Probiotic Niche Specificity and Microbiome Analysis of Different Non-Dairy based Traditional Food Samples Using Metagenomic Approach

Sircar, Bijayanta; Mandal, Manisha; Mandal, Shyamapada

doi:10.30491/jabr.2025.494841.1821

Probiotic Niche Specificity and Microbiome Analysis of Different Non-Dairy based Traditional Food Samples Using Metagenomic Approach

Document Type : Original Article

Authors

Bijayanta Sircar ¹

Manisha Mandal ²

Shyamapada Mandal ¹

¹ Laboratory of Microbiology and Experimental Medicine, Department of Zoology, University of Gour Banga, Malda-732103, West Bengal, India

² Department of Physiology, MGM Medical College and LSK Hospital, Kishanganj, Bihar-855107, West Bengal, India

10.30491/jabr.2025.494841.1821

Abstract

Introduction: People consume different types of traditional dairy and non-dairy-based fermented foods worldwide. The literature review suggests that there are scientifically unexplored diverse non-dairy-based fermented foods. The present study was conducted to determine the taxonomic and metabolic status of beneficial bacteria in various non-dairy-based traditional food samples using a metagenomics approach.
Materials and Methods: Metagenomic analysis of food samples may reveal the presence of many beneficial culturable or non-culturable bacteria through Next Generation Sequencing techniques. In this study, we used six non-dairy-based food products, including two types of idli batter, vegetable fermented mixture, two types of vegetable pickles, and the Indian traditional food Shinni. Phylogenetic relationships, taxonomic plot analysis, presence of enriched genera, core microbiome comparative analysis, species richness in terms of α and β diversity, and functional profiling of the microbiome were also determined in this research work.
Results: All the samples showed a good abundance of probiotic bacterial presence. Specifically, Pediococcus, Weissella, Lactococcus, Acetobacter, and Lactobacillus were statistically more viable genera than others. Functional profiling of the six metagenome samples displayed the top nine KEGG Orthology metabolism and the top fourteen clusters of orthologous genes metabolism.
Conclusions: Variation in the richness and diversity of bacteria in all six samples, along with variations in metabolic functions, indicates the need for further investigation to explore the nutritional value and bioactivity of beneficial bacteria in our region.

Keywords

Non-Dairy Fermented Foods

Next Generation Sequencing

Metagenomic Analysis

Core Microbiome

Bacterial Metabolic Pathway,

Probiotics