{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T01:18:54Z","timestamp":1792804734037,"version":"4.5.0"},"reference-count":49,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T00:00:00Z","timestamp":1770940800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"SRM University AP","award":["SRMAP\/URG\/SEED\/2023-24\/049"],"award-info":[{"award-number":["SRMAP\/URG\/SEED\/2023-24\/049"]}],"id":[{"id":"https:\/\/ror.org\/037skf023","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>India\u2019s diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms\u2014primarily lactic acid bacteria, yeasts, and molds\u2014contribute functional properties that extend beyond food transformation to confer health benefits, including probiotic potential and metabolic regulation. This review integrates classical microbiological studies with modern molecular approaches such as metagenomics, metatranscriptomics, and metabolomics to elucidate the microbial diversity of Indian fermented foods. It highlights how geography, substrates, and ethnic traditions shape region-specific microbial consortia sustained through long-standing ethno-microbiological practices. Special focus is given to the glycemic modulation achieved through microbial fermentation, wherein organic acid production and resistant starch formation lower glycemic index and improve glucose metabolism. These processes, along with enhanced nutrient bioavailability, vitamin synthesis, and immunomodulation, illustrate the broader functional potential of fermentation. The review also examines interactions between food-borne microbes and the human gut microbiota, underscoring implications for personalized nutrition. Finally, it discusses modernization and commercialization strategies and outlines future directions involving multi-omics integration, indigenous starter cultures, and microbiome-based innovations to harness India\u2019s microbial heritage for improved health and sustainable food development.<\/jats:p>","DOI":"10.3390\/foods15040687","type":"journal-article","created":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T10:52:21Z","timestamp":1770979941000},"page":"687","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Decoding the Microbial Diversity of Indian Fermented Foods: Integrating Ethnobiology, Multi-Omics and Functional Insights"],"prefix":"10.3390","volume":"15","author":[{"given":"Priyanka","family":"Samantaray","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, SRM University AP, Amaravati 522 240, Andhra Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8195-6981","authenticated-orcid":false,"given":"Sudeshna","family":"Saha","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, SRM University AP, Amaravati 522 240, Andhra Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,13]]},"reference":[{"key":"ref_1","first-page":"49","article-title":"The ancient Indian alcoholic drink called Sur\u0101: Vedic evidence","volume":"141","author":"McHugh","year":"2022","journal-title":"J. Am. Orient. Soc."},{"key":"ref_2","unstructured":"Bag, A.K. (1997). Fermentation technology. History of Technology of India, The Indian National Science Academy."},{"key":"ref_3","first-page":"250","article-title":"Fermentation in ancient Ayurveda: Its present implications","volume":"6","author":"Sharma","year":"2015","journal-title":"J. Ayurveda Integr. Med."},{"key":"ref_4","first-page":"110","article-title":"Functional properties of lactic acid bacteria in Indian fermented foods","volume":"12","author":"Sharma","year":"2025","journal-title":"Food Sci. Adv."},{"key":"ref_5","first-page":"45","article-title":"Metagenomics of Indian fermented foods and gut microbiome modulation","volume":"19","author":"Patel","year":"2024","journal-title":"Indian J. Microb. Ecol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Ghatani, K., Sha, S.P., Thapa, S., Sarkar, I., Sen, G., and Sen, A. (2024). Investigating bacterial diversity involved in the production of vegetable-based ethnic fermented food of North Bengal and their metabolic pathways with reverse ecology approach. Front. Sustain. Food Syst., 8.","DOI":"10.3389\/fsufs.2024.1322192"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.mimet.2003.11.006","article-title":"PCR-DGGE fingerprinting: Novel strategies for detection of microbes in food","volume":"56","author":"Ercolini","year":"2004","journal-title":"J. Microbiol. Methods"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Dreier, M., Meola, M., Berthoud, H., Shani, N., Wechsler, D., and Junier, P. (2022). High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota. BMC Microbiol., 22.","DOI":"10.1186\/s12866-022-02451-y"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"8604","DOI":"10.1002\/jsfa.13688","article-title":"Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage","volume":"104","author":"Hu","year":"2024","journal-title":"J. Sci. Food Agric."