title: High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator.
abstract: The aim of this work was to investigate the relationship between the structure of gut microbial communities fed with different diets (i.e. high-protein-HP- versus high-fiber-HF-diet) and their functional stability when challenged with mild and acute doses of a mix of amoxicillin, ciprofloxacin, and tetracycline. We made use of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)-a continuous model of the gastrointestinal tract-coupled with 16S-targeted Illumina and metabolomics (i.e. UHPLC-HRMS) analyses. Independently of the diet, the sudden exposure to an acute stress led to a modification of the microbial community structure, selecting for species belonging to Bacillus spp.; Clostridium cluster XIVa; Enterococci; Bacteroides; and Enterobacteriaceae. The antibiotic treatment led to a decrease in the number of operational taxonomic units (at least -10%). Cluster analysis of untargeted metabolic data showed that the antibiotic treatment affected the microbial activity. The impact on metabolites production was lower when the community was preexposed to mild doses of the antibiotic mix. This effect was stronger in the proximal colon for the HF diet and in the distal colon for the HP diet. Different diets shaped different gut microbial communities, which ecologically behaved similarly under stress conditions.
authors.affiliation: Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, Belgium.
authors.forename: Massimo
authors.initials: M
authors.lastname: Marzorati
authors.affiliation: Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, Belgium.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Vilchez-Vargas
authors.affiliation: Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Merelbeke, Belgium.
authors.forename: Julie Vanden
authors.initials: JV
authors.lastname: Bussche
authors.affiliation: Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, Belgium.
authors.forename: Pilar
authors.initials: P
authors.lastname: Truchado
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Ruy
authors.initials: R
authors.lastname: Jauregui
authors.affiliation: Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, Belgium.
authors.forename: Racha Ahmad
authors.initials: RA
authors.lastname: El Hage
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
authors.affiliation: Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Merelbeke, Belgium.
authors.forename: Lynn
authors.initials: L
authors.lastname: Vanhaecke
authors.affiliation: Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Ghent, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Van de Wiele
mesh_terms: D002851:Chromatography, High Pressure Liquid; D016000:Cluster Analysis; D004043:Dietary Fiber / Q000494:pharmacology*; D004044:Dietary Proteins / Q000494:pharmacology*; D000069196:Gastrointestinal Microbiome / Q000187:drug effects* / Q000235:genetics; D006801:Humans; D012336:RNA, Ribosomal, 16S; D013312:Stress, Physiological
chemical_list: D004043:Dietary Fiber; D004044:Dietary Proteins; D012336:RNA, Ribosomal, 16S
keywords: Antibiotic; Functionality; Gastrointestinal tract; SHIME®; Stress