Microbial metabolism in the gut of man and ruminants

Beef, lamb and milk provide important sources of food for mankind.  Ruminant livestock production and the foods that are produced present two main challenges, however. One is environmental, in that ruminants produce large amounts of the greenhouse gas, methane. The second is that dairy and meat products contain a mixture of ‘good’ and ‘bad’ fats in terms of human health. We would like to prevent methane emission and to improve the healthiness of fats in meat and milk.  Coincidentally, both properties are linked via gut microbial activities.

Our research aims are to understand the microorganisms and processes, so that we can change their activities for environmental and health benefits.

Research focus

Methane is a greenhouse gas (GHG), 25 times as potent as carbon dioxide. Ruminants are major methane emitters, contributing 3-4% of global GHG emissions. The methane is derived from microbial fermentation in the rumen, being produced by microbes known as archaea. The archaea convert hydrogen and carbon dioxide produced by bacteria and protozoa to methane. In our Theme 5 work funded by RESAS, the ruminal methanogenic archaea of Scottish cattle and sheep are being characterized, in collaboration with Bob Mayes of the James Hutton Institute and Rainer Roehe of the Scottish Agricultural College. We will assess whether high methane-producing animals possess a different archaeal community to low-methane producers, and dietary and/or host characteristics associated with the differences. Already we have discovered links between the genetic background of the host and its methane emissions and also between the archaeal community and methane emissions.

Hydrogen is also utilized by fatty acid biohydrogenation in the rumen, which leads to a high proportion of health-threatening saturated fatty acids in foods derived from ruminants and to the formation, followed by the destruction, of health-promoting conjugated linoleic acids (CLA), and to the destruction of n-3, health-promoting fatty acids. The primary aim of this part of our research is to improve the fatty acid composition of ruminant milk and meat for human health. In order to achieve this aim, the microorganisms responsible for fatty acid transformations in the rumen are being identified, the fluxes through pathways of biohydrogenation and desaturation measured, the population sizes of the most significant microbial species evaluated, and ways of altering these fluxes and, particularly using plants containing long-chain hydroxy- and epoxy-fatty acids and essential oils, are being investigated. If these objectives can be achieved, it will then be possible, using dietary manipulation or new feed additives, to improve the health profile of fatty acids in ruminant products.

Microbial metabolism in the gut of man has implications for health. In particular, the microbial degradation of protein in the distal colon leads to the formation of toxic products. If amino acids were to be assimilated rather than broken down, much less toxic material would be formed. Protein-rich, low-carbohydrate diets lead to higher genotoxic activity in the colon and to the enrichment of pathogens, including Clostridium perfringens. The factors leading to these developments are being investigated. The possible usefulness of essential oils in promoting gut health, via their effects on commensal as well as pathogenic bacteria, is being investigated in an industrially funded studentship (Mr Dinesh Thapa, Nepal).

The work on plant extracts is based on the results from two EC-funded programmes that I previously coordinated, RUMEN-UP and REPLACE, whose aims were to find alternatives to growth-promoting antibiotics. The new 2012 FP7 project (7.7M Euros) of which I am coordinator is named RuminOmics: Connecting the animal genome, gastrointestinal microbiomes and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production (www.ruminomics.eu). Eleven partners across Europe will attempt to define the relations between host genetics, the ruminal microbiome and emissions using state-of-the-art –omics technologies. While doing so, we aim to develop tools for livestock producers and breeders to help them increase the efficiency of production by lowering polluting emissions.

A new BBSRC-funded project that I lead is a £1.2M Industrial Partnership Award to investigate ‘Sub-acute ruminal acidosis: an interdisciplinary approach to understand and prevent a multifactorial disease’. The overall aims are to explain the underlying mechanism of pathogenesis of SARA, to investigate if microbiome analysis can predict the severity of SARA, and to develop simple, non-invasive methods for monitoring animal behaviour relating to SARA and preventing the condition. Three academic partners, the Universities of Glasgow and Strathclyde and ourselves, three companies, ABVista, Chr. Hansen and Harbro, Quality Meat Scotland and DairyCo are partners in the project.

  • 2011 - TSB Genomics Competition, with Ingenza Ltd. £513,000
  • 2011 - EC FP7, FOOD-SEG partner, €23,219 (of total €999,915)
  • 2012 - Studentship, Commonwealth Scholarship Commission
  • 2012 - FP7 project RuminOmics, coordinator, €7.7M, 2012-2015
  • 2012 - BBSRC IPA Sub-acute ruminal acidosis (SARA). Consortium leader. £1.2M, 2012-2015
  • 2012 - TSB SPARK, methane £5k
  • 2012 - EBLEX (with SRUC) SafeBeef. £280k
  • 2013 - Studentship with SRUC, methane

Halmemies-Beauchet-Filleau, A., Kaireniusm P., Ahvenjarvi, S., Crosley, L.K., Muetzel, S., Huhtanen, P., Vanhatalo, A., Toivonen, V., Wallace, R.J., Shingfield, K.J. (2013) “Effect of forage conservation method on ruminal lipid metabolism and microbial ecology in lactating cows fed diets containing a 60:40 forage-to-concentrate ratio.” Journal of Dairy Science, 96 (4) pp. 2428-2447

Richardson, A.J., McKain, N., Wallace, R.J. (2013) “Ammonia production by human faecal bacteria, and the enumeration, isolation and characterization of bacteria capable of growth on peptides and amino acids.” BMC Microbiology,13 (Art. 6)

Newbold, C.J., Wallace, R.J., Walker-Bax, N.D. (2013) “Potentiation by metal ions of the efficacy of the ionophores, monensin and tetronasin, towards four species of ruminal bacteria.” FEMS Microbiology Letters, 338 (2) pp. 161-167

Morales, E.R., Espinosa, M.A.M., McKain, N., Wallace, R.J. (2012) “Ricinoleic acid inhibits methanogenesis and fatty acid biohydrogenation in ruminal digesta from sheep and in bacterial cultures.”  Journal of Animal Science, 90 (13) pp.4943-4950

Thapa, D., Losa, R., Zweifel, B., Wallace, R.J. (2012) “Sensitivity of pathogenic and commensal bacteria from the human colon to essential oils.” Microbiology – SGM, 158 pp. 2870-2877

Shingfield, K.J., Kairenius, P., Arola, A., Paillard, D., Muetzel, S., Ahvenjarvi, S., Vanhatalo, A., Huhtanen, P., Toivone, V., Griinari, M., Wallace, R.J. (2012) “Dietary fish oil supplements modify ruminal biohydrogenation, alter the flow of fatty acids at the omasum, and induce changes in the ruminal Butyrivibrio population in lactating cows.” Journal of Nutrition,  142 (8) pp. 1437-1448

Additional activities

Research briefs for the Knowledge Scotland web site

Press Releases

13th Feb: New European study to investigate methane production in livestock

Additional Responsibilities

I also participate in the FP7 FOODSEG project (foodseg.net) and the Global Research Alliance, which is a NZ initiative aiming to bring countries together to find ways to grow more food without growing GHG emissions. Recent Technology Strategy Board awards with Ingenza Ltd and Innovent Technology Ltd will enable metagenomic approaches to be taken to solve the methane problem, as well as to find new enzymes of industrial significance.

I serve on the Editorial Advisory Board of Animal Feed Science and Technology and participate in the Centre of Expertise, ClimateXChange.