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Original article
Prebiotic inulin-type fructans induce specific changes in the human gut microbiota
  1. Doris Vandeputte1,2,3,
  2. Gwen Falony1,2,
  3. Sara Vieira-Silva1,2,
  4. Jun Wang1,2,
  5. Manuela Sailer4,
  6. Stephan Theis4,
  7. Kristin Verbeke5,
  8. Jeroen Raes1,2,3
  1. 1Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
  2. 2VIB, Center for Microbiology, Leuven, Belgium
  3. 3Department of Bioengineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Brussels, Belgium
  4. 4BENEO-Institute, Obrigheim, Germany
  5. 5KU Leuven—University of Leuven, Translational Research in Gastrointestinal Diseases (TARGID), Laboratory of Digestion and Absorption, Leuven, Belgium
  1. Correspondence to Professor Jeroen Raes, Department of Microbiology and Immunology, KU Leuven – Campus Gasthuisberg, O&N I Herestraat 49, P.O. Box 1028, Leuven B-3000, Belgium; jeroen.raes{at}


Objective Contrary to the long-standing prerequisite of inducing selective (ie, bifidogenic) effects, recent findings suggest that prebiotic interventions lead to ecosystem-wide microbiota shifts. Yet, a comprehensive characterisation of this process is still lacking. Here, we apply 16S rDNA microbiota profiling and matching (gas chromatography mass spectrometry) metabolomics to assess the consequences of inulin fermentation both on the composition of the colon bacterial ecosystem and faecal metabolites profiles.

Design Faecal samples collected during a double-blind, randomised, cross-over intervention study set up to assess the effect of inulin consumption on stool frequency in healthy adults with mild constipation were analysed. Faecal microbiota composition and metabolite profiles were linked to the study's clinical outcome as well as to quality-of-life measurements recorded.

Results While faecal metabolite profiles were not significantly altered by inulin consumption, our analyses did detect a modest effect on global microbiota composition and specific inulin-induced changes in relative abundances of Anaerostipes, Bilophila and Bifidobacterium were identified. The observed decrease in Bilophila abundances following inulin consumption was associated with both softer stools and a favourable change in constipation-specific quality-of-life measures.

Conclusions Ecosystem-wide analysis of the effect of a dietary intervention with prebiotic inulin-type fructans on the colon microbiota revealed that this effect is specifically associated with three genera, one of which (Bilophila) representing a promising novel target for mechanistic research.

Trial registration number NCT02548247.


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  • DV and GF contributed equally.

  • Contributors Conception and design of the study (ST), data collection (ST, KV and JR), data preparation (MS, ST, JW, DV and KV), data analysis and interpretation (DV, GF and SV-S), writing and critical revision of the manuscript (DV, GF, SV-S, MS, ST, KV and JR). All authors approved the final version for publication.

  • Funding DV is funded by the Agency for Innovation by Science and Technology (IWT). SV-S and JW are supported by a postdoctoral fellowship from Research Foundation Flanders (FWO). The study was funded by BENEO GmbH, Mannheim, Germany, a member of the Südzucker Group. The study results and data contained in the publication have been developed by and/or for BENEO GmbH. BENEO GmbH reserves the exclusive right to use the results and data for possible Health Claim requests.

  • Competing interests MS and ST are employees of BENEO/Südzucker Group. The authors alone are responsible for the content and writing of this article.

  • Ethics approval Landesärztekammer Baden-Württemberg, Stuttgart, Germany.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement Data is made available at the European Genotyping Agency (—study no. EGAS00001002173.

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