Probiotics, Prebiotics and How an Undesirable Gut Microbiota Increases Depression

Written By Erin Stair, MD, MPH ( Dr. Eeks) 


 You are never alone. 

It may not be comfortable to think about, but tons of tiny organisms live inside us and affect our health. The microbiome refers to all of the microorganisms that live in our body. The term microbiota refers to specific populations of microorganisms in specific body parts, such as the gut microbiota. The gut microbiota is huge. There are 10 to 100 times more microorganisms living in each of our guts than our total number of human cells.1  There are more than 1000 species and 7000 subspecies, so next time you are lonely, think about all your gut buddies.

A growing body of research shows that the gut microbiota affects our physical and mental health in many ways, including being linked to depression. Depression may be associated with an altered gut microbiota. Jiang et al analyzed fecal samples from both depressed individuals and individuals who weren’t depressed. Results showed that the depressed individuals’ fecal samples contained increased amounts of harmful bacteria and reduced amounts of beneficial bacteria.2

The type and quantity of microorganisms that make up the gut microbiota are affected by our environment, diet, stress, use of antibiotics and even cleaning products and disinfectants. While our focus is depression, alterations in the gut microbiota are linked to obesity, metabolic syndrome, irritable bowel syndrome, autoimmune disorders, allergies, autism and neurological issues.3 That’s important to note, since chronic health issues can exacerbate an underlying depression.

Research shows that microorganisms in the gut interact with the brain in a bidirectional way. The gut has its own nervous system, the enteric nervous system, often call our second brain because it can function independently of our “real” brain. The enteric nervous system directly communicates with the central nervous system through both the sympathetic nervous system and the vagus nerve, part of the parasympathetic nervous system. The sympathetic nervous system is responsible for gut motility, blood flow, immune cell activation and barrier function. The vagus nerve signals the gut when to “rest and digest” and communicates with the enteric nervous system through multiple nerve endings. The vagus nerve collects information on the health of the gut, including microbial content, and sends this information to the brain.4 Vagus means “wanderer,” and in many ways, it “wanders” around the gut, like a vagabond, collecting information. Alterations in the gut microbiota are sensed by the vagus, communicated to the brain, and have been linked to changes in mood. Studies on animals in which either bacteria were removed from the gut lumen or the vagus nerve severed show that depression, anxiety and stress significantly increase.5
Some microorganisms that make up the gut microbiota can directly produce neuroactive chemicals, such as serotonin, GABA, dopamine and norepinephrine, which can directly affect the central nervous system. The production of these neuroactive chemicals depends on substrates, essentially food, which depends on our diet. Our diets, and even short term dietary changes, can directly influence the types and quantity of bacteria that reside in our gut.6  The walls of a healthy gut form a tight barrier and prevent harmful bacteria and toxins from entering the circulatory system. Damage to the walls can cause increased permeability or a “leaky gut.” Leaky guts enable neurochemical-producing bacteria to enter the circulatory system, thereby creating systemic effects, one possibility being symptoms of depression.

Probiotics are living microorganisms that, in adequate doses, yield health benefits for the host.7 They are often referred to as “good” bacteria and ingesting them may improve the gut microbiota and restore homeostasis. Ingesting probiotics does not automatically translate into health benefits. The dose, strain and durability matters, and more research on these characteristics is warranted. It is theorized that probiotics (and prebiotics discussed below) improve the health of the gut microbiota by promoting the growth of “good bacteria” and limiting the growth of potentially pathogenic bacteria; improving the gut barrier function and improving overall host immunity.