},{"key":"ref_10","first-page":"341","article-title":"Strain-level diversity in traditional Indian fermented foods: Insights from high-throughput sequencing","volume":"11","author":"Das","year":"2024","journal-title":"J. Microb. Biotechnol."},{"key":"ref_11","first-page":"12","article-title":"Multi-omics approaches for functional characterization of fermented food microbiota","volume":"8","author":"Lee","year":"2023","journal-title":"Microb. Biotechnol. Adv."},{"key":"ref_12","unstructured":"Chatterjee, S., and Nair, N. (2023). Spatial localization and functional activities of microbial communities in Indian fermented foods. Front. Microbiol., 14."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1080\/21553769.2016.1249032","article-title":"Diversity of traditional and fermented foods of the Seven Sister states of India and their nutritional and nutraceutical potential: A review","volume":"9","author":"Das","year":"2016","journal-title":"Front. Life Sci."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Tamang, J.P. (2020). Ethnic Fermented Foods and Beverages of India: Science History and Culture, Springer Nature.","DOI":"10.1007\/978-981-15-1486-9"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Steinkraus, K.H. (2004). Industrialization of Indigenous Fermented Foods, CRC Press. [2nd ed.].","DOI":"10.1201\/9780203022047"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Ray, R.C., and Montet, D. (2014). Microorganisms and Fermentation of Traditional Foods, CRC Press.","DOI":"10.1201\/b17307"},{"key":"ref_17","unstructured":"Hutkins, R.W. (2018). Microbiology and Technology of Fermented Foods, Wiley-Blackwell. [2nd ed.]."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/S0963-9969(03)00009-7","article-title":"Cereal-based fermented foods and beverages","volume":"36","author":"Blandino","year":"2003","journal-title":"Food Res. Int."},{"key":"ref_19","first-page":"1","article-title":"Traditional fermentations in tropical countries: What is the future?","volume":"113","author":"Nout","year":"2007","journal-title":"Int. J. Food Microbiol."},{"key":"ref_20","first-page":"1","article-title":"Lactic acid fermentation of vegetables and fruits: Advances in process and health benefits","volume":"2","author":"Filannino","year":"2013","journal-title":"Curr. Opin. Food Sci."},{"key":"ref_21","unstructured":"Battcock, M., and Azam Ali, S. (1998). Fermented Fruits and Vegetables: A Global Perspective, Food and Agriculture Organization of the United Nations. FAO Agricultural Services Bulletin No. 134."},{"key":"ref_22","first-page":"325","article-title":"Studies on microbial profile of some traditional fermented foods and beverages of Assam","volume":"44","author":"Deka","year":"2004","journal-title":"Indian J. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Ray, R.C., and Montet, D. (2014). Traditional fermented beverages from Latin America and the Caribbean. Microorganisms and Fermentation of Traditional Foods, CRC Press.","DOI":"10.1201\/b17307"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1080\/10408398909527507","article-title":"Nutritional improvement of cereals by fermentation","volume":"28","author":"Chavan","year":"1989","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_25","unstructured":"Adams, M.R., and Nout, M.J.R. (2001). Fermentation and Food Safety, Springer Science & Business Media."},{"key":"ref_26","first-page":"187","article-title":"Product characterization of chhurpi, a traditional fermented milk product of the Himalayas","volume":"63","author":"Thapa","year":"2004","journal-title":"J. Sci. Ind. Res."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Paul, A.K., Lim, C.L., Apu, M.A.I., Dolma, K.G., Gupta, M., de Lourdes Pereira, M., Wilairatana, P., Rahmatullah, M., Wiart, C., and Nissapatorn, V. (2023). Are Fermented Foods Effective against Inflammatory Diseases?. Int. J. Environ. Res. Public. Health, 20.","DOI":"10.3390\/ijerph20032481"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"100864","DOI":"10.1016\/j.focha.2024.100864","article-title":"Selected fermented foods of Manipur, India: Traditional preparation methods, nutritional profile, and health benefits","volume":"6","author":"Kabui","year":"2025","journal-title":"Food Chem. Adv."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41575-020-00390-5","article-title":"The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods","volume":"18","author":"Marco","year":"2021","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Tamang, J.P. (2015). Health Benefits of Fermented Foods and Beverages, CRC Press.","DOI":"10.1201\/b18279"},{"key":"ref_31","first-page":"24","article-title":"Fermented foods and beverages of the Indian subcontinent: An ethnobotanical and nutritional review","volume":"7","author":"Nout","year":"2020","journal-title":"J. Ethn. Foods"},{"key":"ref_32","first-page":"63","article-title":"Composition and enzyme inhibitory properties of finger millet polyphenols","volume":"234","author":"Shobana","year":"2012","journal-title":"Eur. Food Res. Technol."