Nestlé is committed to enhancing the quality of consumers' lives through nutritional products that promote health and wellness. It is with this mindset that the company actively pursues research on the human microbiome (the collection of microorganisms that inhabit specific parts of the human body) with the aim to develop functional products that provide microbial-mediated health benefits (see Fig. 1). Nestlé pioneered research on beneficial microorganisms – so called ‘probiotics’, i.e. “live microorganisms that, when administered in adequate amount, confer a health benefit to the host” (WHO expert group, 2011) – identifying lead Lactobacillus sp. and Bifidobacterium sp. strains to be included in a variety of food products such as infant formulae. This approach was further enriched by the development of nutritional products containing blends of microbiome-modulatory substances such as short-chain oligosaccharides (i.e. prebiotics), tailored to promote health through promotion of endogenous beneficial bacteria.

The association between multicellular organisms and prokaryotic microorganisms is not the exception, it is the rule. All organisms – from simple nematodes to complex humans – coexist with a population of microorganisms. These associations might be parasitic, commensalistic or mutualistic. The nature of the interaction might change over time, depending upon host or environmental factors. The dynamics of host–microbe interactions raises interesting questions. Did these associations impart an evolutionary advantage to the host or to the microbe? Can an existing interaction between a host and a microbial system be modulated in a way beneficial to the host? What are the predominant factors that influence the equilibrium between the host and the microbiome? These questions may remain at least partially unanswered for the next few years, but based on data accumulated so far it is already generally accepted that nutrition plays a major part in influencing this dynamic equilibrium.

The spectrum of biological activities that are affected by host-associated microorganisms is currently the subject of extensive investigation among the scientific community. In mammals, data accumulated so far indicate that the microbiome influences a wide range of physiological processes, including digestion, the innate and adaptive immune response, the gastrointestinal endocrine system, or even the central nervous system – to name a few. In humans, nutrition plays a significant part in all of these aspects and over recent years much research has been directed to this area.

From calories to bioactives: Increasing expectations from nutrition

Public awareness of the importance of nutrition to maintain health and prevent disease has significantly increased over the past few decades, paralleled by a significant expansion of research activities in nutritional sciences. In response to these social developments, and sometimes preceding them, the food industry has changed as well. The concept that appetizing food can also be good for your health is at the same time visionary and simple. Instead of treating disease with drugs alone, the nutrition and health industry is providing an increasing range of food-based products with the appropriate nutritional composition to help decrease the risk of developing diseases or improve recovery from illness. With the introduction of food-based nutritional approaches the health sector has more access to diversified solutions spanning from preventative to therapeutic approaches. Growing scientific consensus converges on the idea that contemporary nutritional habits in developed countries, sometimes loosely defined as a ‘Western diet’, characterized by an overconsumption of refined sugars, salt and saturated fat, together with lifestyle changes that include reduced physical activity, contribute to major diseases such as obesity, diabetes and cardiovascular disease. Public health scientists and health economists also argue for prevention as a complementary strategy to treatment with the benefit of reducing healthcare costs.

In view of the constantly increasing interest in the microbiome, the state of the science of nutrition and the human gut microbiome was reviewed and discussed by leading scientists in the field at the 11th Nestlé International Nutrition Symposium in Lausanne in October 2014.

Beneficial gut microbes

Dietary fibres are known to be beneficial to human health, particularly plant fibres that humans cannot digest. Scientists realized that the reason for this perplexing observation is because part of our food is also food for bacteria colonizing the human gut. The complex microbial world living in us (some researchers refer to the 2kg bacterial mass as a major human organ) had until recently defied explanation. However, thanks to new analytical developments largely based on characterization of nucleic acid sequences, the scientific community was able to study the totality of the gut microbes and these organisms have become a new target for the development of beneficial dietary interventions.

