Short Gut Syndrome Patient, Family & Professional Support Groups

Q: Can oral antibiotics for cause diarrhea, dumping, and digestive upset?

Although this issue has not been studied, we receive regular anecdotal reports in our Facebook groups of short gut syndrome patients who have problems with dumping, diarrhea, stomach pain, vomiting, and other digestive symptoms following treatment for routine infections with oral antibiotics, notably amoxicillin.

The use of oral antibiotics is problematic in short gut syndrome. Little research is available on how well oral medications are absorbed. However, what does exist suggests that some antibiotics, namely ciproflaxin, are not absorbed at the same rate as in individuals with functioning guts. Further, the absorption in patients with ultra short gut syndrome was low for all studied antimicrobials.1

Higher doses of some antibiotics may be needed to reach therapeutic levels.1 This can make symptoms even worse for those who are sensitive to these medications.

Anecdotally, short gut individuals and caregivers report an increased sensitivity to antibiotics that causes digestive upset lasting weeks or longer following treatment.

Instead, many patients prefer to receive injectable or infused antibiotics even when treating minor infections such as ear infections, sinus infections, and strep throat.

However, most family practitioners and pediatricians who prescribe treatment for short bowel syndrome are not familiar with this population's unique needs. Patients and caregivers must know this need and advocate for the appropriate treatment.


  1. Korzilius JW, Gompelman M, Wezendonk GTJ, Jager NGL, Rovers CP, Br├╝ggemann RJM, Wanten GJA. Oral antimicrobial agents in patients with short bowel syndrome: worth a try! J Antimicrob Chemother. 2023 Aug 2;78(8):2008-2014. doi: 10.1093/jac/dkad198. Erratum in: J Antimicrob Chemother. 2024 May 16:dkae150. doi: 10.1093/jac/dkae150. PMID: 37390353; PMCID: PMC10393866.

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