Professor Harry Flint


Professor Harry Flint

Role of gut microorganisms in nutrition and health

Fibre and other slowly-digested carbohydrates that are found mainly in plant-based foods make important contributions to human health. These are thought to include helping to maintain gut health and prevent cancer, heart disease and diabetes. Much of their influence occurs through effects on the complex microbial community that colonises our large intestine.

Our research is uncovering the impact of plant fibre and resistant starch on the species composition and metabolism of human gut micro-organisms. This will help us to optimise dietary approaches to benefit human health, including collaborating with plant breeders to identify and develop varieties that maximise health benefits.

The mammalian gut is colonized by a dense and complex microbial community that has a major influence on nutrition and health. The main energy sources for microbial growth in the large intestine of man and farm animals, and also in the rumen, are plant-derived fibre and polysaccharides. Our research employs molecular community analysis, anaerobic microbiology, metabolic profiling and genome data to identify the roles of particular bacteria in the microbial community of the human large intestine. A particular focus is the microbial colonization and degradation of insoluble substrates such as plant cell walls and resistant starch particles (Walker et al 2008), The different groups of micro-organisms that colonize the mammalian gut vary widely in their ability to utilize different carbohydrate sources, reflecting differences in the organization of their degradative enzyme systems, uptake systems and energy metabolism. These differences are now being revealed by analysis of draft genome sequence information from key fibrolytic gut bacteria (Flint et al 2008, Rincon et al 2010). Recently a series of human dietary intervention studies have allowed us to gain unique information on the dynamics of the gut community in response to dietary change, and on the occurrence of inter-individual variation in key bacterial species that appears to influence the fermentation of dietary resistant starch (Duncan et al 2007, Walker et al 2011).

At the same time we are trying to understand the factors that determine metabolic outputs from the gut community. We have been investigating phylogenetic groups responsible for key functions, such as butyrate and propionate formation and lactate utilization, in the human large intestine, using a combination of cultural and molecular approaches. A long-standing line of work (reviewed by Louis & Flint 2009) has defined the major groups responsible for butyrate production in the human colon, including Roseburia spp., Eubacterium rectale, and bacteria related to E. hallii that can convert lactate to butyrate (Duncan et al 2004). Gut pH appears to play an important role in the ecology of these organisms (Duncan et al 2009). Recent work has defined the substrate preferences of another important butyrate-producer Faecalibacterium prausnitzii (Lopez-Siles, in prep) and the new lactate-utilizing species Anaerostipes coli (Allen-Vercoe et al, in prep). These are among the 10 most abundant bacterial species detected in the human intestine by 16S rRNA sequence analysis (Walker et al 2010). In addition we are currently examining the ability of different isolated strains and species to release and transform phenolic compounds present in plant cell wall material.

The ultimate aim is to use this information to understand and enhance the health benefits of plant derived fibre, including the development of new prebiotics. At the same time this work promises to explain why different individuals show contrasting responses to added fibre in their diets that range from intolerance (eg. in some IBS sufferers) to health enhancement.

Research team

Dr Sylvia Duncan - Research Fellow

Dr Indrani Mukhopadhya - Research Fellow

Dr Paul O Sheridan - Research Fellow

Dr Dinesh Thapa - Research Fellow

Dr Eva Soto- Research Fellow

Faith Chung - Post Graduate student


Scottish Government RESAS

  • RESAS themed programme 2011-2016: RINH representative for Food theme (5); Coordinator for WP5.2.RD3.
  • Scottish Government Strategic Partnership project with U. Glasgow on SCFA and satiety [2012-2016]

BBSRC funding

  • Research project grant BB/L009951/1 – ‘Uncovering the molecular strategies that allow human gut symbionts to degrade insoluble dietary and host glycans’ (3 year project due to start in 2014. Part of a collaborative project (Harry Flint - principal applicant) with Dr Nathalie Juge, IFR, Norwich)
  • BBSRC CASE PhD studentship. (2012-2016)-  ‘Development of new targeted prebiotic approaches for optimizing the human intestinal microbiota’ Industrial partner, Cargill (Dr Douwina Bosscher); UoA supervisors Harry Flint and Sylvia Duncan.

EU projects 

  • EU FP7 SATIN (2012-2016) “Satiety control through food structures..” (18 partners - U Aberdeen component £691,343) (with Alex Johnstone). Work package leader.
  • EU FP7 FibeBiotics (2012-2017) “Dietary fibers supporting gut and immune function..” (17 partners  - U Aberdeen component  £300,000) (with Petra Louis).