Some studies show that probiotic consumption improves depressive symptoms. In rats, the probiotic strain Bifidobacterium infantis is shown to significantly reduce stress and depressive symptoms, and the strain Lactobacillus rhamnosus is shown to significantly reduce depressive symptoms after 28 days.8,9  There are a few quality studies on humans with mixed results. I’ll mention two here, each a randomized, placebo controlled, double blind study (RCT), since such a study design is considered the highest level of evidence. One 8-week study compared a probiotic capsule with Lactobacillus helveticus and Bifidobacterium longum with a placebo in individuals with low mood.10 Results showed no significant differences from the control group in subjective measures or biochemical markers. Another RCT showed beneficial mental health effects in petrochemical workers who supplemented with yogurt containing live, active cultures.11 An 8 week long randomized, double blind, placebo controlled study showed that supplementing with probiotics significantly reduced depressive symptoms in individuals diagnosed with major depressive disorder.12 This study is important for three reasons: 1) The study design was solid 2) Participants were required to have an official diagnosis of major depression. (This means they couldn’t self-select into the study, which improves accuracy.) 3) Results showed that probiotics also significantly improved metabolic biomarkers, such as insulin sensitivity.

What foods contain probiotics? Unless altered, most fermented foods contain probiotics. Fermentation is the process by which microorganisms (probiotics being one type) break down carbohydrates into alcohol or acids. Fermented foods were a staple of our ancestors. Before refrigeration and the science of fermentation was understood, food naturally fermented. Therefore, much like the Mediterranean diet ( which I follow), fermented foods are considered part of a traditional diet, or the diet human beings have been eating since the beginning of mankind.

Today you can find many superfoods and functional foods with probiotics, as it’s a booming wellness trend. There are also a ton of supplements in capsule and powder formation. Even though I’m skeptical of supplements, I take a daily probiotic supplement. So does my dog, Barnaby, which could be one reason he is insanely happy. 😉  I didn’t start taking a probiotic supplement for my depression, as the significance of the gut-brain connection wasn’t known when my depression started. I started taking it because I was having irritable bowel symptoms, and nothing was helping. I was bloated and would get sharp abdominal pains after eating any meal. Sometimes when I moved, even just a little bit, my gut sounded sloshy like a swamp. I cut back on gluten, artificial sweeteners, chewing gum and started taking a probiotic supplement. In about three weeks, I noticed a significant change and started to feel a lot better. Years later, learning about its potential antidepressant effects was a bonus.

Here is a list of foods with probiotics. A lot of these are in my refrigerator:
Yogurt with live, active cultures
Some types of cheese
Pickles ( not in vinegar)


Prebiotics are ingredients that create health benefits by increasing the composition and/or activity of specific microflora. All prebiotics are classified as fiber, but not all fiber is prebiotics. For a food ingredient to be classified as a prebiotic, three conditions must be met: 1) The ingredient must resist gastric acidity, hydrolysis by enzymes and absorption in the upper GI tract (Meaning it isn’t digestible) 2) The ingredient is fermented by the intestinal microflora, and 3) The ingredient selectively stimulates the growth and/or activity of intestinal bacteria associated with well-being. Most prebiotics stimulate the growth of Lactobacilli and Bifidobacteria, and it is no coincidence those two genera are in a lot of probiotic supplements.

Like probiotics, prebiotics were heavily consumed by our ancestors. For example, archeological evidence shows that early hunter/gatherer societies ingested high quantities of inulin, a prebiotic fiber found in early dessert plants.13  Research strongly supports inulin as an effective prebiotic, although it has been known to create bloating and gas. A good, tasty source of inulin is Jerusalem artichokes.14  Acacia, the gum from the Acacia tree, is also a good source of prebiotics and fiber. Studies suggest it is one of the more tolerable prebiotics, so if you struggle with gas or bloating, try Acacia.15  Wheat dextrin, a type of prebiotic fiber, has been shown to increase Bifidobacteria and decrease colonies of harmful bacteria in the gut.16  Whole-grain wheat and corn-based cereals have been shown to have prebiotic activity. A randomized controlled trial showed that supplementing with 2 bananas a day produced more Bifidobacteria in the gut, although the result was not statistically significant from the control group that supplemented with water.17  Bananas contain several prebiotic carbohydrates. The group supplementing with bananas, however, did show a statistically significant reduction in side effects, such as bloating, which in itself is a great reason to add more bananas to your diet.

