Bacterial diversity of traditional fermented food, Idli by high thorough-put sequencing

Digambar Kavitake; Mangesh V Suryavanshi; Sujatha Kandasamy; Palanisamy Bruntha Devi; Yogesh Shouche; Prathapkumar Halady Shetty

doi:10.1007/s13197-022-05421-4

Bacterial diversity of traditional fermented food, Idli by high thorough-put sequencing

J Food Sci Technol. 2022 Oct;59(10):3918-3927. doi: 10.1007/s13197-022-05421-4. Epub 2022 Apr 10.

Authors

Digambar Kavitake^#¹, Mangesh V Suryavanshi^#^{2

3}, Sujatha Kandasamy^#¹, Palanisamy Bruntha Devi¹, Yogesh Shouche², Prathapkumar Halady Shetty¹

Affiliations

¹ Department of Food Science and Technology, Pondicherry University, Pondicherry, 605014 India.
² National Centre for Microbial Resource, National Centre for Cell Science, Pune, 416021 India.
³ Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA.

^# Contributed equally.

Abstract

The bacterial composition of naturally fermented Indian food, Idli was studied by high-throughput Illumina amplicon sequencing at different taxonomic levels. Metagenomic investigation revealed fold change with respect to some of the phylotypes in 06^th to 12^th h of fermentation, suggesting the synergistic mode of nutrition. After 12^th h fermentation, bacterial populations were stabilized towards 15^th h fermentation. The bacterial phyla found as Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and others in various proportions with respective to fermentation time. Among these Firmicutes and Proteobacteria were the predominant bacterial associates in this product. Initially at 0^th h time interval Firmicutes (7%) and Proteobacteria (93%) were present adequately in the product which has been changed to Firmicutes (68%), Proteobacteria (31%) at the end of the fermentation (15^th h). Phylum Firmicutes represented various major genus such as Lactococcus, Weissella, Lactobacillus, Enterococcus, Bacillus and Macrococcus whereas Proteobacteria revealed the presence of Enterobacter, Erwinia, Serratia, Pseudoalteromonas, Vibrio and Klebsiella genus. Co-occurrence and Co-exclusion network were developed to ensure the positive and negative association in the eubacterial genus detected in entire batter fermentation event. Some genera like Weissella, Lactococcus and Enterococcus are showing increase in abundances in auxiliary succession events can be established for starter culture development.

Supplementary material: The online version contains supplementary material available at 10.1007/s13197-022-05421-4.

Keywords: Amplicon sequencing; Firmicutes; Idli batter; Microbiome; Proteobacteria.