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4 Functional Medicine Labs to Help Support The Gut Following Antibiotic Treatment

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4 Functional Medicine Labs to Help Support The Gut Following Antibiotic Treatment

While antibiotics can be a lifesaving and necessary medical intervention when used appropriately, they are known to disrupt the diversity and abundance of a healthy gut microbiome. The gut microbiome serves many functions in the human body; dysbiosis can cause disruptions in intestinal and systemic health, leading to a wide array of adverse effects and symptoms. Dietary and supplemental interventions during and after antibiotic therapy can prevent the negative consequences of antibiotic use and preserve gut health and function.


What is the Gut Microbiome?

The intestinal microbiome is the collective group of commensal microorganisms (bacteria, fungi, and viruses) in the large intestine. The gut microbiome begins to form in utero and consists of trillions of microorganisms, predominantly bacteria. Thousands of bacterial species comprise the gut microbiome, each playing a different role in human health and physiology.

A healthy microbiome is responsible for many important physiologic and biological human processes, including digestion, gut barrier function, vitamin and neurotransmitter synthesis, and immune function and regulation. If a disturbance in the balance of beneficial and harmful bacteria occurs within the microbiome due to infection, medications, or lifestyle factors, dysbiosis ensues.

How Do Antibiotics Affect the Gut Microbiome?

The most frequently prescribed class of medication for infectious diseases is antibiotics. Broad-spectrum antibiotics have one job: to kill bacteria. While they primarily target the pathogenic bacteria responsible for the infection, they can't differentiate between the good and bad bacteria in the body. Therefore, when antibiotics enter the system, they inherently will kill beneficial gut microbes and disturb the composition of the gut microbiome. The resulting dysbiosis can have many downstream effects. (1)

As the number of beneficial bacteria in the gut decreases, it creates space for other opportunistic organisms to overgrow within the intestines, causing infection. Fungal overgrowth and Clostridioides difficile infection are possible side effects of antibiotic use.

Another potential consequence of antibiotic use, especially with repeat courses, is small intestinal bacterial overgrowth (SIBO). If certain species of bacteria begin to overgrow in the large intestine as a consequence of dysbiosis, these bacteria can migrate into and colonize the small intestine. (2)

Signs & Symptoms of Poor Gut Health Following Antibiotic Treatment

Dysbiosis associated with antibiotic treatment causes many gastrointestinal and extraintestinal symptoms related to the imbalance between beneficial and harmful bacteria and resulting leaky gut. Disturbances in the gut microbiome have been linked to the development of metabolic diseases, dermatologic conditions, autoimmune diseases, inflammatory bowel disease (IBD), and irritable bowel syndrome (IBS). (1, 3)

Common gastrointestinal symptoms that may occur during or after antibiotic use include (3):

  • Changes in bowel movements: constipation, diarrhea, or both
  • Bloating and abdominal distension
  • Belching and flatulence
  • Abdominal pain and cramping
  • Bad breath (halitosis)
  • Heartburn and acid reflux
  • Nausea and vomiting
  • Food intolerances
  • Mucus in the stool

Because most of the immune system is housed in the gut, dysbiosis can stimulate pro-inflammatory responses and promote the loss of self-tolerance. Immune dysregulation significantly increases intestinal permeability, systemic inflammation, and autoimmunity. Therefore, symptoms outside of the digestive tract can occur secondary to intestinal dysbiotic patterns, including:

  • Fatigue
  • Muscle and joint pain
  • Brain fog, difficult concentration, and poor memory
  • Change in mood: anxiety, depression, irritability
  • Skin rashes: acne, eczema, psoriasis

Functional Medicine Labs to Help Support The Gut Following Antibiotic Treatment

Functional medicine labs can be helpful for patients planning to take or experiencing symptoms after completing a course of antibiotics. These labs can analyze the composition of the gut microbiome and integrity of the intestinal barrier to identify dysbiosis, infection, and intestinal permeability so that personalized treatment plans can be prescribed to correct the imbalances.

Comprehensive Stool Test

A comprehensive stool test is the best way to analyze the gut microbiome. Through culture and PCR testing methods, a comprehensive stool test can diagnose pathogenic intestinal infections (bacterial, fungal, viral, and parasitic) and large intestinal dysbiotic patterns so that appropriate antimicrobial and probiotic therapies can be implemented to remedy the dysbiosis. This intestinal assessment also goes beyond the microbiome to screen for intestinal inflammation, immune function, maldigestion, and imbalances in microbiome metabolites. These results guide specific gut-healing treatment recommendations.

SIBO Breath Test

Antibiotic use and intestinal infections can contribute to the development of SIBO. Ruling out SIBO with a breath test can benefit patients, especially those with lingering gastrointestinal symptoms after discontinuing antibiotics.

Organic Acid Testing

An organic acid test (OAT) measures metabolic byproducts of human, bacterial, and fungal biochemical processes. These results can indicate intestinal dysbiotic patterns and nutritional deficiencies that can inhibit intestinal healing.

Intestinal Permeability

Dysbiosis causes increased intestinal permeability (leaky gut). Leaky gut can be quantified with a blood test that measures immune proteins indicative of intestinal damage and fecal zonulin, the only known protein that reversibly regulates the tight junction spaces between intestinal epithelial cells.


Ways Functional Medicine Can Help Support The Gut After Antibiotic Treatment

Functional medicine doctors recognize the importance of a healthy gut in maintaining overall health. As such, they understand that proactively implementing dietary and supplemental interventions during and after antibiotic treatment can restore the diversity and abundance of the gut microbiome to prevent secondary infections, repair the gut lining, and prevent downstream (unintentional) consequences of antibiotic use. Functional medicine doctors often recommend a 5-R Approach to healing leaky gut, which entails removing offenders, replacing nutrients and enzymes, reinoculating the microbiome, and repairing the gut lining. Specialty lab results guide doctors and patients in knowing precisely what interventions are indicated to customize treatment to each body's functional and cellular needs.