The original hypothesis that host-associated microbes play an important part in our health is more than 100 years old and dates back to Elie Metchnikoff (1908 Nobel Prize in Medicine), who described it in his book “The Prolongation of Life: Optimistic Studies.” Metchnikoff's hypothesis started with an epidemiological observation of his time: Bulgarian people live longer than other Europeans; and Bulgarians eat more yoghurt. Hence one might search for a life-prolonging principle in yoghurt. However, Metchnikoff went a step further and offered a visionary concept that tried to explain the effects of nutrition on health. He defined two main types of gut bacteria, which digest food in the colon in two fundamentally different ways. The first category includes saccharolytic bacteria, which can digest carbohydrates from plant sources into small organic acids. Among those, the lactic acid bacteria, which ferment lactose into lactic acid during yoghurt production, were for Metchnikoff the main bacteria responsible for the above epidemiological observations. Short-chain fatty acids such as acetate, propionate and butyrate – the metabolic end products of the majority of saccharolytic colonic bacteria – are the focus of much current research linking the gut to other organs1. In the second category he classified bacteria that digest animal proteins which leads to harmful metabolic waste products in a process he called “putrefaction”. These products in his hypothesis accelerate the aging process.

A 2014 Nature paper analyzing gut microbiome in the faeces of human volunteers fed alternatively with a carbohydrate-rich, plant-derived diet or a protein-rich, animal-derived diet came essentially to the same conclusions when using an impressive battery of contemporary ‘omics’ analytical approaches, based on state-of-the-art nucleic acid sequencing technologies2.

Nestlé's interest in probiotics

Nestlé research scientists build on Metchnikoff's hypothesis for several reasons. Nestlé manufactures a large quantity of dairy products. For the production of yoghurt, our scientists and technologists have a sound knowledge of industrial milk fermentation by lactic acid bacteria; they curate large collections of bacterial starter strains, many of which are close relatives of gut bacteria. Nestlé is also a leading producer of infant formula – our paediatricians and nutritionists strive to develop formulae that are close to human breast milk. For more than fifty years it has been known that breast milk contains factors that facilitate the establishment of the Bifidobacterium-dominated gut microbiome typically observed in breastfed babies. By association (‘breast is best’) beneficial health effects were attributed to bifidobacteria.

The next goal became to find candidates for promising probiotic (‘health-promoting’) bacteria. With the pioneering work of Minoru Shirota, a Japanese microbiologist who took Metchnikoff's ideas at face value, the first commercial developments took place with a probiotic drink that was introduced to the market in 1935, kick-starting the search for health-promoting bacteria. A few decades later, Nestlé and a handful of other companies that became interested in this area of research screened bacterial strains for candidate probiotic strains with specific properties using a panel of preclinical tests. Nestlé scientists published the first Bifidobacterium sp.3 and the second Lactobacillus sp.4 genome sequence, which allowed genome-based insights into the potential mechanisms of action of beneficial microbes. Genomic comparisons between bacterial strains of the same species that displayed different characteristics were conducted on microarrays, enabling scientists to make preliminary associations linking genes with phenotypes (i.e. bacterial characteristics). In collaboration with the Karolinska Institute in Sweden, we linked only hypothetical open reading frames of the sequenced Bifidobacterium longum strain NCC2705 with protection against rotavirus diarrhoea in a mouse model (unpublished data). Japanese researchers succeeded in linking carbohydrate transporter genes of the same NCC2705 strain with protection against toxigenic Escherichia coli infection5. Comprehensive analyses of bacterial metabolic products revealed that acetic acid excreted by the NCC2705 strain in the gut inhibited the activity of a toxin produced by the pathogenic E. coli (Shiga toxin). This validated the concept proposed by Metchnikoff that metabolic end products of the gut microbiome may be beneficial to the mammal host.

The identification of bacterial genes that encode health-promoting properties is necessary to build greater insight into the mechanisms underlying probiotic functions. However, for the food industry it is even more important to explore the range of health effects that can be achieved with probiotics and the ecoystems they influence.

