Food fermentation has its roots back to ancient generations and is nothing but a means to preserve the food when there are no refrigerators available. Fermented foods are prepared using microbial conversion of major and minor food components, which commonly include dairy based products like curd, south Indian staples such as idli and dosa, fermented soy products from northeast India like kinema and hawaijar, sweet desserts like srikhand and drinks like kombucha and many others. These foods are claimed to have manifold health benefits; however, the claims lack scientific evidence and must be subjected to experimental validation.
In line of this, our group is investigating the effects of fermented food consumption on gastrointestinal (GI) health among traditional fermented food consuming ethnic population of Sikkim, India where fermented foods are an integral part of daily diets, through inspecting and understanding the alteration/modulation in the oral and gut microbiome. Microbiome is a community of characteristic microorganisms colonizing a particular habitat. Oral and gut microbiome, which respectively refers to collection of microorganisms in the oral cavity and GI tract, is reported to be involved in key physiological functions such as digestion and immune functions. The microorganisms produce enzymes which digest food and return important metabolites to human health. The oral and gut microbiome are regulated mostly by diet. For example, healthy eating keeps the microbiome happy and sound. However, any perturbations in microbiota composition can lead to onset of diseases.
In a broadest sense, the impacts of the study may shed insights about the quality and safety of the fermented foods consumed in the region linking to digestive health. The findings may further encourage similar studies across other regions/states of India as well as other parts of the globe where fermented foods and beverages are fundamental part of cultures and traditions. Furthermore, effects of specific fermented foods on the oral and gut microbiome are going to have welcoming opportunities towards development of precision functional foods for healthy life.
But challenges still persist. As these studies are exploratory in nature, it becomes somewhat difficult to collect accurate information on key factors influencing the microbiome, for example, if a subject/patient is really consuming alcohol or a regular smoker or not as alcohol consumption and smoking are both known to influence the microbiome composition. Secondly, what if the information/data we are getting is a cumulative effect of too many factors rather than a single factor which we are studying. Lastly, it is increasingly cumbersome to define control or healthy population as there are so many criteria that need to be considered to declare someone healthy.
For the young minds who are working or interested in working on human microbiomes, I would suggest working in a more planned way keeping in view of the reported challenges. As more and more studies on human microbiomes will grow, scientists and medical practitioners get to know more about the microbiome and their activities with respect to host and environmental factors, it will be likely to apply more rigorous standards. After all, our main aim is to offer better guidance to the general public to take best care of their own microbiomes.
Looking ahead, integrating longitudinal study designs, standardized dietary assessments, and advanced multi-omics analyses will be essential to strengthen causal interpretations. Collaboration between microbiologists, nutritionists, clinicians, and data scientists will further improve study robustness. Such integrative approaches will not only refine our understanding of diet–microbiome interactions but also support evidence-based dietary recommendations, culturally informed nutrition policies, and the development of safe, region-specific functional foods tailored to diverse populations.
