The gut microbiome and the host usually live together in a commensal and symbiotic manner.  However, gut bacteria can potentially be harmful if the ecosystem undergoes abnormal changes with an associated shift in gut microbial composition. This can be caused by numerous external factors, resulting in an alteration of the symbiotic relationship between the gut bacteria and the host.

Gut Microbiome Diversity

The imbalance between the beneficial and pathogenic bacteria in the gut is often referred to as dysbiosis and is associated with several diseases1.

What causes an imbalance in the gut microbiome?

Factors such as diet, ageing, infection, poor diet, international travel and the use of medicinal products including antibiotics can significantly alter the composition of the gut microbiome both on a shorter and longer term.

Gut Microbiome Composition

Are children more affected than adults?

The effect of these factors is more relevant early in life, when the gut microbiome is not yet fully established2.

Do all antibiotics affect the gut microbiome the same way?

The extent to which the gut microbiome changes after antibiotics depends on the chemical nature of the antibiotic or combination of antibiotics and the type of administration, duration and dose as well as the resilience level of the gut microbiome.

The degree to which bacteria in the gut microbiome is impacted by currently available antibiotic interventions varies3. One study showed that the gut microbiome of subjects recovered to near-baseline composition within 1.5 months, after completing a course of antibiotic therapy. There were 9 common genera which were present in all subjects before treatment, that remained below the levels of detection in most of the subjects after 180 days4. Importantly one of the genus that didn’t recover was bifidobacteria. 

Bifidobacteria is an important genus which studies have shown is important for gut health, it also produces metabolites such as lactate and acetate which is particularly important for gut health.

The gut microbiome can confer protection against pathogens, a phenomenon referred to as colonisation resistance which is when good bacteria effectively crowd out the pathogenic bacteria. This positive effect can be severely impaired by antibiotic treatment5.

How to help mitigate the effects of antibiotics on gut health?

  • Promote a diet high in fermentable (prebiotic) fibre. A diet high in whole, plant-based foods, fruit and vegetables will contain non-digestible prebiotic fibre that will help to feed the beneficial bacteria in the gut6.
  • Take supplements to improve gut health. Prebiotics and probiotics may help to reduce the negative effects of antibiotics on the gut microbiome. Increase your intake of natural dietary prebiotics with prebiotic supplements, which help the good bacteria in the gut to thrive, helping to correct an imbalance that may potentially occur. Prebiotics act as a fertilizer, feeding the good gut bacteria, whereas probiotics may seed the gut with beneficial bacteria.

In summary, the use of antibiotics can negatively impact the balance of beneficial bacteria in the gut, which is associated with both acute and chronic conditions. Maintaining good gut health before, during and after taking antibiotics, may help to restore the gut microbiome, thereby maintaining or improving gut health and general wellbeing.

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