A Nestlé-sponsored clinical trial published 20 years ago demonstrated that feeding a blend of bifidobacteria and lactic streptococci protected children against rotavirus diarrhoea6. In a randomized controlled trial at the International Center for Diarrhoeal Diseases Research in Bangladesh (ICDDR,B), Nestlé scientists demonstrated that Lactobacillus paracasei strain NCC2461 (also named ST11) had a significant therapeutic effect on children hospitalized with bacterial, but not with viral, diarrhoea7. Notably, the same strain also mediated a lower nasal congestion in adults with allergic grass-pollen rhinitis in a small proof of concept trial. The effect was attributed to a decrease in allergen-specific antibodies8. In a different clinical setting, Bifidobacterium lactis NCC2818 (see Fig. 2) was also shown to reduce allergic reactions in patients suffering from allergic rhinitis9. Moreover, L. paracasei NCC2461 was shown to decrease skin sensitivity to environmental stresses by increasing the skin barrier function10. Thus, one probiotic strain can have effects on more than one organ system (in this example NCC2461, on gut and nasal mucosa and skin), and different probiotics can affect the same organ while using different effector pathways. While these results provide further evidence that the described health benefits may be attributed to the introduction of a given probiotic strain, much remains to be investigated about their mechanism of action especially with respect to their direct and or indirect roles in biological outcomes.

Nestlé's research to understand mechanisms of action: The case of IBS

A rationalization of the differential effects mentioned is complicated by a limited understanding of the mechanisms of interaction between the gut-associated microbes and our physiology. As part of its efforts to fill this knowledge gap, Nestlé collaborated with scientists at McMaster University in Ontario, Canada, to characterize the role of gut microbes in an experimental model of irritable bowel syndrome (IBS). Oral supplementation of a probiotic B. longum strain (NCC3001) led to a reduction of anxiety-like behaviours, such as fear to explore the environment11. This was paralleled by normalization in the level of brain signalling molecules involved in the response to environmental stimuli. Those data, together with several independent studies reporting an alteration of the intestinal microbiome composition in IBS patients as compared to healthy subjects, suggest a role for the gut-associated microbes in the pathophysiology of this disease.

This hypothesis is further supported by recently obtained results (unpublished) demonstrating transfer of several IBS-related intestinal and behavioural characteristics to germ-free mice after colonization with faecal microbiome from IBS patients, which was not observed in germ-free mice colonized with healthy volunteers' faecal microbiome.

Nestlé's research on prebiotics

As an alternative to providing beneficial microbes directly by means of the probiotic approach, food compounds can be introduced that specifically support the growth of intestinal health-associated bacteria. These substances are called prebiotics. Many plant-derived materials have been explored, including inulin (fructo-polysaccharides present in fibers from many fruits and vegetables), fructo-oligosaccharides (FOS, derived from chicory root) and galacto-oligosaccharides (GOS from soybeans or synthesized from milk sugar). A recent Nestlé clinical trial in children demonstrated that prebiotic supplementation of infant formula with FOS/GOS led to an increase in faecal bifidobacteria, which was also associated with increased faecal acetate, butyrate and propionate, and decreased concentration of pathogenic Clostridium difficile12.

Recent technological developments in analytical sugar chemistry have identified new and potentially bioactive compounds in human breast milk. Advances in synthetic chemistry enabling large-scale production of these compounds have opened up opportunities to improve the nutritional quality of infant formulae. These innovations are based on a very intriguing concept: the “glycan code” in breast milk. In short, this concept tries to explain why oligosaccharides – which are indigestible to babies – are the third-most prominent component in milk, are complex in structure and are variable between species. The hypothesis states that lactating mothers produce breast milk sugar components that help an optimal gut microbiome to develop in the intestines of the newborn soon after birth. Babies acquire gut microbes from their mother and the environment, and it is important for the health of the infant that the correct microbiome establishes itself in early life. Nestlé is conducting controlled nutritional intervention trials with uniquely supplemented infant formula to test the hypothesis.

