Changes in Intestinal Microbiota Tracked Using Next-generation Sequencing Before and after Antimicrobial Administration: An Example of Short-bowel Syndrome.

Although patients with short bowel syndrome may receive antimicrobial therapy for complications associated with abnormal intestinal microbiota, no established criteria for target bacterial screening or antimicrobial susceptibility standards exist. As a result, antimicrobial therapy is often administered without a microbiological evaluation. However, this approach carries uncertainties and risks, as antimicrobials can alter the microbiota in undesirable ways. To address this issue, we administered antimicrobial therapy to a patient with short bowel syndrome associated with chronic metabolic acidosis and monitored the changes in the intestinal microbiota using next-generation sequencing. We report these findings as they provide new insights into short bowel syndrome.