Rewilding the Human Gut: Reintroduction of the Species Lactobacillus Reuteri

There is now substantial evidence that industrialization has resulted in substantial decrease in the bacterial diversity of the gut microbiota (Segata, 2015), likely due to a combination of factors such as use of antibiotics, modern clinical practices, sanitation, and change in dietary habits. However, the only factor for which empirical evidence is exists is the low content of Microbiota-Accessible Carbohydrates (MACs) in Western diets, which are indigestible dietary carbohydrates that become available to the microbes colonizing the intestine (Sonnerburg et al., 2015).

Previous work has confirmed the overall premise of 'microbiome depletion' by demonstrating higher diversity in the fecal microbiota of individuals from rural tribes in Papua New Guinea, which contain an additional of 50 species completely undetectable in North Americans (Martínez et al., 2015). One species detectable in every Papua New Guinean individual by 16S rRNA sequencing but not in a single US control was Lactobacillus reuteri (L. Reuteri). Interestingly, this species, which is also used as a probiotic, was regularly detected in humans in studies conducted around 1960 but is very rarely found in contemporary humans, suggesting a recent decline of the L. reuteri population in Westerners (Walter et al., 2011). Most importantly, L. reuteri is a member of the gut microbiota in many vertebrate species and exerts substantial benefits towards host immune functions and development, as demonstrated in a number of highly cited publications (Zelante et al. 2013; Buffington et al. 2016; Lamas et al. 2016; He et al. 2017).

It is currently unclear what caused the drop in the L. reuteri population. However, it is likely due to the importance of two dietary substrates, the carbohydrates raffinose and rhamnose, that are present at very low amounts in western diet, while being abundant in the diet of Papua New Guineans, a population that consumes a predominantly plant-based diet. Raffinose is a non-digestible oligosaccharide present in root vegetables, yams and beans, and it is an excellent growth substrate for L. reuteri. Rhamnose is a monosaccharide present in cell wall of many plants and can be fermented by enteric bacteria into 1,2-propanediol (1,2-PD), which facilitates the growth of L. reuteri in the presence of raffinose. Interestingly, L. reuteri strains isolated from Papua New Guniea fecal samples grow faster than the western strains MM4-1a and DSM2016T on both raffinose and raffinose+1,2-PD. This demonstrates that strains from Papua New Guinea are different from western isolates, likely due to adaptation to dietary substrates.

The goal of this study is to demonstrate that a bacterial species dominant in the non-westernized microbiome can be 'reintroduced' in the gut of Canadians fed a diet designed to promote the growth of the bacteria. This study will also determine how this 'reintroduction' influences immune function of the host and host-diet-microbiome metabolic interactions, and explore associations between them. The central hypothesis is that an isolate of L. reuteri, originating from rural Papua New Guinea, can be established in the gut of Canadians fed a diet containing the carbohydrates known to facilitate the growth of this microbe. It is also hypothesized that this 'reintroduction' with be associated with immunological and metabolic benefits to the host. To achieve these goals, the following aims are proposed:

1. To conduct a human trial to determine if a Lactobacillus reuteri strain isolated from rural Papua New Guinea (PNG) can be established in the gut of healthy Canadians.

2. To determine if colonization can be improved by feeding/promoting a diet specifically designed to provide growth substrates for L. reuteri.

3. To determine how both L. reuteri and the dietary intervention changes the human microbiome, metabolome, and immune biomarkers of inflammation.

This study will answer the important question if a 'lost species' can be reintroduced into the human gut, and provide potential mechanism how they may reduce the risk of chronic diseases. The availability of L. reuteri isolates from Papua New Guinea that are functionally different from western isolates in their growth on dietary components low in the western diet provides a unique opportunity to characterize strains from a beneficial bacterial species that were not exposed to modern lifestyle.