quite a few ways that we can manipulate them! The following list will help cultivate a healthy microbiota and may help you make better food choices.


Several strains of Bifidobacterium and Lactobacillus have been shown to improve anxiety- and depression-like behavior, which tend to alter eating behavior. In a randomized trial, women who ate a fermented milk product containing probiotics showed reduced activity in the insula and somatosensory cortices (emotional reactivity centers of the brain) in response to an emotional recognition task (33).


Prebiotics are foods that selectively feed certain beneficial microbes over others. Prebiotics have been shown to increase BDNF (34), reduce waking cortisol and alter emotional processing (35), and induce satiety hormones (36). Try fermentable fiber in the form of foods like plantains, onions, garlic, and sweet potatoes, or consider supplementing with inulin or resistant starch.

Focus on Nutrient Density

A diverse microbiota tends to be a healthy microbiota. A diversified, nutrient-dense diet provides substrates to a wide range of microbes that can support your health and prevent any one population from gaining too much ground. Many people find that their cravings subside substantially after adopting a nutrient-dense diet for several months. This is likely mediated by a shift in their gut and oral microbiota.

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Join the conversation

  1. Interesting how bacteria effect our bodies so much. We crave what they like. If this is so maybe we don’t like things they don’t like. Or greater still what kills them could very well kill us too. Makes you think about pesticides, preservatives, chlorine, etc in a whole new light.

  2. I have been following your articles for a couple years and really have turned my health around. I have an old dusty B.Sc. Degree in microbiology, so find this particularly fascinating.
    Getting off of sugar and gluten, and eating real, whole foods has changed my health dramatically. I no longer crave sweet junk food, my severe seasonal allergies are gone, yeast problems are gone, sinus headaches dramatically reduced, I can tolerate some probiotics but not others, and make fermented foods. I have successfully treated my children’s gastric problems with probiotics as well. I have been able to get them off of a cycle of antibiotic use by using herbal gargle of thyme, sage and salt to treat sore throats. This has dramatically reduced antibiotic use which causes so many problems. A urologist treated my daughter’s chronic bladder infections with probiotics, and it has not recurred in three years.
    I used to be addicted to sweets. I would literally get a high off of carmel rolls, but this last holiday season I made them along with various cookies for family and guests and didn’t eat one, it wasn’t even a struggle and I am positive that I have my healthier little gut buddies to thank. I do get the occasional urge which I can satisfy with a couple dates or a paleo desert. I think understanding the source of the cravings and knowing that one can control that is very empowering.

    • Re cravings and whole foods, I’m just finishing off my 27th day of a food program called The Whole 30 (whole30.com) where you completely eliminate added sugars, dairy, grains, beans/legume and alcohol. So you can eat proteins, lots of veggies, limited amounts of fruit (sugar), good fats, nuts and seeds. After 30 days you add in one food group at a time to see whether it has any adverse effect on your gut or mood or aches/pains. It has completely eliminated my sugar cravings and craving for foods which turn into sugar (simple carbs).

  3. The more focus is placed on our MICROBIOTA, the more is discoved about its existence beyond the GUT!

    As a recent article “The microbiota of breast tissue and its assocation with tumors” shows, now other organs are being investigated/studied and this is, I think, just the tip of the iceberg! (Publ. in the Journal of Applied and Environmental Microbiology)

  4. Very nice post here thanks for it .I always like and such a super contents of these post.Excellent and very cool idea and great content of different kinds of the valuable information’s.

  5. I have Ankylosing Spondylitis (AS) which has suddenly worsened considerably after two bouts of urinary infection and subsequently, two doses of antibiotics in close succession. I have been trying to keep to a very low starch diet as recommended by Dr Erhinger of Kings College Hospital, London. He says klebsiella overgrowth in the gut is the problem.
    Everytime I have an inflammatory flare-up, I swear I’ll stick better to the diet. But after two or three days starch free, I find myself compelled to eat something containing starch. I just know that those klebsiella are driving me to do this. My weight goes up by the next morning, probably due to fluid retention.
    Yes, I take a variety of probiotics every day.
    I am presume I have a klebsiella overgrowth and I am looking for something to put it in its place.
    Any suggestions as to what antibiotic and which probiotics? Or any other treatment?

  6. Great article, and very timely. I’m experimenting with this very concept right now. Taking large amounts of probiotics and prebiotics, as well as eating cooked and cooled (resistant) starches. (I have been eating a nutrient dense diet for many years, so that part is not new for me.) I do feel like it’s starting to have a beneficial effect on cravings, including alcohol cravings, as well as mood. I recently did extensive lab testing that showed my gut microbiome lacked diversity and was extremely low in certain important strains. Grace Liu of thegutinstitute.com recommends high doses (fecal implant equivalent doses) of the core strains (like bifidobacteria), and then increasing diversification by adding soil based (prescript assist, fermented foods, etc.). Of course she recommends prebiotics as well. I’ve been finding lots of good info on that site, as well as her podcasts. People have been talking about the important of gut bugs for a long time, but it seems like the recommendations (have some kiefer, take a daily probiotic pill, etc.) have been insufficient to make any significant impact for most people. I’m hoping to see continued work in this area with more potent products and protocols developed.