  • Moraïs, S., Cockburn, DW., Ben-David, Y., Koropatkin, NM., Martens, EC., Duncan, SH., Flint, HJ., Mizrahi, I. & Bayer, EA. 'Lysozyme activity of the Ruminococcus champanellensis cellulosome'. Environmental Microbiology.
    [Online] DOI: 10.1111/1462-2920.13501
  • Duncan, SH., Russell, WR., Quartieri, A., Rossi, M., Parkhill, J., Walker, AW. & Flint, HJ. (2016). 'Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid'. Environmental Microbiology, vol 18, no. 7, pp. 2214-2225.
    [Online] DOI: 10.1111/1462-2920.13158
    [Online] AURA: Duncan_et_al_2016_Environmental_Microbiology.pdf
  • Walker, AW. & Flint, HJ. (2016). 'Editorial: further evidence that proton pump inhibitors may impact on the gut microbiota'. Alimentary Pharmacology & Therapeutics, vol 43, no. 10, pp. 1104-1105.
    [Online] DOI: 10.1111/apt.13596
  • Widder, S., Allen, RJ., Pfeiffer, T., Curtis, TP., Wiuf, C., Sloan, WT., Cordero, OX., Brown, SP., Momeni, B., Shou, W., Kettle, H., Flint, HJ., Haas, AF., Laroche, B., Kreft, J-U, Rainey, PB., Freilich, S., Schuster, S., Milferstedt, K., van der Meer, JR., Groszkopf, T., Huisman, J., Free, A., Picioreanu, C., Quince, C., Klapper, I., Labarthe, S., Smets, BF., Wang, H., Soyer, OS. & Isaac Newton Institute Fellows 'Challenges in microbial ecology: building predictive understanding of community function and dynamics'. The ISME Journal.
    [Online] DOI: 10.1038/ismej.2016.45
  • Sheridan, PO., Martin, JC., Lawley, TD., Browne, HP., Harris, H., 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.
    [Online] DOI: 10.1099/mgen.0.000043
    [Online] AURA: mgen000043.pdf
  • Morais, S., David, YB., Bensoussan, L., Duncan, SH., Koropatkin, NM., Martens, EC., Flint, HJ. & Bayer, EA. (2016). 'Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition'. Environmental Microbiology, vol 18, no. 2, pp. 542-556.
    [Online] DOI: 10.1111/1462-2920.13047

Research briefs for the Knowledge Scotland web site

EU projects

Satin – is a project funded by the European Union Seventh Framework Programme (FP7/2011-2016) under grant agreement n° 289800 to examine Satiety Innovation. This project will examine novel food ingredients on appetite control, with links with the food industry.

Invited Lectures (2010-11) - Harry Flint

  • International Microbiome consortium meeting (MetaHIt), Shenzhen China. March 2010
  • ASM Beneficial Microbes symposium, Miami USA. October 2010.
  • Gut Day, Ghent. October 2010
  • The Role of Microorganisms in Adaptation and Evolution of Humans, Animals and Plants. Meeting to be held in Israel. March 2011
  • The Microbiota in Health and Disease – meeting to be held at Yale University USA. April 2011
  • Today’s Science Tomorrow’s Medicine meeting in Stockholm. October 2011

Additional Activities

Harry Flint is an Associate Editor for Microbiology, and is on the editorial boards of Environmental Microbiology, FEMS Microbiology Ecology and Gut Microbe. Both he and Sylvia Duncan are regular reviewers for a wide range of journals.

Harry Flint is a member of the UK Advisory Committee on Novel Foods and Processes (ACNFP) and was a member of the Organizing Committee for the Rowett-INRA 2010 conference held in Aberdeen

Book Chapters

  • Flint HJ, Duncan SH and Louis P (2009). Gut Microbial Ecology. In Designing Functional Foods ed McClements DJ & Decker EA. Pp. 38-67. Woodhead Publishers.
  • Flint HJ, Duncan SH (2010) Response of the human colonic microbiota to dietary change. Old Herborn University Symposium Monograph No 22
  • Flint HJ, Duncan SH  (2010) Prebiotics and fiber. In ”Probiotics and Prebiotics” - Floch & Kim (ed)
  • Miller MEB, Brulc JM, Bayer EA, Lamed R, Flint HJ, White BA (2009). Advanced technologies for biomass hydrolysis and saccharification using novel enzymes. In Biomass to biofuels: strategies for global industries. Wiley & Sons.
  • Flint HJ, Wallace RJ. (2010). Obesity and colorectal cancer risk: impact of the gut microbiota and weight-loss diets.  Open Obesity Journal.