Senior Research Fellow


Contact Details

work +44 (0)1224 438730
fax +44 (0)1224 438699
The University of Aberdeen Microbial Ecology Group
Rowett Institute
University of Aberdeen
Foresterhill Campus
Scotland, UK
AB25 2ZD

Research briefs for the Knowledge Scotland website

Food Health Innovation Scotland (FHIS) Science Bytes

International Scientific Association for probiotics and prebiotics (https://isappscience.org/)

Blogs by Karen Scott- https://isappscience.org/isapp-blogs/


I gained my BSc (Hons 2:i) in Biochemistry from the University of Aberdeen before continuing to my PhD (Molecular Biology of plant viruses) at what was then the Scottish Crop Research Institute in Invergowrie, Dundee. After my PhD I returned to Aberdeen to the Rowett Institute and have been here ever since.


Research Interests

Investigations into the development and evolution of the gut microbiota

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.

One main research area involves investigating the longitudinal development of the microbiota from birth in a group of infants. Specific techniques including DGGE, NGS and FISH are used to investigate the microbial composition while the activity of the microbiota is established using SCFA analysis and metabolite profiling.

Another key research area is investigating the health benefits that can be derived from increased consumption of oats and barley. The impact of these dietary components are assessed in vitro using bacterial mono- and co-culture, aswell as using mixed batch culture and fermentor systems.  Human studies have also been done to ascertain the effects in vivo.

Finally my group is involved in investigating the incidence, evolution and transferability of specific antibiotic resistance genes between anaerobic gut bacteria. These resistance genes are also useful genetic markers to investigate gene function in key gut anaerobes, and to perfrom genetic manipulation experiments.

Current Research

1. Development of the microbiota (composition and function) from birth,

2. Effect of different cereals as dietary components on the gut microbiota.

3. Manipulation of anaerobic gut bacteria



Through the RESAS work I collaborate with scientists at JHI (Kelly Houston, Nicola Holden), the Moredun (Eleanor Watson), SRUC (Judith Evans) and UHI (Peter Martin).

I also collaborate on various projects with other scientists from different Universities who have mutual interests in the activity of the gut microbiota, or in the prevalence and spread of antibiotic resistance genes.

Research Grants

  • Scottish Government funded HEI Partnership grant - A systems wide approach to the control of Campyobacter in the food chain (focussing on the presence of antibiotic resistance genes)
  • Scottish Government theme funding for RI
  • Commercial funding from Vogel to investigate the effect of a specific prebiotic on gut health
  • Commercial funding to perform anaerobic bacterial isolations

Teaching Responsibilities

I am responsible for teaching various units on the composition and function of the gut microbiota to MSc students and undergraduate 2nd year Medical students. I am also involved in supporting the general science and microbiology undergraduate teaching in the University, contributing to both lecturing and practical course teaching. I also contribute a section on Gut Microbiology to the successful Nutrition and Wellbeing MOOC, accessible learning for anyone interested.

Further Info

External Responsibilities

  • I am the president of ISAPP (International Scientific Association for Probiotics and Prebiotics), the foremost organisation in the world promoting the science behind probiotics and prebiotics (https://isappscience.org/)
  • I am an editor for the Microbiology journal
  • Invited expert on ILSI expert panel - ‘Exploring the role of the major gut microbiota clusters on nutritional and functional benefits of nutrients and nonnutrients’ which resulted in the publication by Ian Rowland, et al 2017. Invited expert on ILSI panel on Microbial Metabolism.
  • Regularly invited to review grant proposals submitted to International award bodies, and scientific manuscripts
  • Regular (2-3 per year) external examiner for PhD theses

Admin Responsibilities

I am the Institute Biological Safety Advisor

I am the primary supervisor for 2 PhD students and the co-supervisor for a further 2 PhD students.