Nutrition and Dietary Considerations Following Antibiotic Treatment

The intake of inflammatory foods, such as refined sugars, alcohol, fried and processed foods, and common food allergens (i.e., gluten and dairy) can exacerbate intestinal inflammation and permeability. A short-term elimination diet of these triggering foods for 2-6 weeks can support intestinal healing and decrease gastrointestinal dysbiotic symptoms. (4)

Although removing food triggers can be important, what you eat is equally, or perhaps more, important in supporting gut function. Emphasizing the intake of fermented, prebiotic, and high-fiber foods promotes healthy bowel movements while also supporting the gut microbiome by reinoculating the large intestine with beneficial bacteria and feeding them with the appropriate nutrients. (4)

Examples of Fermented Foods

  • Kefir
  • Kombucha
  • Sauerkraut
  • Kimchi
  • Pickled vegetables
  • Miso
  • Tempeh
  • Natto
  • Sourdough bread

Examples of Prebiotic Foods

  • Legumes
  • Garlic
  • Onion
  • Under-ripe bananas
  • Jerusalem artichokes
  • Chicory
  • Tomatoes
  • Whole grains
  • Raw honey

Examples of High-Fiber Foods

  • Whole fruits and vegetables
  • Beans
  • Nuts
  • Seeds
  • Whole grains

Best Supplements and Herbs That Support Gut Health After Taking Antibiotics

Many dietary and herbal supplements can accelerate the gut healing process and correct dysbiotic patterns.


Research has indicated that it can take up to six months for the microbiome to recover after a course of antibiotics. Probiotics reinoculate the large intestine with healthy bacterial strains to expedite recovery. Supplementing probiotics during and after antibiotic treatment can make antibiotic treatment more effective, prevent secondary opportunistic infections, and correct dysbiosis caused by antibiotics. (5, 6)


Ginger is antioxidant, anti-inflammatory, and supports gastrointestinal motility. Ginger is also commonly used to symptomatically treat many gastrointestinal side effects of antibiotics, including gas, bloating, abdominal pain, and nausea. (7)


L-glutamine is an amino acid and the preferred fuel source of cells lining the small intestine. Supplemental L-glutamine's ability to restore intestinal barrier function, heal inflammatory gut lesions, and improve gastrointestinal symptoms is supported by a large body of evidence. (8-10)


Butyrate is a short-chain fatty acid, a type of postbiotic that is the primary fuel source for the cells lining the large intestine. Butyrate plays many roles in maintaining a healthy large intestine, including regulating healthy immune responses, reducing intestinal inflammation, stimulating intestinal mucus secretions, and improving gastrointestinal symptoms.


Oregano is a broadly antimicrobial herb that can treat pathogenic and opportunistic infections resulting from antibiotic use. While effective against bacterial, viral, and fungal infections, research has shown that oregano supplementation does not reduce healthy Lactobacillus and Bifidobacterium bacteria concentrations in the gut microbiome. (11)



Antibiotics are a well-known cause of dysbiosis, an imbalance in the healthy balance of microbes in the human microbiome. Functional medicine labs can diagnose and quantify dysbiotic patterns so that appropriate interventions can be implemented to correct the imbalance. Dietary choices and various natural supplements can aid in quickly restoring balance to the gut microbiome, preventing the adverse sequelae of antibiotic use and supporting optimal health.

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1. Kesavelu, D., & Jog, P. (2023). Current understanding of antibiotic-associated dysbiosis and approaches for its management. Therapeutic Advances in Infectious Disease, 10, 204993612311544.

2. Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small Intestinal Bacterial Overgrowth. Gastroenterology & Hepatology, 3(2), 112–122.

3. Maholy, N. (2023b, February 7). How to Create a Gut Healthy Nutrition Meal Plan. Rupa Health.

4. How To Start The Microbiome Diet To Support Your Gut Microbiome. (2023, January 4). Rupa Health.

5. García-Collinot, G., Madrigal-Bujaidar, E., Martínez-Bencomo, M.A., et al. (2020). Effectiveness of Saccharomyces boulardii and Metronidazole for Small Intestinal Bacterial Overgrowth in Systemic Sclerosis. Digestive Diseases and Sciences, 65(4), 1134–1143.

6. Fernández-Alonso, M., Camorlinga, A.A., Messiah, S.E., et al. (2022). Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review. Journal of Medical Microbiology, 71(11).

7. Ginger Benefits. (2022, November 1). Johns Hopkins Medicine.

8. Shu, X., Yu, T., Kang, K., et al. (2016). Effects of glutamine on markers of intestinal inflammatory response and mucosal permeability in abdominal surgery patients: A meta-analysis. Experimental and Therapeutic Medicine, 12(6), 3499–3506.

9. Kim, M., & Kim, H. (2017). The Roles of Glutamine in the Intestine and Its Implication in Intestinal Diseases. International Journal of Molecular Sciences, 18(5), 1051.

10. Zhou, Q., Verne, M., Fields, J.Z., et al. (2019). Randomised placebo-controlled trial of dietary glutamine supplements for postinfectious irritable bowel syndrome. Gut, 68(6), 996–1002.

11. Si, W., Gong, J., Tsao, R., et al. (2006). Antimicrobial activity of essential oils and structurally related synthetic food additives towards selected pathogenic and beneficial gut bacteria. Journal of Applied Microbiology, 100(2), 296–305.

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