We already know that a course of antibiotics introduces damage to the microbial composition of your gastrointestinal (GI) and other (oral, skin, vaginal, bladder, etc.) microbiomes. We witness the deleterious effects in a variety of ways that include increased potential for weight gain and obesity, increased risk for type 2 diabetes, and inflammatory and neurodegenerative conditions. The changes in microbial composition, however, vary with the antibiotic(s) used, the initial state of the microbiome, duration of treatment, and other factors.

Here is a recent study in which the GI microbiomes of healthy volunteer men were tracked serially before and after a course of wide-spectrum antibiotics (vancomycin, gentamicin and meropenem) to document the changes that can occur over time. Stool was therefore analyzed just prior to antibiotic administration, on day 4 after the 4-day course of treatment, then on days 8, 42. and 180.

Among the findings:

  • There was a dramatic reduction in diversity (i.e., number of unique species) after 4-days, gradual recovery over a longer time period. However, a reduction in number of species persisted at 6 months (180 days).
  • There was enrichment in Proteobacteria species (potentially pathogenic fecal species) including Escherichia coli, Veillonella spp., Klebsiella spp., E. faecalis and F. nucleatum. This mix of species is often found in colon cancer samples and are, given emerging evidence, looking like primary causes of many cases of colorectal cancer. These are also the species that dominate in small intestinal bacterial overgrowth, SIBO.
  • There was reduction or loss of beneficial species such as Faecalibacterium prausnitzii, Roseburia hominis, Coprococcus spp. and Eubacterium spp, important for their ability to produce butyrate that mediates many of the beneficial effects of the microbiome such as mental and emotional health, blood glucose and blood pressure control, sleep quality and duration. Most strains of Faecalibacterium did not return at 6 months.
  • Clostridia species increased significantly at day 42, likely due to the loss of beneficial species that allowed this sporulating species to germinate and proliferate, the likely process that allows the dreaded Clostridium difficile to emerge and cause post-antibiotic enterocolitis.
  • Bifidobacteria species, an important collection of beneficial, protective microbes, were lost entirely.

Unfortunately, this analysis was based only on examination of stool samples but no breath testing. I would predict that, had H2 or H2S breath testing been performed, there would have been evidence for small intestinal colonization by fecal microbes, as we know from prior evidence that antibiotics are a major factor leading to SIBO and thereby health conditions outside the GI tract.

The one important new takeaway from this analysis, however, is to pay special attention to the restoration of Bifidobacteria species during and after a course of antibiotics. This is similar to what happens with long COVID in which a depletion of Bifidobacteria occurs and is suspected to underlie the fatigue, mind “fog,” and other symptoms characteristic of this situation. Strategies that you can adopt if you encounter an unavoidable need for antibiotics include:

  • Saccharomyces bourlardii–that I like to make sparkling juices with to amplify microbial counts, while enjoying delicious sparkling juices with little to no residual sugar.
  • Make Lactobacillus reuteri and Lactobacillus gasseri yogurts–as these are species/strains that colonize the small intestine where they produce bacteriocins, natural antibiotics effective in killing Proteobacteria.
  • Consider a probiotic that contains several Bifidobacteria species.
  • Be sure to include sources of inulin/fructooligosaccharides in your diet–as root vegetables, garlic, asparagus, onions, or as commercial powders, as these bloom Bifidobacteria as well as other butyrate-producing species.

Of course, if all of this is new to you, consider getting better acquainted with my prescriptive microbiome strategies through my Super Gut book, my DrDavisInfiniteHealth.com Inner Circle that contains tons of resources and support, or my Microbiome Master Class (no cost to Inner Circle Members).