Dietary influence on functional groups of the gut microbiota

The human gut is colonised by a diverse microbial community that contributes to the digestion of dietary ingredients, especially certain carbohydrates that cannot be digested by the human host. The activities of this microbiota influence human health in several different ways, including via products formed from the breakdown of dietary components. We investigate how human health can be improved through dietary means by modulating the composition and activity of the gut microbiota.

Our research will help to provide scientifically-based dietary advice as well as aid the food industry in developing health-promoting foods.

Research focus

The microbial community in the human large intestine consists of a diverse range of bacteria that break down complex nutrients of dietary and host origin. The members of this ecosystem form a complex metabolic network in which the product of one group can serve as substrate for another group. Overall, this leads to the accumulation of mainly three organic acids, acetate, propionate and butyrate, which are partially absorbed by the colon and serve as an additional energy source for the human host. Butyrate is of special interest, as it serves as the preferred energy source for the colonic wall and thus contributes to the proper functioning of the gut. It has also been claimed to be protective against colon cancer and inflammatory bowel disease through effects on host gene expression and cellular development of the colon. Propionate also influences host physiology and its potential effects on host satiety is of particular interest in view of the current obesity epidemic.

Dietary intakes can influence the microbial gut community and shift the balance between different functional bacterial groups, with potential consequences for host health. Our research concentrates on assessing those changes using molecular techniques, especially quantitative PCR against the 16S rRNA gene as a phylogenetic marker, with a view to establishing the effect of different diets on gut health. In addition we are developing degenerate PCR approaches against functional genes that can be used as phylogenetic markers for specific functional groups of bacteria. This has been successfully applied to investigating the butyrate-producing community in response to intake of the prebiotic inulin (Louis et al, 2010). A further area of interest is the release of dietary plant phenolics from their glycosidic parent compounds by the gut microbiota, which is an essential step in facilitating their health-promoting activities. Techniques used in my lab range from molecular phylogeny and metagenomics to microbial physiology and biochemistry.

Research team

Mrs. Freda Farquharson - Research Assistant
Dr Eva Soto Martin
- Research Fellow
Timo Kramer - PhD student

  • BBSRC TSB CELLDEX - Development of a low calorie bulk sugar replacer. Coordinator Isabella Van Damme, Mars Chocolates; 2014-2017.
  • BBSRC/NERC Sustainable Aquaculture Initiative - Gut health and immune function: the emerging role of gut microbiota in sustainable aquaculture. Coordinator Sam Martin, U. Aberdeen; 2015-2017.
  • Support from Scottish Government themed programme 2011-16
  • Scottish Government funded Strategic Partnership (with U. Glasgow) on the role of short-chain fatty acids as satiety agents; 2011-2016.
  • EU FP7 Collaborative project Fibebiotics: Dietary Fibers supporting gut and immune function – from polysaccharide compound to health claim; 2012-2016.
  • Commercial collaboration with Tereos Syral, Markolsheim, France. Effect of prebiotic intake on constipation, 2013.
  • Staudacher, HM., Lomer, MCE., Farquharson, FM., Louis, P., Fava, F., Franciosi, E., Scholz, M., Tuohy, KM., Lindsay, JO., Irving, PM. & Whelan, K. 'Diet Low in FODMAPs Reduces Symptoms in Patients with Irritable Bowel Syndrome and Probiotic Restores Bifidobacterium Species: a Randomized Controlled Trial'. Gastroenterology, pp. 1-32.
    [Online] DOI: 10.1053/j.gastro.2017.06.010
  • Vollmer, M., Schröter, D., Esders, S., Neugart, S., Farquharson, FM., Duncan, SH., Schreiner, M., Louis, P., Maul, R. & Rohn, S. 'Chlorogenic acid versus amaranth's caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives'. Food Research International, pp. 1-39.
    [Online] DOI: 10.1016/j.foodres.2017.06.013
  • Louis, P. & Flint, HJ. (2017). 'Formation of propionate and butyrate by the human colonic microbiota'. Environmental Microbiology, vol 19, no. 1, pp. 29-41.
    [Online] DOI: 10.1111/1462-2920.13589
  • Watt, E., Gemmell, MR., Berry, S., Glaire, M., Farquharson, F., Louis, P., Murray, GI., El-Omar, E. & Hold, GL. (2016). 'Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies'. Microbiome, vol 4, 61.
    [Online] DOI: 10.1186/s40168-016-0207-9
    [Online] AURA: Extending_colonic_mucosal_microbiome_analysis_assessment_of_...
  • Chung, WSF., Walker, AW., Louis, P., Parkhill, J., Vermeiren, J., Bosscher, D., Duncan, SH. & Flint, HJ. (2016). 'Modulation of the human gut microbiota by dietary fibres occurs at the species level'. BMC Biology, vol 14, 3, pp. 1-13.
    [Online] DOI: 10.1186/s12915-015-0224-3
    [Online] AURA: Inulin_Pectin_Chung_etal_BMCBiology_2016.pdf
  • Ze, X., David, B., Laverde Gomez, J., Dassa, B., Sheridan, PO., Duncan, SH., Louis, PGH., Henrissat, B., Juge, N., Koropatkin, NM., Bayer, EA. & Flint, HJ. (2015). 'Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii'. mBio, vol 6, no. 5, e01058-15.
    [Online] DOI: 10.1128/mBio.01058-15
    [Online] AURA: mBio_2015_Ze_.pdf
Additional activities

Research briefs for the Knowledge Scotland web site