Background: Naturally fermented milk (NFM) products are popular food delicacies in Indian states of Sikkim and Arunachal Pradesh. Bacterial communities in these NFM products of India were previously analysed by high-throughput sequence method. However, predictive gene functionality of NFM products of India has not been studied. In this study, raw sequences of NFM products of Sikkim and Arunachal Pradesh were accessed from NCBI database server. PICRUSt2 and Piphillin tools were applied to study microbial functional gene prediction in combination with the commonly used error-corrected denoising programs like DADA2 and Deblur.Results: Significant functional hits were observed from the Piphillin analysis which included some interesting pathways including GABAergic synapse, glutamatergic synapse and serotonergic synapse, which are known to be probiotic-related, among others that are absent in PICRUSt2 analysis. This study also showed the negative correlation of lactic acid bacteria (LAB) members (Lactococcus, Lactobacillus, Leuconostoc) with most of the disease-related functions, which were on the other hand, positively correlated with unwanted contaminants like Staphylococcus, Bacillus and Pseudomonas.Conclusion: The study explored the potential of microbial functional gene prediction using PICRUSt2 and Piphillin software, and indicated the significance of the presence of LAB in these NFM products of India. Since most LAB members are known to be potential health-promoting bacteria, their negative correlation to many of the disease-related functions also indicates their role in combatting unwanted potential contaminants.