  7. Can you please comment on the product called BRAVO yogurt probiotic? I have read that it’s a very special source of probiotics and other things that help many people use vitamin D. It’s expensive and you need to make your own yogurt with the packet material. Thank-you!

  8. Please comment on a role for fermented foods. Probiotics offer a limited range of microbes in large numbers. Study of kimchee and sauerkraut suggest they contribute hundreds of different microbes. Microbial diversity seems to be the name of the game; Cost and accessibility play a role as well.

    • Hi Bonnie, I feel like you validated yourself within your own question! I always recommend a probiotic for my patients but urge them to cycle to a different brand, ex: Primal Defense to Prescript Assist after 3-4 months. But I also highly encourage the fermented foods. This was how we obtained “probiotics” traditionally without the worry of causing a microbial imbalance by supplementation with low diversity. Ferments like kombucha, sauerkraut, kimchee, beet kvass are now more widely available and aren’t very expensive, especially when fermented at home. I teach my motivated clients how to do it. I personally have noticed a HUGE decrease in carb cravings since I’ve been consuming raw milk and fermented foods. It is amazing and so freeing!!

      • Fay , complex carbs are the body’s main source of fuel . I think you’re implying they are to be avoided which isn’t true . You must consume carbs with protein to prevent going into Ketosis [ an acidic blood Ph ] which is also bad .
        ” Whole” grains are very important they are called the “staff of life” one of the 4 original food groups .Did you see the recent study that came out about how important they are ?.

        • Hi Bill! Thanks for your concern. Since I am a practitioner, I typically don’t have anyone concerned about my diet/health. 🙂
          When I say that I don’t crave carbs, it doesn’t mean that I don’t eat them. It means that I’m not constantly looking for a cookie or the like!! I have also begun to eat less grain-based carbs but it was not something that I purposed to do. I really believe it was a physiological outcome of microbial balance plus the fact that I am eating much more fat. My (contented) brain is thanking me.

          • Fay , whole grains are super important they are a complex carb . A study just came out about them check it out . And the brain is primarily fueled by carbs not fat .
            A high fat from animal meats is not good greatly increase your chance for breast cancer as well as heart attacks . Don’t believe the nonsense you hear today there is no truth out there today as a great man of God predicted for our modern times Isa 59 : 15 Niv bible . Carbs are one of the 3 macro- nutrients how could eliminating one of them be good . And they are one of the 6 essential nutrients . Go google benefits of carbs by Eilleen Lane .

          • Hi Fay and Bonnie & others; I so appreciate your post and this article. As an RD and a patient deep in SIBO tx now following the Cowdon protocol for lyme, have a vested interest in this topic of probiotics, fermented foods and the microbiome. After following low fodmap (Paleo Auto Immune) diet and herbal tx for SIBO and hearing more about long term effects on the microbiome with low fodmap, curious about introducing probiotics such as Saccromyces Boulardi, prescript assist or just using fermented vegetables. I have been on the fence as getting differing opinions from ND’s.

  9. Great article Chris.

    I have IBS and have noticed some interesting things that resonate with this article whilst using a low FODMAP diet. Basically after eating this diet for a few days or a week I tend to, for some inexplicable reason, crave higher FODMAP foods.

    Since the low FODMAP diet should affect the level of microbiota, I thought that maybe this ‘agitates’ the bacteria into increasing appetite for foods that feed them. It’s scary to think that bacteria could have this much control over our body and health.

  10. I just joined food addicts anonymous, which recommends 3 meals a day, 4 Oz protein,1 cup cooked vegies, 1 cup raw veggies, and healthy starch and 1/2 c fruit, but only for breakfast.
    Cheese and cottage cheese are recommended.
    I’ve been wondering why this appears to work, as time goes on. Theory is eat nothing between meals so leptin can be freed up.
    Any opinionsuggestions out there?

  11. Interesting and good to know. Definitely, modern times have given many of us a great availability of food, and adulterated food. It seems to have changed the game of how our bodies respond to all of this. With that said, my experience with regular cravings began abt 15 yrs ago, when tv health advocates talked abt eating many mini meals per day to continually provide nutrients and energy. I went along with this, and all it did for me was to train my brain to WANT food many times a day. I heard a neurologist talk abt how food is an addiction and if we didn’t have the desire for food, we would not eat and starve. Never thought of it that way, but it was helpful to know ad apply to my cravings. Previously, I had a normal addiction to food 3x per day. Now, I craved something to eat 6x day. Because these extra meals occurred at various times, not the exact same times, I began to get the urge to eat maybe 10x per day. I struggled with counting calories, to keep from putting on weight. At one point, I realized that many of these urges to eat came from my brain, some from my stomach. This told me I should try to ignore the brain signals. Not easy, and I sympathize with people who have other addictions. I did find that Vitamin D supplementation cut down the high # of urges, but still I have too many times a day that I want something to eat. Some might call it grazing, but it isn’t enjoyable for me to want food many times a day. It can consume your thoughts, as someone else mentioned. Decided to only eat 2 meals per day recently, and a few nuts with pills in the morning. I am trying to retrain my brain back to 3x per day. I try to keep busy, and my “plan” seems stronger in my head than the urges. That happened gradually over a month’s time. When I was struggling with extra urges for food, I drank water, or took a vitamin of my normal regimen. My brain got something to satisfy the craving, but none of this has been easy. I expect this to take a long time, maybe 1-2 years. I have used probiotics, but didn’t notice less cravings. I will take the info here to incorporate them more often. I had gotten away from regular sleeping habits, and it took two years to retrain those bad habits, so I have learned nothing is going to happen quickly.

