It is becoming increasingly apparent that the microorganisms in the human gut are pivotal to many aspects of our health. Disturbance of the gut microbiota has been linked to a variety of diseases, including colon cancer, diabetes, inflammatory bowel disease, and obesity [1]. Consequently, the gut microbiota has emerged as a potential target for the prevention or treatment of such diseases. Targeted manipulation of the gut microbiota can be achieved by dietary intervention, including through the use of fermented foods, probiotics or prebiotics [2].
A probiotic is a live microorganism that exerts health benefits upon the host when it is ingested at sufficient quantities [3]. Many probiotic strains are consumed as constituents of yoghurt/fermented milk-type drinks or as supplements in the form of capsules. To access the lower gastrointestinal tract, probiotics must first survive transit through the acidic upper gastrointestinal tract. Some probiotic strains can subsequently colonise the gut by adhering to the intestinal epithelial cells [4]. A number of potential mechanisms can contribute to the health benefits of specific strains. These include pathogen inhibition via bacteriocin production or mucosal competitive exclusion, and immunomodulation [5]. Human studies have demonstrated that probiotic strains, such as Bifidobacterium infantis 35624, Lacticaseibacillus casei DN-114001, and Lacticaseibacillus casei Shirota, confer health benefits, including alleviation of the symptoms of irritable bowel syndrome, prevention of antibiotic-associated diarrhoea, or protection against infection [6–8].
Health benefits have also been attributed to several traditional fermented foods and the microbes therein [9]. Particular examples of kefir, a traditional fermented milk product (FMP), have been linked to health benefits, including anti-cholesterolemic, anti-inflammatory, and anti-pathogenic effects [10–12], and several investigations indicate that specific microorganisms in kefir contribute to these effects [13–15]. Despite this promise, it should be noted there has been a relative lack of research into the effects of kefir on human health, with most investigations relying on in vitro or animal models [16].
Prebiotics can also beneficially influence the gut microbiota. Prebiotics are non-digestible oligosaccharides that stimulate the growth of health-promoting commensal microorganisms in the gut [17]. The most frequently studied prebiotics are fructooligosaccharides, galactooligosaccharides, and inulin [18]. Prebiotics naturally occur in various foods, including artichokes, chicory and wheat, but can also be provided in the form of food supplements [19]. Human studies have demonstrated that prebiotics confer various health benefits, including improved satiety, lowered insulin concentrations, and reduced infection [20–22].
Metagenomic and metabolomic sequencing efforts are beginning to improve our understanding of the effects of probiotics, prebiotics and fermented foods on the human gut microbiota and metabolome [23, 24]. However, the majority of studies have been directed at preventing or treating the symptoms of specific diseases [25] and/or evaluating the impact of consumption of high quantities of a probiotic(s), prebiotic(s) and/or fermented food(s) [26]. Few studies to date have analysed the relative impact of supplementing diets with moderate portions of one of these products on the microbiota and metabolome of healthy participants [27].
In the present study, we use metagenomic sequencing and metabolomics to identify changes in the human gut microbiota and metabolome of healthy participants following daily consumption, over 28 days, of either a single portion of a commercial FMP containing the probiotic L. casei, a traditional fermented milk beverage kefir or a diet enriched with the prebiotic inulin.