Short-chain fatty acids and the human gut microbiome

What else can human gut microbes do? Several studies have shown that soluble dietary fibers such as fructooligosaccharides (FOS) can have beneficial effects on body weight and glucose control. FOS is a prebiotic, indigestible by the gut enzymes, but metabolized by bacteria in the colon, i.e. food to our gut commensals. These bacteria produce acetate, propionate and butyrate as metabolic endpoints. Butyrate feeds the colon and induces glucose synthesis in the intestine (intestinal gluconeogenesis), which enters the circulation. Propionate activates receptors (more precisely FFAR3, free fatty acid receptor 3) on the nerves surrounding the portal vein, which transports the nutrients absorbed in the gut to the liver13. The peripheral nerves connect to the brain, which regulates gluconeogenesis in the intestine, illustrating the existence of an active bi-directional gut–brain axis making a positive contribution to our energy balance. Notably, feeding propionate instead of FOS induced similar effects, illustrating the importance of metabolites produced by the gut microbiome.

However, our connection with gut bacteria is more intricate than just providing extra calories. Metabolites of gut bacteria have other important physiological functions, as revealed by a collaborative study between Lausanne University, Novartis, CHUV, EPFL and Nestlé14. Using a mouse model of allergic airway inflammation, it was demonstrated that a diet rich in plant fibers reduced the pathological manifestations in the lung, while these were increased upon feeding mice with a diet low in fiber content. Also in this case, propionate ingestion reproduced the protective effects of a high-fibre diet on the lung, linking health beneficial effects of diets rich in plant fibres to metabolic products of gut bacteria. Similarities in the two systems described above go even further: the first relay in the gut–lung axis is the same as in the gut–brain axis: propionate activates FFAR3. Then, however, the pathways deviate: FFAR3 activation leads to glucose regulation in one case, yet it reduces the capacity of immune cells to mount pro-allergenic properties in the second case. It could be argued that high-fibre diets may produce multiple physiological benefits on both glucose regulation and immune function.

Nestlé's initiative to unravel the microbial metabolome

In collaboration with Imperial College London, Nestlé research has initiated a series of comprehensive metabolite profiling studies (metabolome studies) to identify key functional molecules produced by the gut microbiome. In one of these studies the metabolome of germfree mice was compared with the metabolome from mice colonized with a bacterial community isolated from the stools of a human baby. Colonized mice showed higher gut concentrations of tauro-conjugated bile acids and reduced plasma levels of lipoproteins15, suggesting that the energy harvest from the diet depended on the presence and the type of gut microbiome. It was subsequently investigated how the bacterial-host interaction was influenced after feeding pre-, pro- or symbiotics to mice. Differential effects could be assigned to pre- or probiotic modulation of the gut microbial metabolism, some features being exacerbated upon symbiotic (probiotic + prebiotic) administration. For instance, prebiotic galacto-oligosaccharides (GOS) reduced lipogenesis and triglyceride concentrations, while the probiotic L. rhamnosus NCC4007 strain induced decreased plasma lipoprotein levels16. Interestingly, germ free mice are resistant to weight gain when on a high fat diet. Compared to conventional mice, germ-free mice on a high-fat diet consumed fewer calories, excreted more faecal lipids, weighed less, showed enhanced insulin sensitivity and an altered cholesterol metabolism17. The metabolic events were also studied shortly after the establishment of gut bacteria in germ-free mice. The acquisition of a gut microbiome resulted in rapid increase of body weight; it stimulated glycogenesis and then triglyceride synthesis in the liver. Encouraged by these metabolomics results, we asked whether the knowledge acquired in animal experiments could be applied to humans. The data acquired in human subjects indicate interesting parallels. A 2014 study published by Nestlé scientists reported different urine and stool metabolome profiles between breastfed and milk formula-fed infants, revealing a relationship between processing of dietary proteins by intestinal bacteria and host protein metabolism18. At the other extreme of the lifespan, centenarians showed an increased urinary excretion of bacterial metabolites, suggesting links between gut microbiome composition and longevity19.

