How To Rebuild Your Gut Microbiome After Antibiotics

Summary

Our microbiome is our best friend — it's required for our health, from birth to death. In the last century, antibiotics, ultra-processed foods, pesticides, food additives, mouthwashes, and other aspects of modern life have negatively affected the composition and diversity of our microbial communities. These changes have sparked growing scientific interest in the relationship between the microbiome and our health span.

We should focus on maintaining our healthy microbiome and not degrading it. For those who have lost key microbiome friends, certain practices may help support their recovery. Researchers have a term for this — rewilding — borrowed from conservation biology, where it means restoring species and ecological functions to an ecosystem. Applied to the human body, rewilding means deliberately nourishing microbial diversity and, where possible, helping restore it when it has been depleted.

Viome's Chief Science Officer, Momo Vuyisich, PhD, has spent years studying what that rebuilding process may look like in practice — both with nutritional and lifestyle actions. These practices are beneficial at all times, but especially after your gut has taken a hit, most commonly from antibiotics. His guidance gives the rewilding idea an actionable shape: the everyday habits that support your microbiome and a plan for helping it bounce back.

Why your microbiome needs protection

For most of human history, our bodies were in constant contact with dirt, animals, fermented foods, and each other's germs. We consumed fruits and vegetables coated with microorganisms. That contact wasn't an accident — it's part of how humans co-evolved with microbes and built a symbiotic relationship that supports all aspects of our health: physical, mental, cognitive, and immune.

Our dependence on the gut microbiome is so strong that we have human genes that make special carbohydrates in breast milk (human milk oligosaccharides, or HMOs) that feed specific gut microbes and help the baby develop. Approximately 20% of the carbohydrates in breast milk are HMOs, which the baby cannot digest directly. Instead, they feed the baby's gut microbiome. Our symbiosis with the microbiome starts at birth, and probably even before it.

Our microbiome is essential for our health — physical, mental, cognitive, and immune. A rich (diverse) microbiome contains a large variety of microbes that perform important functions, including protecting us from pathogens, feeding our cells, producing beneficial metabolites, and training our immune system. However, reducing this microbiome richness can lead to the loss of some of these benefits.

Many factors can disrupt the composition and diversity of our microbial communities, but antibiotics are among the most significant. While often lifesaving and medically necessary, antibiotics can deplete beneficial microorganisms alongside those responsible for infection. Research suggests that some changes in microbial composition may persist for months or longer, highlighting the importance of understanding how medications and other environmental factors influence the microbiome.

The underlying idea is that your microbiome isn't static. It's a very complex ecosystem that requires daily maintenance and sometimes rewilding. The bad news is that it's easy to damage, and the good news is that it can often recover.

Prioritizing habits that help maintain a diverse and balanced microbiome is an important part of overall wellness. Following significant gastrointestinal disturbances or antibiotic use, paying attention to dietary and lifestyle factors that support microbial health may be particularly valuable.

The three levers of maintaining and rewilding your microbiome

Whether you're maintaining your healthy microbiome, rebounding from a round of antibiotics, or just trying to undo years of over-sanitizing and eating junk food, the work breaks down into three parallel efforts:

1. Feed what you already have. Your microbes need fuel: fiber (prebiotics), plant antioxidants and polyphenols, amino acids (from proteins), and many other nutrients
2. Reintroduce beneficial microbes. New microbial exposure comes from fermented foods, probiotics, and more contact with the natural world. However, introducing microbes doesn't necessarily mean they will permanently colonize your gut; you have to feed them.
3. Stop unnecessarily disrupting your microbiome. Certain everyday habits and exposures may work directly against everything the first two levers are trying to build.

Lever 1: Feed what you already have

Fibers, polyphenols, and many other nutrients from a wide range of foods, mostly plants, help nourish your gut microbes. Polyphenols and other antioxidants are commonly found in colorful plants, such as carrots, tomatoes, beets, red onions, berries, etc. Fibers are the hard-to-digest carbohydrates found in many whole vegetables, fruits, and grains, as well as mushrooms. Even starchy foods such as rice, potatoes, and corn can provide important fibers (resistant starch).

Dietary diversity is one of the most important principles in gut health. Different microbial species thrive on different fuels, so the more varied your diet, the more opportunities you give a diverse and resilient microbial community to thrive.

Prioritize fiber and plant diversity

Fruits, vegetables, mushrooms, and whole grains contain prebiotic fibers that feed your gut microbiome. As they consume (ferment) these fibers, your microbes produce short-chain fatty acids like butyrate, propionate, and acetate — compounds that nourish your colon's lining, help regulate immune function, reduce inflammation, and support metabolism.

