How Do Antibiotics Effect The Gut Microbiome And How To Restore It


Welcome to my blog entitled ‘How Do Antibiotics Effect The Gut Microbiome And How To Restore It’.

Before we start, other blogs that you might be interested in, include:

Since Alexander Fleming discovered the first antibiotic (penicillin) in 1928, thousands of antibiotic substances have been extracted from natural substances or have been artificially synthesized. The emergence of antibiotics has protected humankind from assaults from various pathogenic bacteria and saved millions of lives during the last century. However, extensive use of antibiotics also negatively impacts human health (1).

A growing number of studies have shown that antibiotics can result in microbial dysbiosis

And the disruption of gut microbiota in neonates and adults contributes to numerous diseases, including diabetes, obesity, inflammatory bowel disease, asthma, rheumatoid arthritis, depression, autism, and superinfection in critically ill patients (1).

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How Do Antibiotics Effect The Gut Microbiome

Antibiotics can effect gut microbiota through direct or indirect mechanisms.

Antibiotics are intentionally administered for the depletion of pathogenic (bad) bacteria; however, due to their broad-spectrum activities, subsets of commensal (friendly) microbes are also indiscriminately killed or inhibited.

Notably, different antibiotics or their combinations have different antimicrobial spectra and will result in different changes to the microbiome.

For example:

  • Vancomycin decreases fecal microbial diversity and the absolute number of gram-positive bacteria, particularly the Firmicutes phylum.
  • Amoxicillin does not change total bacterial numbers and microbial diversity significantly.
  • A combination of antibiotics containing ampicillin, gentamicin, metronidazole, neomycin, and vancomycin not only reduced the total number of bacteria but also dramatically shifted the composition of gut microbiota

The secondary metabolites produced by some species of microbiota may be necessary nutrients for other colonizers. For example, Bifidobacterium adolescentis are able to utilize fructooligosaccharides and starch to produce lactate and acetate. Butyrate-producing anaerobes cannot directly utilize fructooligosaccharides and starch but can utilize lactate and acetate as growth substrates.

Therefore, B. adolescentis can facilitate the proliferation and expansion of butyrate-producing species in vivo by cross-feeding.

This cross-feeding-dependent symbiotic relationship is also found in Rhodopseudomonas palustris and Escherichia coli, Methanobrevibacter smithii and Bacteroides thetaiotaomicron, and Eubacterium rectale and B. thetaiotaomicron.

Otherwise, some metabolites accumulated in the gut may be toxic to other microbes, and microbial biotransformation of these toxic metabolites may be restricted to specific species. One of the most striking examples is conjugated bile acids, which can inhibit the growth of bacteria in the duodenum and jejunum. Deconjugation by Lactobacilli, Bifidobacteria, Clostridium, and Bacteroides is the key step in reducing the toxicity of bile acid. Deconjugated bile acids can be further used by bacteria or reabsorbed by the liver for bile acid enterohepatic circulation.

Thus, loss of specific populations of microbiota may lead to the alteration of metabolites and the microenvironment in the gut, which in turn affect the growth of other members of the gut microbiota.

The Negative Effects Of Antibiotics On The Gut Microbiome And Immune System

Negative effects on the gut microbiome include (1):

  • Increase in antibiotic-resistance genes
  • Change in bacterial metabolites
  • Disrupted bacterial signaling and antimicrobial peptide secretion
  • Gut immune cell dysregulation
  • Host systemic immunity dysfunction

Antibiotics, The Gut Microbiome And Brain Health

Research has also started to discuss the potential role antibiotics may play in influencing Alzheimer’s disease (9).

It has recently been hypothesised that Alzheimer’s may be associated with a dysbiosis of microbes in the intestine. In fact, the intestinal flora is able to influence the activity of the brain and cause its dysfunctions.

Given the growing interest in this topic, a recent review set out to analyse the role of antibiotics in relation to the gut microbiota and AD.

Alteration of the gut microbiota can induce changes in brain activity, which raise the possibility of therapeutic manipulation of the microbiome in AD and other neurological disorders.

Antibiotics, Mitochondria And Psychiatric Conditions

Clinical usage of several classes of antibiotics is associated with moderate to severe side effects due to the promotion of mitochondrial dysfunction. The CNS is extremely dependent on delivery of molecular oxygen for maintaining a required level of metabolic activity, as reflected by the high concentration of neuronal mitochondria. Thus, it is not surprising to find several distinct behavioral abnormalities conforming to established psychiatric criteria that are associated with antibiotic usage in humans.

Ways To Restore The Gut Microbiome After Antibiotics

We can consider the following interventions to restore the microbiome (1):

  • Prebiotics both in dietary and supplement form
  • Probiotics such as saccharomyces boulardii
  • A diverse diet adequate in fibre and polyphenols
  • Fecal microbiota transplants in unique/extreme cases
  • Exercise
  • Stress management
  • Sleep

Test Your Microbiome

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It is increasingly clear that antibiotic effect the diversity, composition and function of the microbiome and thus influence various aspects of systemic health ranging from immunity to energy production and brain health. Fortunately we are understanding more and more how our lifestyle can positively (and negatively) influence all three of these aspects.


  1. Facing a new challenge: the adverse effects of antibiotics on gut microbiota and host immunity: click here
  2. Antibiotics as deep modulators of gut microbiota: between good and evil: click here.
  3. Antibiotics alter the gut microbiome and host health: click here.
  4. Gut Microbiome and Antibiotics: click here.
  5. Antibiotic-induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review: click here.
  6. Role of Microbiome and Antibiotics in Autoimmune Diseases: click here.
  7. Protection of the Human Gut Microbiome From Antibiotics: click here.
  8. A review of antibiotics, depression, and the gut microbiome: click here.
  9. Antibiotics, gut microbiota, and Alzheimer’s disease: click here.
  10. Effects of Antibiotics on Gut Microbiota: click here.
  11. Antibiotics May Trigger Mitochondrial Dysfunction Inducing Psychiatric Disorders: click here.
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