Antibiotics can adversely alter gut microbiome for a year

Antibiotics can have complex and long lasting effects on the human microbiome with consequences that increase the risk for inflammatory bowel disorders. Research just published in mBio (American Society For Microbiology) offers evidence that certain antibiotics have diverse effects depending on the local bodily habitat, and most importantly that changes in the intestinal microbiome that cause deficient production of butyrate can persist for a year. The authors began with an intent to investigate the effect of antibiotics on different physical habitats (niches):

"Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial."

They sequenced the genes of the microbial species present in feces and saliva at baseline, immediately after exposure to one of the antibiotics, and 1, 2, 4, and 12 months after administration of the antibiotics or placebo.

Damage to the gut microbiome by antibiotics impairs butyrate production

Butyrate (butyric acid) is the main energy substrate (food) for the cells that line the colon. It is crucial for their health and deficiency is a know risk factor for inflammatory bowel disease and colon cancer. The authors' data show that the salivary microbiota were barely affected but the gut microbiome took a severe hit:

"The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance."

A single course of antibiotics is all it takes

Commenting on their results the authors state:

"Many health care professionals use antibiotic prophylaxis strategies to prevent infection after surgery. This practice is under debate since it enhances the spread of antibiotic resistance. Another important reason to avoid nonessential use of antibiotics, the impact on our microbiome, has hardly received attention. In this study, we assessed the impact of antibiotics on the human microbial ecology at two niches. We followed the oral and gut microbiomes in 66 individuals from before, immediately after, and up to 12 months after exposure to different antibiotic classes. The salivary microbiome recovered quickly and was surprisingly robust toward antibiotic-induced disturbance. The fecal microbiome was severely affected by most antibiotics: for months, health-associated butyrate-producing species became strongly underrepresented. Additionally, there was an enrichment of genes associated with antibiotic resistance. Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome."

Clinical note

For individual and public health it's clear that non-essential antibiotic use should be assiduously avoided. In cases where they are necessary, practitioners should be attentive to the possibility that butyrate-producing strains may be severely diminished for as long as year, increasing the risk for inflammatory bowel disorders and colon cancer. Probiotic replenishment during and after antibiotic use is a sound standard of care microbiome rehabilitation is still uncertain. Comprehensive stool tests for microbial ecology that include measurement of butyrate and other short-chain fatty acids are readily available. The authors conclude:

"In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome."