Investigations into the metabolism of different substrates by gut bacteria

The human large intestine is home to the largest and most diverse group of bacteria in the human body. These bacteria play an important role in maintaining human health, fermenting plant fibres and other non-digestible carbohydrates, and releasing compounds that have direct or indirect benefits to human health.

We are interested in investigating the interactions between different bacterial groups, how populations and bacterial activities change through life, and how they respond to the availability of specific growth substrates.

Understanding the impact of specific dietary components on gut bacteria will help us to formulate health advice for the general population.

Research focus

Scottish grains and ancient varieties video

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The microbial community in the human large intestine consists of a diverse range of bacteria that are predominantly obligate anaerobes.  One approach utilised a differential expression technique combined with microarrray analysis to investigate gene expression in Roseburia inulinivorans. We have successfully reintroduced some of these bacteria in a simulated human colon system against a background of total colonic microbiota. Thus there is a real potential for manipulating the balance of the gut microbiota improve health both by prebiotic and probiotic approaches. However we first need to improve our knowledge of the composition of the normal microbiota. This has been done in my work using new techniques targeting the 16S rDNA gene to enumerate numbers of specific bacterial groups using both fluorescent in situ hybridisation (FISH) and pyrosequencing.

My research also aims to determine key substrates that are the preferred energy source of specific beneficial gut bacteria, and identify the genes involved in their metabolism. One approach utilised a differential expression technique combined with microarrray analysis. The microarray approach successfully identified a novel fucose utilisation pathway, a novel mechanism for the utilisation of long chain inulin for growth, and was also used to identify genes involved in the interactions between bacteria, and between bacteria and the human host.

The information from these studies can ultimately be used to develop new pro/pre/synbiotic approaches to manipulate the gut flora with the aim of improving human health. A related research interest is gene transfer between gut bacteria, specifically the transfer of antibiotic resistance genes. These genes provide a model for the spread of genetic information between bacteria in an ecosystem, and between ecosystems, and illustrates the high frequency with which gene transfer events occur between bacteria.

Research team

Ms Jenny Martin - Research Assistant


Factors influencing transgene survival and transfer in the rumen. Grant holders – Karen Scott (RINH) and Jamie Newbold (University of Aberystwyth). Funded by the FSA.

  • Walsh, AM., Crispie, F., Daari, K., O‚ÄôSullivan, O., Martin, JC., Arthur, CT., Claesson, MJ., Scott, KP. & Cotter, PD. 'Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks'. Applied and Environmental Microbiology, vol 83, no. 14.
    [Online] DOI: 10.1128/AEM.01144-17
  • Gibson, GR., Hutkins, R., Sanders, ME., Prescott, SL., Reimer, RA., Salminen, SJ., Scott, K., Stanton, C., Swanson, KS., Cani, PD., Verbeke, K. & Reid, G. 'Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics'. Nature Reviews Gastroenterology & Hepatology, pp. 1-12.
    [Online] DOI: 10.1038/nrgastro.2017.75
    [Online] AURA: nrgastro.2017.75.pdf
  • Ashton, JJ., Colquhoun, CM., Cleary, DW., Coelho, T., Haggarty, R., Mulder, I., Batra, A., Afzal, NA., Beattie, RM., Scott, KP. & Ennis, S. (2017). '16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease'. Medicine, vol 96, no. 26, e7347, pp. 1-10.
    [Online] DOI: 10.1097/MD.0000000000007347
    [Online] AURA: 16S_sequencing_and_functional_analysis_of_the.62.pdf
  • Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I. & Tuhoy, K. 'Gut microbiota functions: metabolism of nutrients and other food components'. European Journal of Nutrition.
    [Online] DOI: 10.1007/s00394-017-1445-8
    [Online] AURA: ILSIMicrobiota_paper.pdf
  • Chappell, A., Scott, KP., Griffiths, IA., Cowan, AA., Hawes, C., Wishart, J. & Martin, P. (2017). 'The agronomic performance and nutritional content of oat and barley varieties grown in a northern maritime environment depends on variety and growing conditions'. Journal of Cereal Science, vol 74, pp. 1-10.
    [Online] DOI: 10.1016/j.jcs.2017.01.005
  • Sheridan, PO., Martin, JC., Lawley, TD., Browne, HP., Harris, HMB., Bernalier-Donadille, A., Duncan, SH., O'Toole, PW., Scott, KP. & Flint, HJ. (2016). 'Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes'. Microbial Genomics, vol 2, no. 2, 43, pp. 1-16.
    [Online] DOI: 10.1099/mgen.0.000043
    [Online] AURA: mgen000043.pdf
Additional activities

Research briefs for the Knowledge Scotland web site

Additional Responsibilities

Treasurer of the International Scientific Association for Probiotics and Prebiotics (ISAPP).