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The Gut Microbiome and Antibiotics


The gut microbiome can influence certain diseases and conditions, including allergies, inflammatory bowel disease, and even some mental health disorders.

What is the gut microbiome?
The gut microbiome refers to the collection of microorganisms, including bacteria, viruses, fungi, and other microbes, that live in our digestive tract, primarily in the large intestine
(1). The bacteria in our body are incredibly diverse and are approximately equal to the number of cells we have in our body (2). The gut microbes play a crucial role in maintaining our overall health and well-being. They help us digest food, produce essential nutrients, regulate our immune system, and protect against harmful pathogens.

Although the microbiome contains a lot of organisms that we often think of as dangerous, the vast majority of these microbes are working together with us in a mutualistic relationship, meaning we benefit from their presence, and they benefit from us as well. They assist in breaking down complex carbohydrates, fiber, and other substances that our bodies cannot digest on their own, producing short-chain fatty acids and other byproducts that have important downstream effects on our health.

Furthermore, the gut microbiome influences our immune system. It helps develop our immune cells, ensuring they can respond to pathogens, and distinguish between what is harmful and what is not. The gut microbiome can influence certain diseases and conditions, including allergies, inflammatory bowel disease, and even some mental health disorders.

Factors that influence the composition of the gut microbiome include diet, genetics, lifestyle, and environmental exposures. For example, a diet rich in fiber tends to promote a beneficial gut microbiome. On the other hand, a diet high in fats can negatively affect the diversity and balance of the gut microbiome (1).






By providing rapid and accurate diagnostic information at the point of care, point-of-care biomarker testing has the potential to improve health outcomes and save lives.

How do antibiotics affect the gut microbiome
The development of antibiotics is one of the most important breakthroughs in healthcare history, and they are incredibly important, lifesaving medications. However, that does not mean they are without any side-effects. Overprescribing of antibiotics is rapidly leading to antibiotic resistance, which occurs when the pathogenic microbes evolve to become resistant to antibiotic treatment. Antibiotic resistance, however, is not the only threat that antibiotics poses. Studies have shown that broad-spectrum antibiotics can affect around 30% of gut bacteria, causing dysbiosis to occur. Dysbiosis is defined as “disturbance in composition and function” of the microbiome

What are the health consequences of this?
It has been established that antibiotics are having a significant impact on the gut microbiome, but what does this mean for our health? One important consequence of microbiome dysbiosis is the increased risk for infections. When the microbiome is disrupted, there is less competition between microbes due to decreased diversity, and therefore it becomes easier for pathogenic bacteria to colonize, or for already present pathogenic bacteria to spread and increase in abundance. Along with this, after antibiotic use, the dysbiosed   gut provides a prime home for resistant bacteria

Furthermore, a disrupted microbiome can lead to chronic inflammation through various different mechanisms, which may contribute to many diseases that are related to inflammation (4). Antibiotic use has been linked to obesity, depression, atopic, inflammatory, and autoimmune diseases, and metabolic syndrome, which is suggested to be mediated by the disruption to the microbiome (3,5,6). Studies have found that probiotics have decreased inflammation levels in patients with depression, metabolic syndrome, rheumatoid arthritis, and coronary artery disease, suggesting that the microbiome has a direct effect on inflammation levels in the body (4).

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Nutritionists can help individuals incorporate a variety of foods that nourish the gut microbiome.

How to help a client who must take antibiotics?
If a client needs to take antibiotics, one way to replenish and support their gut microbes is through their nutrition. Probiotic supplementation can help them introduce more mutualistic bacteria into the gut, and prebiotic foods, such as fermented and high fiber foods, can help them nourish the gut microbes and encourage new growth

Furthermore, it may be useful to monitor CRP levels, which is a biomarker of inflammation, in order to track changes in inflammation that might occur due to dysbiosis. It also may be used for tracking the effectiveness of interventions that are addressing microbiome dysbiosis, since interventions targeting the microbiome have been successful in lowering inflammation levels (4).

What benefits can nutritionists provide when dealing with microbiome dysbiosis?
Personalized Dietary Recommendations:
By assessing an individual's current eating habits and health goals, a nutritionist can identify areas for improvement and suggest dietary changes to promote a healthier gut microbiome. This may include incorporating foods that are rich in fiber, prebiotics, and probiotics, which are known to support the growth of beneficial gut bacteria

Balancing Macronutrients:
Achieving a balanced intake of macronutrients is important for a thriving gut microbiome
(9,10). Nutritionists can help identify and address any nutrient deficiencies that may be impacting the health of the gut microbiome, ensuring that individuals receive adequate nutrition for optimal gut function.

Identifying Food Sensitivities:
Food sensitivities or intolerances have also been associated with the gut microbiome
(11). Nutritionists can assist in identifying potential food triggers that may be causing gut inflammation or discomfort. By pinpointing these sensitivities, individuals can make informed dietary adjustments, eliminating or reducing problematic foods, which may alleviate gut inflammation (11).

Gut-Friendly Meal Planning:
Nutritionists can help individuals incorporate a variety of foods that nourish the gut microbiome. This may involve integrating fermented foods like yogurt, kefir, sauerkraut, and kimchi into meals, as these are rich sources of probiotics, which help maintain a healthy gut environment (8). Additionally, nutritionists can suggest specific recipes and meal ideas that prioritize gut health while still catering to an individual's taste preferences and dietary restrictions.

References 1.Gomaa EZ. Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek. 2020 Dec;113(12):2019–40. 2.Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body [Internet]. bioRxiv; 2016 [cited 2023 May 23]. p. 036103. Available from: 3.Francino MP. Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Front Microbiol [Internet]. 2016 [cited 2023 May 15];6. Available from: 4.Potrykus M, Czaja-Stolc S, Stankiewicz M, Kaska Ł, Małgorzewicz S. Intestinal Microbiota as a Contributor to Chronic Inflammation and Its Potential Modifications. Nutrients. 2021 Oct 28;13(11):3839. 5.Vallianou N, Dalamaga M, Stratigou T, Karampela I, Tsigalou C. Do Antibiotics Cause Obesity Through Long-term Alterations in the Gut Microbiome? A Review of Current Evidence. Curr Obes Rep. 2021 Sep 1;10(3):244–62. 6.Hao WZ, Li XJ, Zhang PW, Chen JX. A review of antibiotics, depression, and the gut microbiome. Psychiatry Res. 2020 Feb 1;284:112691. 7.Tan GSE, Tay HL, Tan SH, Lee TH, Ng TM, Lye DC. Gut Microbiota Modulation: Implications for Infection Control and Antimicrobial Stewardship. Adv Ther. 2020 Oct 1;37(10):4054–67. 8.What You Should Eat During and After Antibiotics [Internet]. Healthline. 2017 [cited 2023 May 23]. Available from: 9.Jardon KM, Canfora EE, Goossens GH, Blaak EE. Dietary macronutrients and the gut microbiome: a precision nutrition approach to improve cardiometabolic health. Gut. 2022 Jun 1;71(6):1214–26. 10.Oliphant K, Allen-Vercoe E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome. 2019 Jun 13;7(1):91. 11.Caminero A, Meisel M, Jabri B, Verdu EF. Mechanisms by which gut microorganisms influence food sensitivities. Nat Rev Gastroenterol Hepatol. 2019 Jan;16(1):7–18.

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