4 Simple Ways to Optimize Your Microbiome - Probiotics
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4 Simple Ways to Optimize Your Microbiome

What does it really mean to have a healthy gut? In a nutshell, it means having the right bacterial balance in your microbiome. You see, your microbiome consists of trillions of microbes that live inside your gut and work around the clock producing mood-regulating, brain-stimulating, and immune-boosting chemicals, as well as supporting healthy digestion and helping to keep premature aging at bay. Here are our top tips to optimize your microbiome and keep it in peak shape.

Eat more plants. Plant foods containing fiber are the best fuel for your gut bacteria. A plant-based diet is also linked with greater diversity of gut bacteria. That is why a plant-based diet that includes a variety of whole grains, legumes, vegetables, and fruit increases the microbial diversity in your microbiome. Legumes, for example, contain a type of fiber called prebiotics, which feed your good gut bacteria and produce short-chain fatty acids.1 Combined with probiotics, prebiotics provide long-term sustainable nourishment to your microbiome. Whole grains contain something called polysaccharides which provide bulk and absorb water to promote healthy bowel movements. Fruits and veggies also contain simple sugars which draw water into the gut to assist the movement of fiber and help to prevent constipation.2 

The importance of the body’s gut microbiome has become a major topic for anyone interested in health and wellness—and with good reason. The microbiome is a vital biological infrastructure that acts like a health operating system for the entire human body. It’s home to trillions of bacteria, fungi, and other microbes that help run processes far beyond your digestive tract.

What Is the Microbiome—Why Does It Matter for Your Overall Health?

The gut microbiome refers to the community of microorganisms living mainly in your large intestine. These microbes ferment the food you eat, producing compounds that circulate through your bloodstream and interact with nearly every organ system in your body. In fact, a 2024 review in World Journal of Methodology explains that, while gut microbes influence digestion, these belly bugs also affect your immune system, brain, lungs, heart, and metabolism. What’s more, the composition of this community shifts in response to your diet, age, and lifestyle.1 In other words, what’s happening in your gut doesn’t stay in your gut—it ripples outward, shaping your inflammation levels, your immune response, and even your mood.

Simple Strategies for Better Gut Health

Because the state of your gut microbiome readily responds to your daily habits, it’s relatively easy to improve it with a handful of simple lifestyle changes. And that’s good news for anyone with less-than-optimal habits. Here are four evidence-backed ways to support a healthier microbiome:

Eat a diverse, nutrient-dense diet. When it comes to your diet, variety matters. The American Gut Project, a large-scale citizen-science effort involving thousands of everyday people working with scientists, sequenced the gut bacteria of more than 4,000 people around the world and compared it to their reported eating habits, activity levels, and health backgrounds. The researchers found that people who ate a wider variety of plant foods each week tended to carry a more diverse population of gut bacteria than people who ate a narrow rotation of the same few foods.2

A diverse microbiome matters because different species of bacteria specialize in breaking down different plant compounds—whether it’s fiber, polyphenols, or resistant starches—and each produces its own set of beneficial byproducts. Practically, this means you should rotate your produce, whole grains, legumes, nuts, seeds, and herbs throughout the week rather than eating the same foods every day. A good rule of thumb is to strive to eat 30 different types of plants each week to maximize microbiome diversity. Here is a cheat-sheet to get you started:

  • Fruits & Vegetables:All fresh, frozen, or canned varieties (different colors of the same vegetable, like red and green peppers, count separately).
  • Legumes & Beans:Chickpeas, lentils, black beans, kidney beans, and edamame.
  • Whole Grains:Oats, brown rice, quinoa, barley, and whole-wheat products.
  • Nuts & Seeds:Almonds, walnuts, chia seeds, pumpkin seeds, and flaxseeds.
  • Herbs & Spices:Basil, oregano, cinnamon, turmeric, and cumin.
  • Extras:Coffee, tea, extra virgin olive oil, and dark chocolate (70%+ cocoa) also contribute beneficial plant polyphenols.