},{"key":"ref_33","first-page":"862","article-title":"Preparation and functional properties of decorticated finger millet (Eleusine coracana)","volume":"105","author":"Shobana","year":"2007","journal-title":"Food Chem."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2446","DOI":"10.1002\/fsn3.846","article-title":"Fermentation and germination improve nutritional value of cereals and legumes through activation of endogenous enzymes","volume":"6","author":"Nkhata","year":"2018","journal-title":"Food Sci. Nutr."},{"key":"ref_35","first-page":"94","article-title":"Health benefits of fermented foods: Microbiota and beyond","volume":"70","author":"Marco","year":"2021","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_36","unstructured":"Patel, R., and Reddy, P. (2024). Microbial succession in Indian fermented foods: A molecular perspective. Front. Microbiol., 15."},{"key":"ref_37","first-page":"45","article-title":"Probiotic potential of traditional Indian fermented foods: A bibliometric review","volume":"13","author":"Sharma","year":"2025","journal-title":"Food Nutr. J."},{"key":"ref_38","first-page":"109843","article-title":"Indigenous fermentation: Microbial communities and functional traits","volume":"382","author":"Gupta","year":"2025","journal-title":"Int. J. Food Microbiol."},{"key":"ref_39","first-page":"1717","article-title":"Impact of fermented foods on the seasonal stability of the gut microbiota in Indian populations","volume":"16","author":"Webb","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Sivamaruthi, B.S., Kesika, P., Prasanth, M.I., and Chaiyasut, C. (2018). A Mini Review on Antidiabetic Properties of Fermented Foods. Nutrients, 10.","DOI":"10.3390\/nu10121973"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"100381","DOI":"10.1016\/j.focha.2023.100381","article-title":"Probiotic potential of fermented foods and their role in non-communicable diseases management: An understanding through recent clinical evidences","volume":"3","author":"Nithya","year":"2023","journal-title":"Food Chem. Adv."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/j.jff.2016.04.031","article-title":"Randomized clinical trial: The effect of fermented milk with the probiotic cultures Lactobacillus acidophilus La-5\u00ae and Bifidobacterium BB-12\u00ae and Beneo dietary fibres on health-related quality of life and the symptoms of irritable bowel syndrome in adults","volume":"24","author":"Smid","year":"2016","journal-title":"J. Funct. Foods"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1038\/s41467-025-56014-6","article-title":"Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population","volume":"16","author":"Jeyaram","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e24501","DOI":"10.1016\/j.heliyon.2024.e24501","article-title":"A review of biogenic amines in fermented foods: Occurrence and health effects","volume":"10","author":"Turna","year":"2024","journal-title":"Heliyon"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1007\/s10068-023-01305-1","article-title":"Prevalence of antibiotic resistance in lactic acid bacteria isolated from traditional fermented Indian food products","volume":"32","author":"Ojha","year":"2023","journal-title":"Food Sci. Biotechnol."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Duche, R.T., Singh, A., Wandhare, A.G., Sangwan, V., Sihag, M.K., Nwagu, T.N.T., Panwar, H., and Ezeogu, L.I. (2023). Antibiotic resistance in potential probiotic lactic acid bacteria of fermented foods and human origin from Nigeria. BMC Microbiol., 23.","DOI":"10.1186\/s12866-023-02883-0"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e00368-19","DOI":"10.1128\/AEM.00368-19","article-title":"Diversity and succession of microbiota during fermentation of the batter of idli","volume":"85","author":"Mandhania","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"250424","DOI":"10.1155\/2014\/250424","article-title":"Fermented fruits and vegetables of Asia: A potential source of probiotics","volume":"2014","author":"Swain","year":"2014","journal-title":"Biotechnol. Res. Int."},{"key":"ref_49","first-page":"109774","article-title":"Relative abundance of halophilic archaea and bacteria in diverse salt-fermented foods","volume":"131","author":"Das","year":"2020","journal-title":"LWT-Food Sci. Technol."}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/4\/687\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T11:32:51Z","timestamp":1770982371000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/4\/687"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,13]]},"references-count":49,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["foods15040687"],"URL":"https:\/\/doi.org\/10.3390\/foods15040687","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,13]]}}}