In this 36-week randomized cross-over trial, a low-fat vegan diet led to greater reductions in body weight compared with a Mediterranean diet. The relative abundance of Bacteriodetes decreased and Eubacteria increased on both diets. The relative abundance of Lachnospiraceae increased, the Firmicutes to Bacteroidetes ratio increased and the butyrate-producing bacteria decreased on the Mediterranean diet. The relative abundance of Proteobacteria decreased, and Enterobacteria and Ruminococcus increased on the vegan diet. Changes in body weight correlated positively with changes in relative abundance of Firmicutes and Lachnospiraceae on both diets. In addition, changes in body weight correlated negatively with changes in relative abundance of Enterobacteria on the Mediterranean diet and Eubacteria on the vegan diet.
We hypothesized a greater increase in the abundance of Bacteroidetes relative to Firmicutes on both diets. However, in the present study, we found Bacteroidetes to significantly decrease in both groups and the ratio of Firmicutes to Bacteroidetes to increase. This contradicts the current literature which shows a higher abundance of Bacteroidetes in vegans and vegetarians compared to omnivores (23–25). For instance, in one study, the bacterial composition of Indian adults was compared to that of Chinese adults. Both groups ate a diet that emphasized whole, plant-based foods, however, the Chinese adults ate more animal fat and protein. The microbiomes of the Indian adults were found to have nearly four times the percentage of Bacteroidetes than in the Chinese adults, 16.39% versus 4.27%, respectively (p = 0.001). This may be explained by their lower intake of animal products (25), which supports our initial hypothesis.
Additionally, it has been shown that the Bacteroidetes to Firmicutes ratio correlates negatively with BMI, meaning a greater abundance of Bacteroidetes relative to Firmicutes is associated with a lower BMI (26). Compared to non-obese individuals, obese individuals have been shown to have a three-fold less relative abundance of the Bacteroidetes phylum and a greater abundance of Firmicutes (27). Although we observed the opposite: the body weights of the vegan participants decreased significantly while the ratio of Firmicutes to Bacteroidetes increased, we did note a moderate, positive association between changes in body weight with changes in relative abundance of Firmicutes on both diets.
In this study, the relative abundance of Prevotella increased insignificantly under both interventions, with a greater increase under the Mediterranean diet. This finding supports our second hypothesis as well as the current literature. Plant-based foods are high in a type of carbohydrate called polysaccharides. Prevotella is a polysaccharide-degrading bacteria, and thus, a diet high in polysaccharides is beneficial for bacterial substrate utilization (28, 29). Additionally, significant associations between vegetable-based diets and the abundance of Prevotella have been shown (30).
Our third hypothesis, which predicted an increase in the abundance of Faecalibacterium prausnitzii on the vegan diet, was also correct, although the increase was insignificant. Faecalibacterium prausnitzii has been shown to be more abundant on vegetarian and vegan diets (31). Populations that consume higher amounts of resistant starch in place of protein and fat, which reflects the diet composition of this study’s vegan intervention, have greater abundance of Faecalibacterium prausnitzii (32). High-fiber diets most likely support the growth of Faecalibacterium prausnitzii due to the role that this species plays in degrading plant polysaccharides and starch to produce health-promoting short chain fatty acids (33, 34). While we observed a decrease in Faecalibacterium prausnitzii under the Mediterranean diet, a Mediterranean-style diet, in addition to a high-fiber diet and a vegetable-rich macrobiotic diet, has been associated with an increased in Faecalibacterium among individuals with type 2 diabetes (34).
We also observed significant changes in the relative abundance of butyrate producing bacteria, Enterobacteria, Ruminococcace and Proteobacteria. Based on the current literature, we would expect to see an increase in butyrate producing bacteria, however, we observed a significant decrease on the Mediterranean diet. Butyrate, along with acetate and propionate, is a short chain fatty acid that has been shown to increase in individuals with the hightest adherence to a Mediterranean diet (35) and in individuals following a strict vegan or vegetarian diet (30).
The significant increase in Enterobacteria under the vegan diet is also in opposition to previous research. Zimmer et al. noted lower Enterobacteriaceae species in vegans than controls (36). Kim et al also observed a decrease with a strict vegetarian diet (28). However, we did observe a negative correlation between changes in body weight and changes in relative abundance of Enterobacteria on the Medtierranean diet (r=-0.32; p = 0.02) that remained significant after adjusting for changes in energy intake (r=-0.34, p = 0.02).
It is less clear as to how to results of Ruminococcace line up against previous research as there is less of a clear trend. In one study examining changes in microbiota on an animal based diet versus a plant based diet, the animal based diet decreased Ruminococcus (37). Conversely, Ruminococcus was associated with omnivorous diets, as opposed to vegan vegetarian diets, in another study (30). Lastly, our Protobacteria results are supported by other studies. A study examining the microbiome of undernourished and obese children in Mexico found a positive correlation between proteobacteria and fat intake, in addition to greater abundance of Rroteobacteria in obese children. This is consistent with our study findings, with Proteobacteria being decreased after the low-fat vegan dietary intervention, and is in line with the significant weight loss in this group (38). In another study, which examined microbiota in relation to Mediterranean diet adherence, lower intake of polysaccharides was related to a higher relative abundance of Rroteobacteria (P = 0.028) (35).
Study strengths and limitations
The strengths of the study include the randomized cross-over design and the reasonably long study duration provided sufficient time for adaptation to the diet and to capture microbiome changes. The weekly classes provided for participants also were a strength in facilitating adherence. Despite the long trial length, we achieved a high level of retention (84%), in accordance with our previous findings (39). Importantly, the results of this free-living study are applicable for general population.
We also need to admit some limitations. Dietary adherence was high, but it has been shown previously that self-reported data may not always accurately reflect real dietary intake (40). However, it is reassuring that the reported changes in dietary intake were accompanied by changes in body weight and gut microbiome. Furthermore, our participants were generally health-conscious individuals who were willing to change their diet. Therefore, they may not be representative of the general population, but rather of a population seeking advice how to lose weight.