Chew thoroughly to jumpstart digestion. Did you know that digestion doesn’t start in your stomach? It actually starts in your mouth. When you chew, food is mechanically broken down into smaller particles. This increases the surface area that your digestive enzymes can act on, while saliva itself contains enzymes that begin breaking down carbohydrates and fats before you even swallow.

This was shown in a randomized crossover trial published in the American Journal of Clinical Nutrition. Scientists had healthy adults chew whole almonds and then they analyzed the resulting food particles. They found that the size and structure of chewed almond particles directly determined how much of the nut’s fat became accessible for digestion, with less thorough chewing leaving more nutrients trapped inside intact plant cells that passed through the digestive system largely undigested.3 An earlier study found that chewing a small handful of almonds 40 times instead of 10 or 25 times significantly reduced fat excretion in stool, meaning the body absorbed up to a third more energy and nutrients.4

The takeaway: food that isn’t broken down well in the mouth arrives in the gut less accessible to both your own digestive enzymes and your gut bacteria. Slowing down and chewing more thoroughly—especially if you’re eating fibrous or fatty whole foods like nuts, seeds, and vegetables—gives your digestive system, and your microbiome, a better starting point.

Focus on fiber. Dietary fiber—like that found in fruits, vegetables, and whole grains—is arguably the single most direct fuel source for your gut bacteria. Unlike other nutrients, fiber passes through the small intestine undigested and arrives in the large intestine largely intact. Once there, beneficial bacteria ferment the fiber, producing short-chain fatty acids (SCFAs) such as butyrate, propionate, and acetate.

A 2022 systematic review in the journal Nutrients concluded that dietary fiber intake reliably increases SCFA production and shifts the composition of gut bacteria toward beneficial species in healthy adults.9 These SCFAs (also called postbiotics) boast several important health benefits:

  • Energy source.Butyrate acts as the primary fuel source for the cells lining the large intestine, helping them stay healthy and energized.5
  • Strengthens the intestinal barrier. SCFAs strengthen the intestinal lining, maintaining optimum barrier tightness and preventing harmful toxins or pathogens from leaking into the bloodstream.5
  • Provides anti-inflammatory effects. SCFAs reduce inflammation in the gut and support key immune cells. These actions lower the risk of digestive disorders and help manage conditions like ulcerative colitis.6
  • Controls pathogens. By making the gut slightly more acidic, SCFAs create an unfavorable environment for harmful oxygen-loving bacteria.7
  • Improves mineral absorption. The acidic environment and increased cellular surface area help the body absorb vital minerals like calcium, magnesium, iron, and zinc.8

The problem is, most Americans aren’t getting nearly enough fiber from the foods they eat. According to the American Society for Nutition, adults should strive to consume 25-38 grams of fiber daily. Yet, only 5 percent of men and 9 percent of women are meeting these targets.10 While increasing the amount of fiber you eat can be a delicious way to hit your numbers, it’s not always practical. Fortunately, there’s another category of fiber called prebiotics that selectively feed beneficial bacteria like Bifidobacterium. Clinical trials demonstrate that prebiotics and synbiotics (supplements that combine prebiotics and probiotics) significantly decrease systemic inflammatory markers, like C-reactive protein, by elevating SCFA production.11 Because prebiotics are available as supplements and as part of synbiotic supplements, adding them to your daily routine can be a convenient way to ensure you’re getting all the benefits SCFA provide.

Add a daily shelf-stable probiotic. While diet shapes your existing gut bacteria, probiotics introduce additional live microorganisms that can interact with your gut ecosystem and immune system directly. But it’s important to note that not all probiotic strains are studied equally. This is why strain-specific research matters.

