Your Post-antibiotic Recovery Plan: Diet, Supplement and Lifestyle Changes to Make

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    Taking antibiotics can negatively impact your gut microbiome. We'll discuss which dietary and lifestyle changes to focus on to restore your microbiome.

    What is the gut microbiome?

    The gut microbiome is all of the bacteria residing in the digestive tract that carry out various functions for the body overall. These bacteria act like an ecosystem that helps the body with nutrient absorption, digestion, immune function, and several other systems. Since the bacteria work as a team in a synergistic relationship with your gut, they must be in proper balance to enable a healthy gut. If the natural balance of bacteria in the microbiome gets thrown out of balance, the gut can become irritated & dysfunctional.

    Good bacteria versus bad bacteria

    While “bacteria” can have a bad reputation, not all bacteria are bad. In fact, the human body has an estimated 100 trillion good bacteria, many of which live in the gut.

    Good bacteria are researched beneficial strains of bacteria that help our bodies carry out various essential functions. For example, good bacteria use the food we consume to produce several key vitamins in our gut, like vitamin K2.

    Probiotic bacteria are those that naturally already live in the human gut and provide benefits to the gut. Some beneficial species of bacteria include Lactobacillus and Bifidobacterium.

    “Bad” bacteria may refer to bacteria that cause negative effects when present in any amount or others that may be disruptive when present in amounts larger than normal.

    Gut bacteria’s influence on immune health

    In addition to supporting digestive health, probiotic bacteria have also been studied for their effect on the immune system. A balance of healthy gut bacteria can provide optimal immune support by promoting cells of the innate and adaptive immune system such as toll-like receptors, dendritic cells, lymphocytes, and macrophages.

    On the other hand, disruptions in gut bacterial balance, caused by antibiotic treatments or improper diet, can impact immune function.

    What are antibiotics?

    Antibiotics are prescribed medications for various health issues that involve bacterial overgrowth. These medications have proven to be life-saving in many ways. In recent years, however, there is increased understanding of the potential side effects of antibiotics especially relating to the gut microbiome.

    Effects of antibiotics on your gut microbiome

    Antibiotics can negatively disrupt the balance of good bacteria in the gut microbiome. These negative effects include:

    • A decrease in gut bacterial species diversity
    • Altered metabolic activity
    • Potential for increase in antibiotic-resistant microbes
    • Potential for increased susceptibility to yeast imbalances

    Common side effects from antibiotics

    Some common side effects of antibiotics include digestive symptoms such as nausea and changes in bowel movements. Some of these side effects can be avoided when taking antibiotics with some food.

    Other side effects may include rash or yeast imbalances. Side effects can range from minor to severe health problems. Be sure to talk with your doctor if you develop any side effects or allergic reactions while taking an antibiotic, and only take antibiotics exactly as prescribed.

    Restoring your gut microbiome

    In the event that you need to take antibiotics, you can take simple steps to help restore your gut microbiome through dietary and lifestyle changes.


    Adjusting what you eat can have a profound impact on your gut microbiome and help restore your gut after antibiotic treatment.

    Eat fiber-rich foods

    Research shows that diets deficient in fiber can worsen the reduced microbial diversity that often occurs with antibiotic use and cause delays in recovery.

    Foods rich in fiber include vegetables, fruits, nuts, seeds, whole grains, and legumes like lentils and beans. Some may experience digestive upset when consuming a lot of fiber after antibiotic treatment, so gradually increasing fiber in the diet over several days may be helpful.

    Eat fermented foods

    Fermented foods contain beneficial microbes that alter the food through the process of fermentation. This fermentation process often results in the production of healthy metabolites like enzymes and nutrients.

    In a 10 week clinical trial with 36 adults, Stanford researchers found that eating a diet rich in fermented foods increases gut microbial diversity.

    Fermented foods include fermented dairy, like yogurt and kefir, as well as sauerkraut, kimchi, kombucha, miso, and others.

    Eat foods high in collagen

    Collagen is a type of protein found in skin, muscles, bones, and connective tissues that provides the structure and strength of these body parts. Collagen supplements come from animal or marine sources and may help to promote collagen function in our own bodies.

    One study found that incorporating collagen into the diet can promote healthy digestive function in healthy women. The participants took 20 grams of collagen peptide supplement daily, in two split doses, and 93% of the women experienced reduction in digestive symptoms, including bloating.

