Learn 8 science-backed ways to bounce back after antibiotics—diet, fermented foods, HMOs, smart probiotic timing, and more.
Content Outline
1. Finish your course and give it time
2. Diversify your diet with a variety of fiber
5. Seed your gut with beneficial bacterial strains
6. Consider human milk oligosaccharides for targeted bifidogeneic support
What are antibiotics?
Antibiotics are a type of powerful medication given to clear bacterial infections. They work by killing bacteria or stopping them from growing or multiplying, sometimes by interfering with their DNA, their cell walls, or protein synthesis. Several types of antibiotics are available, including:
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broad spectrum – effective against a wide range of bacteria, including gram-positive and gram-negative types, such as tetracyclines and fluoroquinolones, but can wipe out both good and bad bacteria [1]
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narrow spectrum – effective against specific types of bacteria and has a less damaging effect on the body’s beneficial bacteria by only targeting those responsible for causing an infection [2]
Why recovery matters after antibiotics
Antibiotics are an essential part of the medical toolkit, but they can reduce the abundance and diversity of beneficial gut microbes for months, especially after repeated or broad-spectrum courses. A less diverse microbiome can have several negative consequences, including diarrhoea, temporary food intolerances, and even a greater chance of stomach upset due to dysbiosis, or an imbalanced gut microbiota [3].
Antibiotic-induced dysbiosis can last for years and even leave you susceptible to chronic conditions, such as obesity, asthma, allergies, and metabolic changes [4]. Some people may also never fully recover without the help of therapies, including probiotics, prebiotics, and synbiotics.
What disruption looks like
8 ways to recover from antibiotics
If you have ever had antibiotics, either recently or in the past, and you’ve never thought about rebuilding or resetting your gut microbiome, now is a great time to do it. Rebuilding your good bacteria colonies not only restores balance but also helps to reduce or prevent digestive issues, like diarrhoea, and strengthens your gut to deal with invading pathogens, so there’s less chance of you getting sick.
Here, we look at 8 easy but scientifically backed ways to help boost your gut microbiota after antibiotics.
1. Finish your course and give it time
It’s essential that you complete the antibiotic course you have been given exactly as it has been prescribed. If you don’t, then there is a risk that the infection will come back, and you may need further antibiotic courses, which will disrupt your microbiome further
The disruptive effects of antibiotics in the gut can last for up to 2 years [5]. So, it is essential that you only take antibiotics when necessary, take them for as long as they have been prescribed, and then give your gut time to recover.
2. Diversify your diet with a variety of fiber
Fiber is the microbiome’s fuel because, although it cannot be digested by your body, your gut bacteria can break it down to help stimulate their growth and activity levels. Research suggests that individuals who consume more soluble fiber have fewer antibiotic-resistant genes compared to those who consume less [6].
Alongside fiber, resistant starch is also essential for boosting short-chain fatty acid (SCFA) production, particularly butyrate, which supports gut barrier integrity. These factors are important for rebuilding your microbiome, especially after antibiotics [7].
3. Fermented foods daily
Fermented foods naturally contain healthy bacterial species, such as Lactobacilli, which help to restore the gut microbiota following antibiotic use. They also have numerous other health benefits, including a reduced risk of heart disease, type 2 diabetes, and obesity [8].
Incorporating fermented foods into your daily diet can help rebuild and bolster your colonic ecosystem following antibiotics by repopulating health-promoting bacteria, improving microbial diversity and supporting your wider gut health. Examples of fermented foods include:
4. Take probiotics
Probiotics are live cultures or “good” bacteria that provide health benefits when consumed in large enough quantities. They are found in some fermented foods, like yoghurt, but are also available in supplement form. Probiotics help to maintain a healthy balance of microbes in your gut, and can improve digestion and support immune function [9].
A recent study found that daily supplementation of a combination of Bifidobacteria, Lactobacilli, and Saccharomyces boulardii for 10 days alongside antibiotic use successfully reduced antibiotic-associated disturbances. This was because the antibiotics protected against diversity loss and lowered the antibiotic-resistance capacity in the re-growth population [10].
5. Seed your gut with beneficial bacterial strains
When restoring your gut microbiome after antibiotics, it’s important not only to add probiotics but also to “seed” your gut with specific strains and prebiotics that are known to effectively recolonize and promote health. Research shows that certain species and strains, such as Bifidobacterium longum, Bifidobacterium breve, Lactobacillus rhamnosus, and Saccharomyces boulardii, are more resilient and can help re-establish balance following antibiotic use.
