Assessing gaps in science and innovation

On the 30th - 31st of May 2016, Douwina Bosscher (Cargill) attended a workshop "The Microbiome, Diet and Health: Assessing Gaps in Science and Innovation". Here she led a session on "Advances and barriers for valorisation of gut microbiome research - Industry R&D perspective".

The workshop was organised by OECD, the Buisness and Industry Advisory Committee (BIAC), and the Department of Economy, Science and Innovation (EWI) of the Flemish Government, Belgium in Brussels, Belgium. 

Below is an abstract of Bosscher's presentation.


The human microbiome is a rapidly emerging market driven by the steep growth of investments in research and development in both academic and industry circles. The prompt translation of new scientific discoveries in the general press raises consumer awareness, which is critical for market acceptance of new products with health positioning. Digestive health is as a universal consumer concern. Food and beverages with digestive health as prime positioning accrued value of sales of US$77.2 billion globally in 2014 - making it the third most popular positioning platform behind general wellbeing and weight management (Euromonitor, 2014).

Projects like the Human Microbiome Project (HMP) funded by the National Institutes of Health (USA) (>$150MM) and MetaHIT (~$22MM) funded by the 7th Framework Program (FP-7) of the European Commission, clearly have set the scene; while the more recent FP-7 MetaCardis (~$15MM) (1), FP-7 MyNewGut (~$10MM) (2), amongst others, keep advancing this field. In addition, numerous academic-industry partnerships have been created. It is fair to state that during the last decade there has been an explosion in both basic and applied microbiome research.

Target indications for human gut microbiome research are enteric infections (C. difficile-associated), inflammatory bowel disease and irritable bowel syndrome; but extend to extra-intestinal sites such as immune disorders (allergy, chronic inflammatory states), infectious diseases, obesity and metabolic disorders and, more recently also neurological disorders. Given the wide range of conditions and diseases affected by the functioning of the gut microbiome; industry interest ranges from food ingredient producers, consumer goods companies, pharma industry, medical device companies, to biotech and technology service providers (-‘omics’).

Food companies have been mainly leveraging their scientific insights and research investments into the development of pre- and probiotics. The latter being a live organism which, when administered in adequate amounts confers a health benefit to the host (FAO/WHO Expert Consultation Report, 2011). Prebiotics are non-digestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, thus improving a host health (Gibson and Roberfroid, 1995). Studies have primarily focused on stimulating growth of lactic acid producing bacteria such as bifidobacteria and lactobacilli – as indicators of a healthy gut microbiota, by utilizing in-vitro simulations of gut microbial fermentations, animal studies (including the use of gnotobiotic breed animals) or through clinical trials, utilizing molecular techniques to quantify target organisms.

Ongoing developments in –omics technologies (particularly metabolomics and the development of the next generation of sequencing technologies or metagenomics) provide newest technological tools to comprehensively characterize the human microbiome and its functioning. The building of a publicly accessible database with reference genomes (HMP, MetaHIT) is critical in this effort. Hence worldwide initiatives that contribute to this body of knowledge either by government sponsored programs of even single academic or private initiatives should be encouraged. At the same such insights have revealed the extreme complexity of the functioning of bacterial ecosystems in the human gut. Adequate interpretation of such complex datasets have made the field of bioinformatics critical to capture new insights generated. It is clear that such technological developments go hand in hand with generating newest scientific insights into how the gut microbiota impacts health and disease.

Institutions and/or corporate entities need to overcome the technologic and scientific challenges on how to effectively valorize investments made. Indeed, to impact public health scientific insights need to be translated into consumer messaging which can be achieved by governments into dietary recommendations or, by industry through new product launches with health positioning. For food ingredient companies’ new ingredient development and/or scientific substantiation of health benefits are critical drivers of innovation pipelines. However, effective consumer messaging on the associated health benefits is essential (i.e. health claims); which under the current environment forms a barrier esp. in the field of digestive health.

In addition, science in this field evolves at extreme speed which gives rise to uncertainty of previously executed research. Mapping of metagenomic reads of European gut microbiomes to reference genomes revealed in 2011 the existence of enterotypes that were to characterize individuals in their microbial community composition (Arumugan et al., Nature). More recently, gut microbial richness (expressed by gene number) showed to be inversely correlated with dysregulation of metabolic markers such as insulin resistance and dyslipidaemia, marked overall adiposity and more pronounced inflammatory phenotype (Le chatelier et al., 2013, Nature). Interestingly, loss of richness has been shown to be partially corrected by dietary interventions (Cotillard et al., 2013, Nature). There is an urgent need to find consensus in the scientific community about gut microbiome markers (taxonomic and/or functional) with predictive value for risk for certain disease. With such biomarkers handy this field can advance from establishing correlations between microbiota composition (and/or functioning) and disease states (essential to generate hypotheses) towards identifying causal relationships. Consequently, translations can be made on the impact of diet, or beneficial effect of certain functional foods, for wellbeing and disease prevention through a modulation of the gut microbiota.

In parallel, insights are being generated on the impact of external influencers, beyond diet, such as circadian rhythms and physical activity. Confounding factors related to data generation are for example handling of fecal sample preparations, calling for a universal standardization of study designs and protocols.

This is a highly competitive field. The presentation will include examples of barriers to overcome to further advance this field and Cargill’s contribution herein. This through a well-balanced project portfolio of corporate funded (applied) research and our partnering into multidisciplinary research consortia focused on both applied and basic research. Examples of our participation into consortia are the previously named 7th European Framework programs MetaCardis (1) and MyNewGut (2).


(1)MetaCardis investigates the role of gut microbes in cardiometabolic diseases. The main investigatory approach is metagenomics and the use of clinical and experimental studies:

(2)MyNewGut Project investigates the microbiome's influence on energy balance and brain development/function put into action to tackle diet-related diseases and behavior: