Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production
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The diet provides carbohydrates that are non-digestible in the upper gut and are major carbon and energy sources for the microbial community in the lower intestine, supporting a complex metabolic network. Fermentation produces the short-chain fatty acids (SCFAs) acetate, propionate and butyrate, which have health-promoting effects for the human host. Here we investigated microbial community changes and SCFA production during in vitro batch incubations of 15 different non-digestible carbohydrates, at two initial pH values with faecal microbiota from three different human donors. To investigate temporal stability and reproducibility, a further experiment was performed 1 year later with four of the carbohydrates. The lower pH (5.5) led to higher butyrate and the higher pH (6.5) to more propionate production. The strongest propionigenic effect was found with rhamnose, followed by galactomannans, whereas fructans and several α- and β-glucans led to higher butyrate production. 16S ribosomal RNA gene-based quantitative PCR analysis of 22 different microbial groups together with 454 sequencing revealed significant stimulation of specific bacteria in response to particular carbohydrates. Some changes were ascribed to metabolite cross-feeding, for example, utilisation by Eubacterium hallii of 1,2-propanediol produced from fermentation of rhamnose by Blautia spp. Despite marked inter-individual differences in microbiota composition, SCFA production was surprisingly reproducible for different carbohydrates, indicating a level of functional redundancy. Interestingly, butyrate formation was influenced not only by the overall % butyrate-producing bacteria in the community but also by the initial pH, consistent with a pH-dependent shift in the stoichiometry of butyrate production.
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Compositional data are still useful and can correlate well with absolute quantifications obtained with techniques such as qPCR.
“Compositional data are still useful, and can correlate well with absolute quantifications obtained with techniques such as qPCR 28,29 .”
From Human microbiome myths and misconceptions (2023) · cites this paper as [29]
The ‘Relationship between microbiota composition and SCFA formation’ section reports that sequencing results agreed well with qPCR results and that most corresponding groups had significant correlations. However, those correlations used relative qPCR data, not absolute quantifications; the Statistical analysis section likewise specifies percentages of total bacteria. Page numbers are not available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThere are important functionalities that are conserved across many different human microbiota species, such as short-chain fatty acid production.
“While there are important functionalities that are conserved across many different human microbiota species, such as short-chain fatty acid production 29 ,”
From Human microbiome myths and misconceptions (2023) · cites this paper as [29]
Rhamnose is a non-digestible carbohydrate that has a propionogenic, as opposed to butyrogenic, effect.
“Rhamnose is a non-digestible carbohydrate that has a propionogenic (as opposed to butyrogenic) effect26.”
From Nivolumab plus ipilimumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial (2022) · cites this paper as [26]
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- Authors
- Reichardt, N., Vollmer, M., Holtrop, G., Farquharson, F. M., Wefers, D., Bunzel, M., Duncan, S. H., Drew, J. E., Williams, L. M., Milligan, G., Preston, T., Morrison, D., Flint, H. J., & Louis, P.
- Affiliations
- University of Aberdeen (GB)
- Biomathematics and Statistics Scotland (GB)
- Karlsruhe Institute of Technology (DE)
- University of Glasgow (GB)
- Scottish Universities Environmental Research Centre, University of Glasgow, Rankine Avenue , East Kilbride, UK
- Scottish Universities Environmental Research Centre (GB)
- Corresponding author
- Louis, Petra
- ORCID
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-01
- Volume
- 12
- Issue
- 2
- Pages
- 610-622
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC5776475
- OpenAlex
- W2774698525
- Cited by
- 249
- References
- 50
- Citations by year
- 2026: 29 · 2025: 30 · 2024: 27 · 2023: 29 · 2022: 35 · 2021: 32 · 2020: 36 · 2019: 19 · 2018: 12
- FWCI
- 7.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The ISME Journal (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion, cc-by-sa)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
- Funders
- Scottish Government
- University of Aberdeen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Microbial Metabolites in Food Biotechnology
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- fecal microbiota, short-chain fatty acids, butyrate production, propionate production, acetate, non-digestible carbohydrates, dietary fiber fermentation, rhamnose, galactomannan, fructans, glucan, Eubacterium hallii, Blautia, propylene glycol, pH dependence, interindividual variability, functional redundancy
- MeSH terms
- Bacteria, Butyrates, Dietary Carbohydrates, Eubacterium, Fatty Acids, Volatile, Feces, Fermentation, Galactose, Humans, Mannans, Propionates, Rhamnose, Reproducibility of Results, Microbiota
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