Post Antibiotic Treatment: Restoration of Intestinal Balance

Antibiotics are essential for fighting infections, but they are not selective. They destroy beneficial intestinal bacteria as well as harmful ones, reduce microbial diversity and disrupt the natural balance in the intestine. This disorder can trigger permanent changes in the microbiome, give harmful bacteria room to multiply, and contribute to side effects such as indigestion and occasional diarrhea. Biodiversity and culturable* bacteria decline sharply immediately after antibiotic treatment. While some microbes return to normal within about two months in most healthy adults, others remain, the underlying taxonomy, resistome**, and metabolism often remain altered, accompanied by increased antibiotic resistance.¹

These antibiotic-induced changes in microbial composition can affect host health. Microbial diversity decreases, intestinal flora functions change, and the formation and selection of antibiotic-resistant strains is favored. This makes the host more susceptible to pathogens such as Clostridioides difficile. As antibiotic use continues to increase, antibiotic resistance remains an urgent global concern. Therefore, it is crucial to understand the comprehensive effects of antibiotics on intestinal flora and health.² Bacteria that are particularly at risk during antibiotic treatment include so-called „keystone species." These closely linked microorganisms, although sometimes found in relatively small numbers, exert a disproportionate influence on the stability and function of the entire intestinal ecosystem. The loss of these species not only reduces diversity but can also trigger a major structural change in the entire microbial community.³ These essential bacteria are also vital for intestinal barrier integrity, immune system support, and metabolic regulation. Their decline after prolonged antibiotic use can therefore significantly disrupt the intestinal environment.⁴⁻⁵

Die Wiederherstellung der Darmflora nach einer Antibiotikabehandlung bedeutet, sich auf die Wiederherstellung der mikrobiellen Diversität und die Linderung damit verbundener Symptome zu konzentrieren. Dazu gehört auch, Schlüsselarten die Möglichkeit zu geben, sich wieder anzusiedeln. Probiotika und Präbiotika spielen dabei eine zentrale Rolle. Präbiotika sind insbesondere Ballaststoffe, die das Wachstum und die Aktivität nützlicher Bakterien fördern und so zur Wiederherstellung der mikrobiellen Diversität und zu einem gesunden Darmmilieu beitragen.

Supplement your food supplements with prebiotic-rich foods. Download our free, gut-friendly shopping list to get started.


For those who have recently had an antibiotic: The JANISER® booster treatment (one bottle of 500ml) is available until November 30, 2026 for CHF 99.50 (EU: 99.50 €) instead of CHF 145 (EU: 145 €). Freight-free!

*These bacteria can be cultured (cultured) in a laboratory dish using traditional microbiological methods. That is, they can be isolated and propagated on a nutrient medium. This is important because not all intestinal bacteria can be cultivated in this way. A large proportion of intestinal microbes are not culturable by standard methods „and can only be detected by DNA sequencing.

**This refers to the totality of all antibiotic resistance genes within a microbial community, in this case the genes carried by the intestinal bacteria that enable them to survive after antibiotic exposure. You can think of it as the „genetic toolbox" of the gut for antibiotic resistance. After antibiotic treatment, the resistome may remain altered even if bacterial biodiversity has recovered. This means that the surviving and returning bacteria may carry more resistance genes than before. This is one reason why antibiotic use leads to increasing antibiotic resistance over time.

  1. https://www.sciencedirect.com/science/article/pii/S2211124722004016
  2. https://onlinelibrary.wiley.com/doi/10.1002/mbo3.1260
  3. https://www.mdpi.com/2072-6643/14/1/137
  4. https://www.frontiersin.org/journals/cell-and-developmental-biology/articles/10.3389/fcell.2021.719072/full

Image: Polina Tankilevitch

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