List of Prebiotic Foods:
Jerusalem Artichokes
Supplements (Inulin, Acacia, Wheat dextrin)

An extra note for the ladies:
1. Premenstrual syndrome can exacerbate underlying depression. Research strongly shows that calcium significantly reduces PMS symptoms, including low mood. Studies show that prebiotics may increase calcium absorption. If you suffer from PMS and want to manage it naturally, I recommend loading up on prebiotic foods and calcium at least two weeks before your expected period.
2. Probiotics for post-partum blues: Depression and anxiety are common after giving birth. A randomized, double blind, placebo-controlled study showed that pregnant women who supplemented with Lactobacillus rhamnosus HN001 through pregnancy and six months after giving birth had significantly reduced symptoms of depression and anxiety than the control group.18

An extra note for anyone with anxiety:
While the focus of this blog is depression, eating fermented foods with probiotics is also associated with a significant reduction in anxiety.19


I hope this blog helps shed some light on the gut microbiota and depression. For what it’s worth, adding probiotics and prebiotics to your diet can’t hurt.  If you already take pro/pre biotics, feel free to share your experiences in the comments below.  🙂

PS: What brand of Probiotics do I use?  See below.




1. Sanchez, B., Delgado, S., Lourenco, A., et al. (2016) Probiotics, gut microbiota, and their influence on host health and disease. Food Research.
2. Jiang, H., Ling, Z., Zhang, Y., et al. (2015) Altered fecal microbiota composition in patients with major depressive disorder. Brain, Behavior and Immunity.
3. Albenberg, L., and Wu, G.(2014) Diet and the Intestinal Microbiome: Associations, functions and implications for health and disease. Gastroenterology.
4. O’Mahony, S., Clarke, G., Borre, Y., Dinan, G., et al. (2015) Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behavioral Brain Research.
5. Grimonprez, A., Raedt, R., Baeken, C., et al. (2015) The antidepressant mechanism of action of vagus nerve stimulation: Evidence from preclinical studies. Neuroscience & Behavioral Reviews.
6. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ (2013) Diet rapidly and reproducibly alters the human gut microbiome. Nature.
7. Schlundt J (2001) Health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. Report of a joint FAO/WHO expert consultation on evaluation of health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. FAO/WHO
8. Desbonnet,L. (2010) Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience.
9. Bravo, JA, et al. (2011) Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci U S A.
10. Romiin, A., Rucklidge, J., Kuijer, R., et al. (2017) A double-blind, randomized, placebo-controlled trial of Lactobacillus helveticus and Bifidobacterium longum for the symptoms of depression. Australian and New Zealand Journal of Psychiatry.
11. Mohammid, A., Jazayeri, S., et al. (2016). The effects of probiotics on mental health and hypothalamic-pituitary-adrenal axis: A randomized, double-blind, placebo-controlled trial in petrochemical workers. Journal of Nutritional Neuroscience.
12. Akkasheh, G., Zahrakashani, D., et al. (2016). Clinical and metabolic response to probiotic administration in patients with major depressive disorder: A randomized, double-blind, placebo-controlled trial. Nutrition.
13. Leach, J.D and Sobolik, K.D. (2010). High dietary intake of prebiotic inulin-type fructans in the prehistoric Chihauhuan desert. Br.J of Nutrition.
14. Li, W., Zhang, J., Quing, C., et al. (2015). Extraction, degree of polymerization determination and prebiotic effect evaluation of inulin from Jerusalem artichokes. Carbohydrate Polymers.
15. Nakov, G., Georgieva, D., et al. (2015). Prebiotic effects of inulin and acacia gum. ( Review). As retrieved from:
16. Carlson, J., Hospattankar, A., et al. (2015). Prebiotic effects and fermentation kinetics of wheat dextrin and partially hydrolyzed guar gum in an in vitro batch fermentation system. Foods.
17. Mitsou, E., Kougia, E., et al. (2011). Effect of banana consumption on fecal microbiota: a randomized controlled trial. Anaerobe.
18. Slykerman, I., Wickens, K., Thompson, J., et al. (2017). Effect of Lactobacillus rhamnosus HN001 in Pregnancy on Postpartum Symptoms of Depression and Anxiety: A randomized double-blind placebo-controlled trial. EbioMedicine
19. Hilimire, M., DeVylder, E., Forestell, C. (2015). Fermented foods, neuroticism, and social anxiety: An interaction model. Psychiatric Research.

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