    Collagen is a rich source of the amino acid glycine, which is essential for production of the antioxidant glutathione, which can help manage oxidative stress. During disruptions to the intestines, like during the use of antibiotics, collagen may help to support the health of the gut lining.


    Among the most highly touted supplements on the market for digestive support, probiotics provide beneficial effects on the composition and function of the intestinal microbiome.

    Our Care/of Probiotic Blend supplement combines three highly studied probiotic strains: Bifidobacterium lactis (BB-12), Lactobacillus rhamnosus GG, and Lactobacillus acidophilus (LA-5). They have been shown to help colonize the gut with helpful bacteria in order to support a healthy digestive system.

    Particularly, Lactobacillus strains can enhance the strength and function of the intestinal barrier, the protective lining along the gastrointestinal tract.

    Certain strains of probiotic bacteria can help manage loose stools that often occur with antibiotic use. A meta-analysis of 82 randomized control trials found that probiotic use was associated with a reduction in antibiotic-associated diarrhea.

    Probiotic supplements can be taken during & after antibiotic treatment to help restore the microbiome. However, be sure to take probiotic supplements and antibiotic medications several hours apart.


    Prebiotics are special types of fibers and other compounds in certain plant foods that serve as food for good bacteria to grow.

    Healthy gut bacteria can create peptides called bacteriocins to manage competition with unhealthy microbes. Prebiotics is a promising way to promote the growth of healthy gut bacteria to strengthen the environment of the gut microbiome.

    Foods and supplements containing prebiotics can help ease bloating, balance good bacteria in the gut, promote healthy bowel movements, and allow probiotics to work more effectively.

    Prebiotics are naturally found in many plant foods high in fiber as well as rich in polyphenols. Some examples of prebiotic foods and supplements include garlic, apples, oats, mushrooms, and chicory root.

    A healthy lifestyle

    Healthy lifestyle factors including stress management and reduction, getting enough sleep, and regular physical activity are all known to support a healthy gut.

    Aim to reduce and manage occasional stress. High levels of stress can promote disruptions in gut bacterial balance through alterations in stress hormones, immune system, and the nervous system response.

    Get adequate sleep each night. Healthy amounts of sleep are associated with microbial diversity and a stronger immune system. Research indicates the connections between gut microbiome health and sleep includes changes in the immune system and cognition.

    Be active regularly. Research suggests that exercise leads to beneficial effects on the gut microbiome. Exercise can enhance healthy levels of gut bacteria and enrich microbial diversity.

    How long would it take to restore gut flora after taking antibiotics

    Currently no specific standard timeline exists to predict when the gut microbiome will be restored after taking antibiotics. In general, however, most studies report that it can take about three months, but can be less or more depending on lifestyle, diet, duration of antibiotic use and use of other medications.

    Final takeaways

    Antibiotics can provide important support for certain bacterial overgrowths. However, they may cause unwanted side effects and changes to the gut microbiome. You can help restore your gut microbiome through diet and lifestyle changes. Foods and supplements containing probiotics, prebiotics, and collagen can restore gut bacterial balance and strengthen the gastrointestinal tract. In addition to diet, lifestyle support like reducing stress, getting adequate sleep, and regular physical activity can further promote gut microbiome restoration and should be included in your post-antibiotic recovery plan.

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    Dr. Carla Montrond Correia ND, CNS
    Medical Content Manager
    Dr. Montrond-Correia is a licensed naturopathic physician and a certified nutrition specialist (CNS). She holds degrees from University of Bridgeport, Georgetown University, and University of Saint Joseph, and supplemented her education with internships in the health and wellness space. She's focused on research, herbal medicine, nutrigenomics, and integrative and functional medicine. She makes time for exercise, artistic activities, and enjoying delicious food.
    Our Editorial Staff
    Freelance Contributor
    The Care/of Editorial Team is made up of writers, experts, and health enthusiasts, all dedicated to giving you the information you need today. Our team is here to answer your biggest wellness questions, read the studies for you, and introduce you to your new favorite product, staying up to date on the latest research, trends, and science. Each article is written by one of our experts, reviewed both for editorial standards by an editor and medical standards by one of our naturopathic doctors, and updated regularly as new information becomes available.