The target: Try to consume 20 different whole plant foods and mushrooms per week. This is a practical goal for encouraging dietary diversity, not a scientifically established minimum. Don't stress if you don't achieve this high bar. Just do the best you can.

Look for specific prebiotic sources

Foods particularly rich in important prebiotic fibers include:

• Onion family: onions, garlic, leeks…

• Root veggies: Jerusalem artichokes, beets, parsnips, jicama…

• Fruits: apples, pears, mangos, berries, bananas (especially slightly underripe)...

• Whole grains: wheat, oats, rye…

• Legumes: lentils, beans, chickpeas, soy beans (edamame and tempeh)

• Other vegetables: asparagus, artichokes, broccoli, Brussels sprouts, cabbage, cauliflower…

• Leafy greens: kale, spinach, mustard greens, collard greens…

• Mushrooms

Tip: Do not fall for wheat-based products with names such as "whole grain" or "21 grains" without checking the ingredients. Read the nutritional ingredients. The very first ingredient must be whole wheat, whole oats, or whole rye. The number of grains advertised on the package doesn't tell you how much whole grain the product actually contains.

Get enough fiber

Fiber has a target range. About 20-40 grams a day is a useful goal for many adults.

If you're starting from very little, ease in — increase your fiber intake gradually, by about 5 grams a day at a time, allowing several days or longer between increases depending on your tolerance. Some fibers can cause bloating and other unpleasant effects, especially when increased too quickly.

Viome customers can use their personalized food recommendations as a guide.

An easy way to consume much of your daily fiber is to eat overnight oats or granola with added oat and wheat bran most mornings. Combine that with modest portions of whole plants and mushrooms during the day, and you are set.

Polyphenols

Polyphenols are natural compounds found in plants that play an important role in supporting a healthy gut microbiome and your metabolism. Unlike many nutrients that are absorbed in the small intestine, a substantial portion of dietary polyphenols reaches the colon, where gut microbes break them down into smaller, biologically active compounds. This creates a mutually beneficial relationship: polyphenols can promote the growth and activity of beneficial microbes while influencing the production of microbial metabolites that support gut barrier function, healthy inflammatory responses, and contribute to overall health. Different polyphenols interact with different microbes, so eating a wide variety of colorful plant foods helps support a diverse and healthy gut microbiome.

Foods rich in polyphenols include:

• Berries: blueberries, blackberries, raspberries, strawberries, cranberries…

• Other fruits: pomegranates, grapes, cherries, plums, apples, citrus fruits…

• Vegetables: red onions, artichokes, broccoli, red cabbage, spinach…

• Nuts and seeds: walnuts, pecans, almonds, flaxseeds, chestnuts…

• Legumes: beans, lentils, soybeans

• Herbs and spices: cloves, cinnamon, oregano, rosemary, thyme, turmeric…

• Beverages: green tea, black tea, coffee…

• Other foods: extra virgin olive oil, dark chocolate, cocoa…

Recipe: High fiber, high polyphenol, and high protein breakfast

½ cup (approximately 50 g) rolled oats or granola (fiber and protein vary by product)

⅓ cup (40 g) oat bran (approximately 7 g of fiber, 7 g of protein)

½ cup (30 g) wheat bran (approximately 12 g of fiber, 4 g of protein)

A handful of walnuts

Berries of your choice

Yogurt (protein varies by type and serving size)

Lever 2: Reintroduce beneficial microbes

Fermented foods and probiotic supplements can introduce new microbial strains into your gut. This may be particularly relevant following antibiotics use, which can alter microbial populations. However, most of them also require prebiotics to colonize and provide health benefits.

Eat fermented foods regularly

Traditionally fermented foods — sauerkraut, kimchi, kefir, plain yogurt, natto, and kombucha deliver live bacterial and yeast cultures. Look for products labeled as containing "live and active cultures." Pasteurization or cooking after fermentation can kill live microorganisms, although some beneficial fermentation products may remain. Yogurt made from pasteurized milk can still contain live cultures added during production.

Consider probiotic supplements

Bifidobacteria and Lactobacilli are among the most widely studied probiotics. Research has explored various probiotic species and strains in the context of digestive health and the period following antibiotic use.* However, evidence regarding the optimal timing of probiotic consumption relative to antibiotic therapy remains mixed. Some approaches suggest waiting 1–2 weeks after completing antibiotics before introducing probiotics, although current evidence is insufficient to establish a definitive recommendation. Further research is needed to better understand the relationship between probiotic timing and microbial recovery.

Different strains offer different benefits, and research supports several in particular:

• Bacillus subtilis and Bacillus coagulans — spore-forming bacteria that are highly resistant to stomach acid, allowing more of them to reach the gut alive.* Their clinical benefits depend on the specific strain and formulation.

