Effects of different foods and cooking methods on the gut microbiota: an in vitro approach

Abstract Background Dietary interventions are likely tools for modulation of the gut microbiota but the large inter-individual variability in gut microbiota composition leads to different host responsiveness and the impact of a particular food cannot be assessed. In contrast, in vitro fermentation models allow characterization of the fecal microbiota when fermenting a large number of different foods. Furthermore, cooking methods also directly influence the effects of food on gut microbiota composition. The aim of this study was to investigate the gut microbiota growing on representative foods of the Mediterranean and Western diets as well as the influence of cooking methods using in vitro fermentations. Results We performed in vitro digestions and fermentations of 55 foods, raw or cooked using up to 5 cooking methods, for a total of 159 combinations, employing fecal material from three healthy adults as inoculum. The composition of the bacterial communities was determined by sequencing the 16S rRNA gene. Foods derived from plants or animals had significantly different impacts on the abundances of bacterial taxa. Animal and vegetable fats, fish and dairy products led to the greatest shifts in microbial composition. Specifically, an increase in the beneficial bacteria Faecalibacterium, Blautia and Roseburia was identified in animal and vegetable fats. However, butter, dairy products and fish also resulted in higher abundances of Lachnoclostridium, which has been associated to several diseases. With respect to cooking methods, only frying and roasting had strong and common effects across all food categories. In general, fried foods showed more differences than other cooking methods, and Ruminococcus was particularly responsive to the cooking method employed. Conclusions Despite substantial differences in baseline microbiota composition, some shared effects were detected across the three analyzed individuals, such as the substantial impact of high-fat foods on the abundance of health-relevant bacteria. Cooking methods effects on the gut microbiota resulted to be highly individualized and food-dependent, making them challenging to investigate and integrate into personalized diet. Further characterization of the responses of the fermentative microbiota to food-cooking method combinations will enable the refinement of dietary interventions aimed at gut microbiota modulation, paving the way towards personalized nutrition.