The gastrointestinal tract and the microbes colonizing it form a complex ecosystem that has various effects on the well-being of the host. In addition to acute infections, the composition of the gastrointestinal microbiota has been suspected to influence the etiopathogenesis of many chronic diseases, such as rheumatoid arthritis and inflammatory bowel diseases. It has been suggested that the bacterial colonization of the gastrointestinal tract is genetically determined. Using gas-liquid chromatography of bacterial cellular fatty acids we show in this study that modulation of the microbiota by a course of antibiotics is followed by regeneration of the murine intestinal flora depending on the genotype of the host. The mice used in our study were acclimatized to identical living conditions before treatment with ciprofloxacin and clindamycin for 1 week via drinking water. Within a few days of finishing the antibiotic course, the cellular fatty acid profiles of fecal samples resembled those of the pre-course community, showing a considerable indigenous recovery potential. Colonization of the gastrointestinal tract appeared to be genetically regulated since differences in communities between the mouse strains were observed. Our results are in harmony with earlier observations, indicating that the gut community is not established by chance and that it is influenced by host-derived factors. © 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
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