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Contributions to Journals


  • Rowland, I., Gibson, G., Heinken, A., Scott, K., Swann, J., Thiele, I. & Tuhoy, K. (2018). 'Gut microbiota functions: metabolism of nutrients and other food components'. European Journal of Nutrition, vol. 57, no. 1, pp. 1-24.
    [Online] DOI: https://doi.org/10.1007/s00394-017-1445-8
    [Online] AURA: Gut_microbiota_functions.pdf
  • Walsh, AM., Crispie, F., Daari, K., O’Sullivan, O., Martin, JC., Arthur, CT., Claesson, MJ., Scott, KP. & Cotter, PD. (2017). 'Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks'. Applied and Environmental Microbiology, vol. 83, no. 16, e01144-17.
    [Online] DOI: https://doi.org/10.1128/AEM.01144-17
    [Online] AURA: AEM01144_17R1_Merged_PDF.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: https://doi.org/10.1097/MD.0000000000007347
    [Online] AURA: 16S_sequencing_and_functional_analysis_of_the.62.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: https://doi.org/10.1016/j.jcs.2017.01.005
    [Online] AURA: 1_s2.0_S0733521017300139_main_1_.pdf
  • Gibson, GR., Hutkins, R., Sanders, ME., Prescott, SL., Reimer, RA., Salminen, SJ., Scott, K., Stanton, C., Swanson, KS., Cani, PD., Verbeke, K. & Reid, G. (2017). '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, vol. 14, pp. 491-502.
    [Online] DOI: https://doi.org/10.1038/nrgastro.2017.75
    [Online] AURA: Expert_consensus_document.pdf
  • Costea, PI., Zeller, G., Sunagawa, S., Pelletier, E., Alberti, A., Levenez, F., Tramontano, M., Driessen, M., Hercog, R., Jung, F-E, Kultima, JR., Hayward, MR., Coelho, LP., Allen-Vercoe, E., Bertrand, L., Blaut, M., Brown, JR.M, Carton, T., Cools-Portier, S., Daigneault, M., Derrien, M., Druesne, A., de Vos, WM., Finlay, BB., Flint, HJ., Guarner, F., Hattori, M., Heilig, H., Luna, RA., van Hylckama Vlieg, J., Junick, J., Klymiuk, I., Langella, P., Le Chatelier, E., Mai, V., Manichanh, C., Martin, JC., Mery, C., Morita, H., O'Toole, PW., Orvain, C., Patil, KR., Penders, J., Persson, S., Pons, N., Popova, M., Salonen, A., Saulnier, D., Scott, KP., Singh, B., Slezak, K., Veiga, P., Versalovic, J., Zhao, L., Zoetendal, EG., Ehrlich, SD., Dore, J. & Bork, P. (2017). 'Towards standards for human fecal sample processing in metagenomic studies'. Nature Biotechnology, vol. 35, pp. 1069–1076.
    [Online] DOI: https://doi.org/10.1038/nbt.3960
  • 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: https://doi.org/10.1099/mgen.0.000043
    [Online] AURA: mgen000043.pdf
  • Hansen, R., Scott, KP., Khan, S., Martin, JC., Berry, SH., Stevenson, M., Okpapi, A., Munro, MJ. & Hold, GL. (2015). 'First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota'. PLoS ONE, vol. 10, no. 7, e0133320.
    [Online] DOI: https://doi.org/10.1371/journal.pone.0133320
    [Online] AURA: journal.pone.0133320.pdf
  • Walker, AW., Martin, JC., Scott, P., Parkhill, J., Flint, HJ. & Scott, KP. (2015). '16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice'. Microbiome, vol. 3, 26.
    [Online] DOI: https://doi.org/10.1186/s40168-015-0087-4
    [Online] AURA: Infant_Bifids_Protocols_Microbiome2015.pdf
    [Link] http://www.microbiomejournal.com/content/3/1/26
  • Scott, KP., Antoine, J-M, Midtvedt, T. & van Hemert, S. (2015). 'Manipulating the gut microbiota to maintain health and treat disease'. Microbial Ecology in Health and Disease, vol. 26, pp. 25877.
    [Online] DOI: https://doi.org/10.3402/mehd.v26.25877
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