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Ceftriaxone and Rifaximin are first choice perioperative antibiotics in gastrointestinal surgery targeting fundamental processes of intestinal bacteria; however, may also have negative consequences for the host cells. In this study, we investigated their direct effect on mitochondrial functions in vitro, together with their impact on ileum, colon and liver tissue. Additionally, their impact on the gastrointestinal microbiome was studied in vivo, in a rat model. Rifaximin significantly impaired the oxidative phosphorylation capacity (OxPhos) and leak respiration in the ileal mucosa, in line with increased oxidative tissue damage and histological changes following treatment. Ceftriaxone prophylaxis led to similar changes in the colon mucosa. The composition and diversity of bacterial communities differed extensively in response to antibiotic pre-treatment. However, the relative abundances of the toxin producing species were not increased. We have confirmed the harmful effects of prophylactic doses of Rifaximin and Ceftriaxone on the intestinal mucosa and that these effects were related to the mitochondrial dysfunction. These experiments raise awareness of mitochondrial side effects of these antibiotics that may be of clinical importance when evaluating their adverse effects on bowel mucosa.<\/jats:p>","DOI":"10.3390\/ijms23095064","type":"journal-article","created":{"date-parts":[[2022,5,3]],"date-time":"2022-05-03T08:26:35Z","timestamp":1651566395000},"page":"5064","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Mitochondrial Side Effects of Surgical Prophylactic Antibiotics Ceftriaxone and Rifaximin Lead to Bowel Mucosal Damage"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8837-2375","authenticated-orcid":false,"given":"B\u00e1lint","family":"Bar\u00e1th","sequence":"first","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"},{"name":"Department of Traumatology, University of Szeged, 6725 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3700-5668","authenticated-orcid":false,"given":"D\u00e1vid K.","family":"J\u00e1sz","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tamara","family":"Horv\u00e1th","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5713-8471","authenticated-orcid":false,"given":"Bence","family":"Bar\u00e1th","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Szeged, 6725 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3705-0461","authenticated-orcid":false,"given":"Gergely","family":"Mar\u00f3ti","sequence":"additional","affiliation":[{"name":"Institute of Plant Biology, Biological Research Center, ELKH, 6726 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerda","family":"Strifler","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriella","family":"Varga","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0530-763X","authenticated-orcid":false,"given":"Lilla","family":"S\u00e1ndor","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Domonkos","family":"Per\u00e9nyi","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Szabolcs","family":"Tall\u00f3sy","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3793-9647","authenticated-orcid":false,"given":"Tibor","family":"Donka","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P\u00e9ter","family":"J\u00e1vor","sequence":"additional","affiliation":[{"name":"Department of Traumatology, University of Szeged, 6725 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mih\u00e1ly","family":"Boros","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4746-9792","authenticated-orcid":false,"given":"Petra","family":"Hartmann","sequence":"additional","affiliation":[{"name":"Institute of Surgical Research, University of Szeged, 6724 Szeged, Hungary"},{"name":"Department of Traumatology, University of Szeged, 6725 Szeged, Hungary"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,5,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Hong, S., Fanning, K., Harris, K., Frohlich, K., and Agris, P. 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