The Effect Of Antibiotics On Your Gut Microbiome

Antibiotics have saved millions of lives by reducing or eliminating pathogenic bacteria. However, we are now learning that overusing antibiotics can have the unintended consequence of also reducing or removing resident bacteria that are important for gut health and increasing the abundance of antibacterial resistance genes.

Antibiotics come in many different forms. Some can target a wide range of bacteria (broad-spectrum), while others will target only a few types of bacteria (narrow-spectrum). Broad-spectrum antibiotics are the most commonly prescribed because often the microorganism causing an infection is unknown. Use of broad-spectrum antibiotics has been observed to have several impacts on gut health, including:

– reducing microbial diversity in the gut^1-5

– reducing protective species such as Bifidobacterium spp.^1,2,6

– promoting the colonisation of opportunistic pathogens such as Clostridioides difficile that can cause antibiotic-associated diarrhea^7-9

In infants and young children, antibiotic use has also been linked to an increased risk of asthma and weight gain^1,10.

In a healthy gut microbiome, the resident microorganisms help protect against invasion by opportunistic pathogens through a process called colonisation resistance. This involves different methods to inhibit pathogens, such as:

• producing antimicrobial compounds
• outcompeting pathogens for space in the gut
• maintaining the mucus layer so pathogens cannot reach intestinal cells
• training the immune system to respond to pathogens^11,12

When the resident gut microorganisms are reduced during antibiotic use, these protective functions may stop occurring, providing an opportunity for pathogenic bacteria to colonise.

After an antibiotic course, recovery of the gut microbiome can take some time. In general, after short-term antibiotic use (between five and ten days), studies have observed it can take at least one to two months for most bacterial groups to recover to pre-antibiotic levels^2,3,13-16. However, these studies have also shown that even after two to four years, some bacterial groups do not recover completely and antibacterial resistance genes can also persist at increased levels for at least one to two years following antibiotic use^13,14,16,17. Therefore, even a short course of antibiotics can have long-term effects on the gut microbiome.

There is increasing clinical evidence that taking probiotics during and after antibiotic use can decrease the risk of invasion by opportunistic pathogens and the development of antibiotic-associated diarrhea^18-20. However, there is still some debate about whether probiotics promote or inhibit the recovery of native gut microbiota.

Some studies have observed taking probiotics during and after antibiotic usage can slow the return of native gut microbes²¹, while other studies have observed the opposite^23,24. A recent systematic review on the topic concluded that based on current evidence, probiotic supplementation during antibiotic therapy does not influence the recovery of microbial diversity²⁵. This means that probiotics likely do not improve or inhibit recovery. The review did note however that studies to date are limited and there was considerable variability in the probiotic strains, doses, and length of time tested. Thus, as more research is conducted in this area, it is possible these findings may change.

Another good general strategy to improve gut health following antibiotics is to make certain you feed your gut microbiome with diverse types of fibre-rich foods, that will allow your beneficial resident microbiota to grow back. A meta-analysis of four cohorts of people that took antibiotics found a group of key bacteria that were associated with faster recovery of the gut microbiome. The common factor in these recovery-associated bacteria was an increased ability to produce enzymes that break down carbohydrates²⁶. Fibre is the main source of carbohydrates that reach the gut. This means that eating a wide variety of foods that are high in fibre , such as fruits, vegetables, legumes, nuts, seeds and whole grains may help speed the recovery of your gut microbiome.