Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota

Wing Sun Faith Chung, Alan W. Walker, Joan Vermeiren, Paul O. Sheridan, Douwina Bosscher, Vicenta Garcia-Campayo, Julian Parkhill, Harry J. Flint, Sylvia H. Duncan* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

32 Citations (Scopus)
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The diversity of the colonic microbial community has been linked with health in adults and diet composition is one possible determinant of diversity. We used carefully controlled conditions in vitro to determine how the complexity and multiplicity of growth substrates influence species diversity of the human colonic microbiota. In each experiment, five parallel anaerobic fermentors that received identical faecal inocula were supplied continuously with single carbohydrates (either arabinoxylan-oligosaccharides (AXOS), pectin or inulin) or with a ‘3-mix’ of all three carbohydrates, or with a ‘6-mix’ that additionally contained resistant starch, β-glucan and galactomannan as energy sources. Inulin supported less microbial diversity over the first six days than the other two single substrates or the 3- and 6-mixes, showing that substrate complexity is key to influencing microbiota diversity. The communities enriched in these fermentors did not differ greatly at the phylum and family level, but were markedly different at the species level. Certain species were promoted by single substrates, whilst others (such as Bacteroides ovatus, LEfSe p=0.001) showed significantly greater success with the mixed substrate. The complex polysaccharides such as pectin and arabinoxylan-oligosaccharides promoted greater diversity than simple homopolymers, such as inulin. These findings suggest that dietary strategies intended to achieve health benefits by increasing gut microbiota diversity should employ complex non-digestible substrates and substrate mixtures.
Original languageEnglish
Article numberfiy201
JournalFEMS Microbiology Ecology
Issue number1
Early online date9 Oct 2018
Publication statusPublished - 1 Jan 2019

Bibliographical note

This work was largely funded by a PhD studentship award (BB/J012351/1) from the Biotechnology and Biological Sciences Research Council (BBSRC-CASE) with Cargill as commercial partner. JP and 16S rRNA gene sequencing costs were funded by the Wellcome Trust (grant number WT098051). The Rowett Institute receives financial support from the Scottish Government Rural and Environmental Sciences and Analytical Services (RESAS)


  • microbial diversity
  • bacteroidetes
  • firmicutes
  • CAZymes
  • dietary carbohydrates


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