title: Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders.
abstract: Sections of fecal cylinders were analyzed using fluorescence in situ hybridization targeting 180 bacterial groups. Samples were collected from three groups of women (N=20 each) treated for bacterial vaginosis with ciprofloxacin+metronidazole. Group A only received the combined antibiotic regimen, whereas the A/Sb group received concomitant Saccharomyces boulardii CNCM I-745 treatment, and the A_Sb group received S. boulardii prophylaxis following the 14-day antibiotic course. The number of stool cylinders analyzed was 188 out of 228 in group A, 170 out of 228 in group A/Sb, and 172 out of 216 in group A_Sb. The colonic biomass was organized into a separate mucus layer with no bacteria, a 10-30μm broad unstirred transitional layer enriched with bacteria, and a patchy fermentative area that mixed digestive leftovers with bacteria. The antibiotics suppressed bacteria mainly in the fermentative area, whereas abundant bacterial clades retreated to the transitional mucus and survived. As a result, the total concentration of bacteria decreased only by one order. These effects were lasting, since the overall recovery of the microbial mass, bacterial diversity and concentrations were still below pre-antibiotic values 4 months after the end of antibiotic treatment. Sb-prophylaxis markedly reduced antibiotic effects and improved the recovery rates. Since the colon is a sophisticated bioreactor, the study indicated that the spatial anatomy of its biomass was crucial for its function.
authors.affiliation: Laboratory for Molecular Genetics, Polymicrobial Infections and Biofilms, Department of Medicine, Section of Gastroenterology, Hepatology and Endocrinology, Charité University Hospital, CCM 10117 Berlin, Germany. Electronic address: alexander.swidsinski@charite.de.
authors.forename: Alexander
authors.initials: A
authors.lastname: Swidsinski
authors.affiliation: Laboratory for Molecular Genetics, Polymicrobial Infections and Biofilms, Department of Medicine, Section of Gastroenterology, Hepatology and Endocrinology, Charité University Hospital, CCM 10117 Berlin, Germany.
authors.forename: Vera
authors.initials: V
authors.lastname: Loening-Baucke
authors.affiliation: Laboratory for Molecular Genetics, Polymicrobial Infections and Biofilms, Department of Medicine, Section of Gastroenterology, Hepatology and Endocrinology, Charité University Hospital, CCM 10117 Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schulz
authors.affiliation: Department of Nutritional Biochemistry, University of Potsdam, Institute of Nutritional Science, Nuthetal, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Manowsky
authors.affiliation: Department of Obstetrics and Gynaecology, Ghent University Hospital, Ghent, Belgium.
authors.forename: Hans
authors.initials: H
authors.lastname: Verstraelen
authors.affiliation: Department of Microbiology, Labor Berlin - Charité Vivantes GmbH, Sylter Strasse 2, 13353 Berlin, Germany.
authors.forename: Sonja
authors.initials: S
authors.lastname: Swidsinski
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D000981:Antiprotozoal Agents / Q000627:therapeutic use*; D018533:Biomass; D019149:Bioreactors / Q000382:microbiology*; D002939:Ciprofloxacin / Q000627:therapeutic use*; D016360:Clostridioides difficile / Q000187:drug effects*; D005243:Feces / Q000382:microbiology*; D005260:Female; D000069196:Gastrointestinal Microbiome; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008795:Metronidazole / Q000627:therapeutic use*; D019936:Probiotics / Q000627:therapeutic use*; D012440:Saccharomyces / Q000254:growth & development*; D016585:Vaginosis, Bacterial / Q000188:drug therapy* / Q000382:microbiology
chemical_list: D000900:Anti-Bacterial Agents; D000981:Antiprotozoal Agents; D008795:Metronidazole; D002939:Ciprofloxacin
keywords: Antibiotics; Bioreactor; Clostridium difficile; Colonic microbiota; FISH; Saccharomyces boulardii