While antibiotics can be a lifesaving and necessary medical intervention when used appropriately, they are known to affect the diversity and abundance of a healthy gut microbiome. The gut microbiome serves many functions in the human body; disruptions can affect intestinal and systemic health, leading to a wide array of effects and symptoms. Dietary and supplemental interventions during and after antibiotic therapy may help support gut health and function.
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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, an imbalance may ensue.
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 target 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 may affect beneficial gut microbes and disturb the composition of the gut microbiome. The resulting imbalance can have many downstream effects. (1)
As the number of beneficial bacteria in the gut decreases, it creates space for other opportunistic organisms to grow within the intestines. 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 imbalance, these bacteria can migrate into and colonize the small intestine. (2)
Signs & Symptoms of Changes in Gut Health Following Antibiotic Treatment
Imbalances associated with antibiotic treatment may cause many gastrointestinal and extraintestinal symptoms related to the imbalance between beneficial and harmful bacteria. Disturbances in the gut microbiome have been linked to various health conditions. (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, imbalances can stimulate pro-inflammatory responses. Therefore, symptoms outside of the digestive tract can occur secondary to intestinal 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 imbalances so that personalized plans can be developed to address the imbalances.
Comprehensive Stool Test
A comprehensive stool test is a way to analyze the gut microbiome. Through culture and PCR testing methods, a comprehensive stool test can identify intestinal patterns so that appropriate therapies can be considered to address the imbalance. 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-supportive recommendations.
SIBO Breath Test
Antibiotic use and intestinal changes 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 patterns and nutritional considerations that can support intestinal health.
Intestinal Permeability
Imbalances may affect intestinal permeability. This can be assessed with a blood test that measures immune proteins indicative of intestinal changes and fecal zonulin, the only known protein that reversibly regulates the tight junction spaces between intestinal epithelial cells.
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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 may help support the diversity and abundance of the gut microbiome. Functional medicine doctors often recommend a 5-R Approach to supporting gut health, which entails removing offenders, replacing nutrients and enzymes, reinoculating the microbiome, and supporting the gut lining. Specialty lab results guide doctors and patients in knowing precisely what interventions are indicated to customize support 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 affect intestinal health. A short-term elimination diet of these triggering foods for 2-6 weeks may support intestinal health. (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 may support the gut healing process and help manage imbalances.
Probiotics
Research has indicated that it can take up to six months for the microbiome to recover after a course of antibiotics. Probiotics may help reinoculate the large intestine with healthy bacterial strains. Supplementing probiotics during and after antibiotic treatment may support antibiotic treatment and help manage imbalances caused by antibiotics. (5, 6)
Ginger
Ginger is antioxidant, anti-inflammatory, and supports gastrointestinal motility. Ginger is also commonly used to help manage many gastrointestinal side effects of antibiotics, including gas, bloating, abdominal pain, and nausea. (7)
L-Glutamine
L-glutamine is an amino acid and the preferred fuel source of cells lining the small intestine. Supplemental L-glutamine's potential to support intestinal barrier function and improve gastrointestinal symptoms is supported by a large body of evidence. (8-10)
Butyrate
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 supporting healthy immune responses and reducing intestinal inflammation.
Oregano
Oregano is a broadly antimicrobial herb that may help manage pathogenic and opportunistic organisms. While effective against bacterial, viral, and fungal organisms, research has shown that oregano supplementation does not reduce healthy Lactobacillus and Bifidobacterium bacteria concentrations in the gut microbiome. (11)
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Summary
Antibiotics are a well-known factor that can affect the balance of microbes in the human microbiome. Functional medicine labs can help identify patterns so that appropriate interventions can be considered to support balance. Dietary choices and various natural supplements may aid in supporting the gut microbiome and overall health.
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