• Bifidobacterium breve and Bifidobacterium longum — common gut residents linked to digestive comfort and immune support.*

• Bifidobacterium longum strain infantis - a particularly important probiotic in early childhood development of the immune system.* This strain naturally consumes human milk oligosaccharides.

• Lactobacillus plantarum (now called Lactiplantibacillus plantarum) — a versatile species found naturally in fermented vegetables and used in certain probiotic products.

• Saccharomyces boulardii — a beneficial yeast, rather than a bacterium, that has been studied for its role in digestive health and the ability to reduce antibiotic-associated diarrhea.*

• Akkermansia muciniphila - shown to positively impact metabolic health, whether in live or dead form.* Also produces acetate and propionate.*

Butyrate producers*:

• Faecalibacterium prausnitzii

• Roseburia intestinalis

• Anaerostipes caccae

• Clostridium butyricum

• Many others

People with compromised immune systems or serious underlying illnesses should consult their healthcare professional before taking live probiotic supplements.

Reintroduction goes beyond diet and supplements

Our environment is a great source of microorganisms.

Spending time outdoors, gardening, and being around animals can increase our exposure to environmental microbes. This kind of "rewilding" is an emerging and still under-researched idea. You can simply spend more time outdoors and in contact with soil and nature, while maintaining normal food safety and hand hygiene.

Lever 3: Stop unnecessarily disrupting your microbiome

Feeding your microbiome well works best if you're not simultaneously undermining it. Some exposures can disrupt microbial communities or hinder their return to balance, whether or not you've recently taken antibiotics.

These include:

• Unnecessary antibiotic use

• Excessive alcohol consumption

• Ultra-processed foods

• Food preservatives (such as benzoates and sorbates) and emulsifiers (such as polysorbates)

• Pesticides

• Unnecessary use of antiseptic mouthwash, which can affect beneficial oral microbes

• Excessive use of antibacterial products when ordinary hygiene is sufficient

Use antibiotics only when truly necessary

Antibiotics are sometimes lifesaving, but many don't distinguish between harmful and beneficial bacteria — a single course can dramatically reduce microbial diversity, sometimes permanently. Reserve them for situations where they are medically indicated, including confirmed or strongly suspected bacterial infections and certain preventive uses. Talk to your doctor about whether a prescription is truly necessary versus precautionary, especially when symptoms may be caused by a viral illness.

Look for food additives

Emulsifiers: Common emulsifiers like carboxymethylcellulose and polysorbate-80 have been linked in experimental research to disruption of the gut's protective mucus layer and shifts toward more inflammatory bacterial populations.

Preservatives: Preservatives such as benzoates and sorbates are used in many packaged foods to inhibit microbial growth and extend shelf life. Some have demonstrated negative effects on microorganisms.

One of the worst uses of preservatives is in fermented foods. There are brands of sauerkraut that, instead of enriching your microbiome with live microorganisms, actually deplete your microbiome due to the added preservatives.

Artificial sweeteners: Sweeteners such as sucralose, saccharin, and aspartame have been shown in some studies to alter gut bacterial composition and, in certain circumstances, influence glucose tolerance. If you consume large amounts of artificially sweetened foods and beverages, reducing your intake may be worth considering.

Pesticides: If you consume the outer layer of fruits and vegetables, choosing organic produce when possible can reduce exposure to certain pesticide residues. Conventionally grown produce can carry pesticide residues, and some pesticides have been shown in experimental studies to affect microorganisms.

Reconsider antiseptic mouthwash use

Some antiseptic mouthwashes reduce the oral bacterial population broadly — including species that play a beneficial role in health and the production of nitric oxide, a molecule involved in cardiovascular regulation.

Rewilding is a practice, not a one-time fix

The through-line here is simple: your microbiome isn't something you fix once and move on from. It responds, continuously, to what you eat, how you clean your home and body, and how much contact you have with the natural world.

A healthy microbiome isn't built overnight, and it isn't necessarily destroyed overnight either — it responds to the sum of your daily choices. Feed it a wide variety of plants, introduce live cultures through fermented foods and selected probiotics when appropriate, and reduce unnecessary chemical and antimicrobial exposures that may disrupt it.

Antibiotics are sometimes necessary and can be lifesaving — but treating gut recovery as a deliberate, food-first practice afterward, rather than an afterthought, may help support the recovery process.

Spending more time in nature and eating a lot more plants isn't a lifestyle fad — it's closer to how humans lived for most of history, before modern life changed our relationship with microbes.

The most important strategy is to protect and nourish the microbiome you already have. Do this consistently, and your microbiome often has a remarkable capacity to recover — even after a disruptive event like a course of antibiotics.