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

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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 06th to 12th h of fermentation, suggesting the synergistic mode of nutrition. After 12th h fermentation, bacterial populations were stabilized towards 15th 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 0th 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 (15th 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.

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Data availability

Sequencing data have been deposited to NCBI Sequence Read Archive under accession number: SRP174635 and BioProject ID: PRJNA511947.

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Acknowledgements

We acknowledge Department of Food Science and Technology, Pondicherry University, Pondicherry and National Centre for Microbial Resource, National Centre for Cell Science, Pune for providing support and requirements to this study. DK and PBD are thankful to University Grants Commission, New Delhi for Senior Research Fellowship (1532/OBC-PWD/NET-DEC.2015) and Kothari Post-Doctoral Fellowship (201920-BL/19-20/0192) funding.

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Author notes

  1. Digambar Kavitake, Mangesh V. Suryavanshi and Sujatha Kandasamy the authors are have contributed equally.

Authors and Affiliations

  1. Department of Food Science and Technology, Pondicherry University, Pondicherry, 605014, India

    Digambar Kavitake, Sujatha Kandasamy, Palanisamy Bruntha Devi & Prathapkumar Halady Shetty

  2. National Centre for Microbial Resource, National Centre for Cell Science, Pune, 416021, India

    Mangesh V. Suryavanshi & Yogesh Shouche

  3. Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA

    Mangesh V. Suryavanshi

Authors
  1. Digambar Kavitake
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  2. Mangesh V. Suryavanshi
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  3. Sujatha Kandasamy
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  4. Palanisamy Bruntha Devi
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  5. Yogesh Shouche
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  6. Prathapkumar Halady Shetty
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Contributions

DK, SK, PHS, MVS and YS contributed in planning and designing of this research framework. SK and DK collected the samples and performed DNA isolation experiments. MVS and YS has processed 16S rRNA amplicons sequencing and performed detailed bioinformatics analysis. DK, MVS, SK, PBD, YS and PHS analyzed, drafted and corrected the data for manuscript. All authors read and approved the final manuscript.

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Correspondence to Prathapkumar Halady Shetty.

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Authors are assuring that the work is original and has not been published elsewhere; either completely or in partial format and the manuscript has not been submitted to any other journal. The present study did not include any animal or human studies.

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Kavitake, D., Suryavanshi, M.V., Kandasamy, S. et al. Bacterial diversity of traditional fermented food, Idli by high thorough-put sequencing. J Food Sci Technol 59, 3918–3927 (2022). https://doi.org/10.1007/s13197-022-05421-4

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  • DOI: https://doi.org/10.1007/s13197-022-05421-4

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