Developing tangible perspectives

Where is the future of microbiome research leading? Some microbiologists now see humans as a multi-organism consortium. For more doubtful scientists it remains to be proven to what extent our phenotype is co-determined by the microorganisms that inhabit our gut. Skeptics have already voiced their opinions. William P. Hanage is a Harvard epidemiologist who, in a 2014 Nature comment, called for a good dose of caution towards the conclusions of many published microbiome studies, underlining that association is not causation20. It is safe to predict that the microbiome field will be progressively integrated into established health research and applications. As molecular mechanisms start to be identified in the context of human disease, the field will probably move away from having its own identity and be incorporated by scientists and clinicians who can associate the findings in their areas of expertise.

Experimental therapies such as faecal transplants, which have been effective in fighting recurrent Clostridium difficile intestinal infections, demonstrate the importance of gut microbiome equilibrium for human health. Microbial transplantation is still in an experimental stage and clinicians would benefit from a better understanding of the mechanisms involved, which might allow future interventions with defined microbial communities or microbiome-derived compounds. Perhaps the best way to summarize the future for microbiome research is that there will be a progressive integration into the mainstream of epidemiological and medical research while concentrating on microbiome function rather than its composition. The challenge will be the application of new analytical tools to couple patient populations with treatments or clinical decision-making. Therefore, the microbiome has the potential to play a part in the evolution of personalized medicine. In the future, microbiome characteristics may be used to indicate whether a subject might react positively to a medical or dietary intervention, or which treatment might be best adapted to a person's physiology.

The microbiome is currently being associated with a range of conditions, including anxiety, autism, inflammation and obesity. How can we intervene to change microbial ecology in a way that would provide a therapeutic benefit? If we consider the human microbiome as an ecosystem, there will be underlying principles defined in ecosystems such as soil, lakes, rivers, and oceans that will serve as guides. It seems certain that as our understanding of human microbial ecology develops, we will be able to identify the molecular mechanisms underlying associations, determine key points of intervention and demonstrate efficacy in randomized clinical trials.

Overall, the field of microbiome research and its impact on human health is too important for scientists interested in nutrition and health to be ignored. At Nestlé we have selected two approaches. Scientists at the Nestlé Research Center in Lausanne are conducting prospective nutritional and health studies with frequent sampling of diverse microbiome together with a detailed documentation of health outcome (selected studies to be found in ClinicalTrials.gov under the following registration identifiers: NCT01276626, NCT01715246, NCT01581957, NCT01983072, NCT02031887, NCT01880970, NCT01971671, NCT02021058, NCT02223585). In partnership with the Epigen consortium, Nestlé participates in a large, long-term birth cohort study in Singapore, to characterize how delivery mode and gestational age influence infant gut microbiome and health-related parameters (ClinicalTrials.gov identified: NCT01174875). In parallel, we organized a smaller birth cohort study in Bangladesh with ICDDR,B, an institution that has a significant database on nutrition, health and disease in its population. ICDDR,B is renowned for translating research into interventions that lead to a measurable health improvement in their population. With these prospective data and by taking advantage of existing cohorts in Europe and beyond, we will test predictions of the literature concerning microbiome-health associations. For those associations, which we can confirm for the investigated population, we will design nutritional intervention trials targeting microbiome changes and test for predicted health benefits.

At the Nestlé Institute of Health Sciences Lausanne, which is the bio-analytical arm of Nestlé Research, we are investigating microbe–host interactions for the promising microbiome–health associations with respect to their mechanisms of action by deploying state-of-the-art ‘omics’ technologies and informatics systems approaches for multiple data analytics integration. With this double-pronged approach, we are excited by the prospect of delivering new knowledge in food compositions and nutritional interventions that promote human health by working in concert with host-associated microbes.

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