  12. I learn almost as much reading the comments as I do the article . I’m 59, and after a lifetime of junk and bad eating, now gerd, I have changed my eating. I’ve lost weight, controlled eating urges. I’m still learning, thanks to all who have taught me!

  13. After rounds and rounds of antibiotics starting from a young age, I couldn’t walk by my refrigerator without eating something. My days and nights were spent incessantly worrying about what I was going to eat next and what I was going to eat next. I finally, at 35, dosed myself with high amounts of just acidophilus (sp) and within a week, all craving completely ceased. For the first time in my life, I could just exist mostly in peace. And I ate when I was hungry and stopped when I was full. I am now 45 and its still the same. I continue to take probiotics in high numbers at least several times a week. “Discovering” probiotics was one of the best things that ever happened to me, but I don’t believe I would have had the same results just taking 1 a day or even 1 3x a day. I had to take lots.

    • I agree and so does Dr. Ohi rrawho makes his own probiotics that you may have seen. He says people need to take loading doses of probiotics in order to take over the bad bacteria in the gut. He is a researcher and he has cured Crohn’s disease and IBS by taking 10 to 20 pills a day for several months of probiotics. I used to be lactose intolerant so I took 10 pills a day for a month and a half and now I no longer have the problems I used to have with Dairy, which was massive diarrhea and bloating.

    • That’s very interesting! May I ask what kind of doses you took and what your maintenance dose is? Thanks!

  14. I’ve found an unexpected result of meditation/relaxation was eating less leading to effortless weight loss!
    Thanks for the article, very interesting.

  15. Chris, could you comment on all of this in relation to SIBO? Specifically, what if someone has had a great nutrient-dense diet (for years) but has microbes in the small intestine? Then, more probiotics or prebiotics are contraindicated because the microbes land in the wrong place. I’ve been told “too much of a good thing” re: fermented foods, etc. What if the SIBO is resistant to treatment? My understanding is that usually SIBO can’t be treated by diet alone, but do these more recent studies change that view? Thanks!

    • Maybe look at the work of Gerard Mullins: Gut Balance Revolution, where he eliminates certain foods, inc probiotics in the first phase of his plan, to bed rid of Small Intestine Bacterial Overgrowth.

  16. This is the second time this week I’ve said “Far Out”
    Whatta in-situ-ful concept and who woulda thunk. essentially aliens are controlling me and that’s why I’m fat with no energy and tired all the time. But now I can wrestle control back. thanks

  17. Great article, Chris. It’s quite believable that our microbiome attempts to control our cravings and the best way to control the microbiome is to increase it’s diversity via probiotics, prebiotics, and nutrient density.

    I’m imagining that foods that are essentially probiotic are sour, foods that are prebiotic will have lots of fiber which is tasteless, and foods that are nutrient dense with phytonutrients are anything but sweet, and often bitter. In other words, functional, but never-craved foods. When people adjust themselves to these foods, and these alone as their total whole-food diet, they find they are satisfied metabolically and cravings don’t reappear. What may then appear is true gut-guidance toward what is lacking in the way of minerals, macro-nutrients, etc.

    I’ve heard several people, always ones without cravings but on nutrient rich diets, say they “listen to their gut”. They are always talking about guidance, not cravings. I think I experience this at times when I eat too little protein. This is quite different from cravings though.

    I’d love to see you follow up this great article on cravings with one about the possibility that there is a different type of guidance available from the gut once a person balances their foods and microbes such that they lose the cravings. Do you have experience and testimonies of others on this possibility?

    Thanks for all the great ideas and inspiration!


    • Great Article Chris, thank you for the fascinating connections.

      There is a product that I have used which contains Inulin and I have used as part of an Intestinal cleansing programme in the past:


      gentle and effective and I hadn’t realised what additional properties the mixture had as a food source for the beneficial gut bacteria until I re-read the supporting information.

    • Glenn-

      I have experienced this. When I purge the sugar which takes about a week or two, I can feel my gut telling me what to eat.

      But it’s hard to stay in that place without some major discipline. While the cravings do fade, they dont eliminate.

      So it’s especially hard in American culture, with social and emotional eating, advertising, always on the run, and raising kids.