The Hidden Driver of SIBO and Chronic Gut Dysfunction: Bile Acid Malabsorption, Dysbiosis, and the Mitochondrial Cascade — Part V: The Antibiotic Paradox—Why Antimicrobials Worsen the Underlying Mechanism

The Short-Term Benefit, the Long-Term Cost Antibiotics are the standard-of-care treatment for SIBO. For the first weeks to months following antibiotic therapy, many patients improve: bacterial overgrowth is reduced, hydrogen and methane production falls, symptoms improve. But here is the paradox that virtually no SIBO literature adequately addresses: antibiotics do not differentiate between pathogenic SIBO organisms and the specific commensals required for bile acid metabolism. When you prescribe rifaxomicin, neomycin, or herbal antimicrobials (berberine, oregano oil, etc.), you are not selectively eliminating Klebsiella or E. coli . You are eliminating large swaths of the anaerobic bacterial community&#8212;indiscriminately. This includes the remaining Clostridium scindens , C. hiranonis , Eubacterium , Bacteroides , and other organisms that express BSH and the bai operon. The antimicrobial therapy thus exacerbates the very enzymatic deficit that drove the SIBO in the first place. What the Literature Shows Wahlstr&#246;m et al. (2016, Gut) studied the effects of broad-spectrum antibiotics on the human microbiota and bile acid metabolism: Before antibiotics: secondary bile acids were abundant; primary bile acid fecal concentration was low and stable After antibiotics: secondary bile acids essentially disappeared. Primary bile acids accumulated 10-fold. The study followed patien