One combination that has been tested in randomized, placebo-controlled human trials is Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2. In a crossover trial of older adults published in the Journal of the American College of Nutrition, researchers found that taking this three-strain probiotic combination for three weeks reduced inflammatory cytokines, which are small proteins released by immune cells that promote and boost inflammation in the body. This probiotic trio also led to a favorable shift in the composition of gut bacteria compared with a placebo.12 In a separate, larger randomized controlled trial published in the American Journal of Clinical Nutrition, the same probiotic blend improved the quality of life in adults with self-reported seasonal allergies when taken daily for eight weeks. This suggests that the benefits of this specific probiotic blend extend beyond the gut to immune-mediated symptoms elsewhere in the body.13

A daily probiotic featuring this specific, clinically studied strain combination can be a convenient way to complement dietary changes, particularly since shelf-stable formulations don’t require refrigeration and are easier to take consistently. To get the most from your probiotic, it’s also smart to check the label to ensure that the strains it contains are guaranteed to be viable at the time of consumption.

Bringing It Together

None of these four habits work in isolation—they reinforce each other. Eating a diverse diet gives your existing gut bacteria the raw material they need. Thorough chewing ensures that material is actually accessible for digestion and fermentation. Adding fiber through food and prebiotic supplementation feeds the beneficial bacteria already in your microbiome. And a well-studied probiotic can introduce additional strains to support the ecosystem you’re feeding. Research clearly shows that these small, consistent changes can make major improvements to your gut microbiome. And that, in turn, can support better overall health.

References

  1.  Salvadori M, Rosso G. Update on the gut microbiome in health and diseases. World Journal of Methodology. 2024;14(1):89196.
  2. McDonald D, Hyde E, Debelius JW, et al. American gut: an open platform for citizen science microbiome research. mSystems. 2018;3(3):e00031-18.
  3. Grundy MM, Grassby T, Mandalari G, et al. Effect of mastication on lipid bioaccessibility of almonds in a randomized human study and its implications for digestion kinetics, metabolizable energy, and postprandial lipemia. American Journal of Clinical Nutrition. 2015;101(1):25-33.
  4. Cassady BA, Hollis JH, Fulford AD, et al. Mastication of almonds: effects of lipid bioaccessibility, appetite, and hormone response. American Journal of Clinical Nutrition. 2009;89(3):794-800.
  5. Chakraborty P, Laird AS. Understanding activity of butyrate at a cellular level. Neural Regeneration Research. 2025;20(8):2323-4.
  6. Sankarganesh P, Bhunia A, Kumar AG, et al. Short-chain fatty acids (SCFAs) in gut health: Implications for drug metabolism and therapeutics. Medicine in Microecology. 2025;25:100139.
  7. Sun Y, O’Riordan MX. Regulation of bacterial pathogenesis by intestinal short-chain fatty acids. Advances in Applied Microbiology. 2013;85:93-118.
  8. Gut microbiota modulation of mineral absorption. Nature Index. Available at: https://www.nature.com/nature-index/topics/l4/gut-microbiota-modulation-of-mineral-absorption
  9. Vinelli V, Biscotti P, Martini D, et al. Effects of dietary fibers on short-chain fatty acids and gut microbiota composition in healthy adults: a systematic review. Nutrients. 2022;14(13):2559.
  10. ASN Staff. Most Americans are not getting enough fiber in our diets. The American Society for Nutrition. 2021. Available at: https://nutrition.org/most-americans-are-not-getting-enough-fiber-in-our-diets/
  11. McLoughlin RF, Berthon BS, Jensen ME, et al. Short-chain fatty acids, prebiotics, synbiotics, and systemic inflammation: a systematic review and meta-analysis. American Journal of Clinical Nutrition. 2017;106(3):930-45.
  12. Spaiser SJ, Culpepper T, Nieves C Jr, et al. Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2 ingestion induces a less inflammatory cytokine profile and a potentially beneficial shift in gut microbiota in older adults: a randomized, double-blind, placebo-controlled, crossover study. Journal of the American College of Nutrition. 2015;34(6):459-69.
  13. Dennis-Wall JC, Culpepper T, Nieves C Jr, et al. Probiotics (Lactobacillus gasseriKS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2) improve rhinoconjunctivitis-specific quality of life in individuals with seasonal allergies: a double-blind, placebo-controlled, randomized trial. American Journal of Clinical Nutrition. 2017;105(3):758-67.

This article is for informational purposes only. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment and should never be relied upon for specific medical advice.