A further study found that three Lactobacillus strains—L. plantarum, L. casei, and L. rhamnosus —are able to restore antibiotic-induced alterations in the microbiome and metabolic profile in mice.
These bacterial strains help reinforce the gut barrier, support immune modulation, and improve the production of short-chain fatty acids (SCFAs) that nourish your gut lining. Alongside this, you should focus on a diverse diet rich in prebiotic and fermented foods to nourish beneficial bacteria and encourage their growth and activity.
Some of the dietary strategies you should follow to help seed your gut include:
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Plant-based, high-fiber foods, such as onions, garlic, leeks, bananas, apples, oats, asparagus, wholegrains, and legumes
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Increase your intake of fermented foods, like kefir, kimchi, yogurt, sauerkraut, and kombucha
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Choose polyphenol-rich foods, including berries, dark chocolate, nuts, seeds, and green tea
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Select scientifically-backed prebiotic supplements, particularly human milk oligosaccharides (HMOs)
6. Consider human milk oligosaccharides for targeted bifidogeneic support
Human milk oligosaccharides (HMOs), like 2’-fucosyllactose (2’-FL) and Lacto-N-neotetraose (LNnT), are unique, non-digestible carbohydrates that are naturally present in human milk. They act as prebiotic sources, feeding the beneficial gut species, particularly Bifidobacteria, to increase the abundance and diversity of the microbiome.
A 2016 study found that supplementation of 2’-FL and/or LNnT promoted the growth of Bifidobacteria, improved the diversity of the microbiota, and could be a valuable tool for restoring balance in an imbalanced gut [11]. In older adults, HMO supplementation increased Bifidobacterium levels, high-density lipoprotein (HDL) or good cholesterol, and blood insulin levels, suggesting that HMOs could promote healthy aging. This is interesting because older adults in nursing homes are frequently prescribed antibiotics [12].
Although post-antibiotic clinical trials involving HMOs are limited, these prebiotic supplements benefit in supporting the integrity of the gut barrier and the ability to support the abundance and function of beneficial species, such as Bifidobacteria, make them a promising and gentle option in the recovery period following antibiotic use.
7. Eat prebiotic foods
While fiber feeds many gut microbes, it’s not the only way to keep them nourished. Prebiotics are components in certain foods that your body cannot digest, and instead, they feed your good gut bacteria [13].
Prebiotic-rich foods include:
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onions
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garlic
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leeks
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asparagus
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Jerusalem artichokes
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bananas
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oats
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legumes
Penumutchu and colleagues found that prebiotic fibers can reduce the impact of antibiotic treatment on the gut microbiome composition and function [14]. Therefore, through their ability to modulate the gut microbiota, prebiotics could be a potential therapeutic option for protecting beneficial microbes during antibiotic treatment [15].
8. Move your body
Exercise is a great way to boost microbial diversity and SCFA production. A review by Koutouratsas et al., suggested that physical activity positively altered the microbiome composition in such a way that it was partially corrective for those with inflammatory bowel disease [16]. For this reason, exercise could be a great way to bolster the colonic ecosystem following antibiotic treatment. More recent research in animals has found that moderate exercise can reduce the colonization of pathogens, such as MRSA [17].
Ideally, you should aim to complete at least 150 minutes of moderate intensity exercise each week. Good activities include:
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brisk walking
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cycling
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swimming
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dancing
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team sports
Key takeaway
Antibiotics are an important treatment option if you have a bacterial infection, and in the worst cases, can be life-saving. However, they can reset your gut microbiome, leaving you susceptible to dysbiosis and illness. So, if you have ever had antibiotics and have never reset your gut, or you are currently treating a bacterial infection, you should focus on eating plenty of fiber and prebiotic-rich foods.
Adding fermented foods, taking probiotics, and supplementing your diet with HMOs can all help to seed, build, and bolster your microbiome. Combining these strategies with nutritious whole foods, rest, and movement, your ecosystem will naturally and gradually regain its balance.
Written by: Leanne Edermaniger, M.Sc. Leanne is a professional science writer who specializes in human health and enjoys writing about all things related to the gut microbiome.
