Unraveling Tempeh through omics: a scoping review of fermentation pathways and functional health benefits

1. Romulo, A & Surya, R. Tempe: a traditional fermented food of Indonesia and its health benefits. Int. J. Gastron. Food Sci. 26, https://doi.org/10.1016/j.ijgfs.2021.100413 (2021).

2. Frias, J., Peñas, E. & Martinez-Villaluenga, C. Fermented Pulses in Nutrition and Health Promotion. https://doi.org/10.1016/B978-0-12-802309-9.00016-9 (Elsevier Inc., 2017).

3. Tamam, B. et al. Proteomic study of bioactive peptides from Tempe. J. Biosci. Bioeng. 128, 241–248 (2019).

   Google Scholar 

4. Astawan, M., Cahyani, A. P. & Wresdiyati, T. Antioxidant activity and isoflavone content of overripe Indonesian tempe. Food Res. 7, 42–50 (2023).

   Google Scholar 

5. Yarlina, V. P. & Astuti, D. I. Characterization of vitamin B₁₂, folate, and isoflavones of soybean Tempeh with the pure isolate Rhizopus oryzae, Rhizopus oligosporus, and Rhizopus stolonifer as functional food,”. Teknol. Pangan Media Inf. Dan Komun. Ilm. Teknol. Pertan. 12, 95–105 (2021).

   Google Scholar 

6. Herawati, H. et al. Characteristics of GABA (Gamma Amino Butyric Acid), antioxidant and sensory quality of modified Tempeh. Int. J. Food Prop. 26, 3532–3543 (2023).

   Google Scholar 

7. Sarkar, S., Sha, S.P. & Ghatani, K. Metabolomics of ethnic fermented foods and beverages: understanding new aspects through Omic techniques. Front. Sustain. Food Syst. 7, https://doi.org/10.3389/fsufs.2023.1040567 (2023).

8. Rezac, S., Kok, C.R., Heermann, M. & Hutkins, R. Fermented foods as a dietary source of live organisms. Front. Microbiol. 9, https://doi.org/10.3389/fmicb.2018.01785 (2018).

9. Gao, Y. et al. Metabolomics approaches for the comprehensive evaluation of fermented foods: a review. Foods 10, 1–18 (2021).

   Google Scholar 

10. Yarlina, V. P., Djali, M., Andoyo, R., Nurmilah, S. & Lani, M. N. Metagenomic insights into enhancing protein content and digestibility in Jack Bean (Canavalia ensiformis) Tempeh: unraveling microbial dynamics during fermentation. Appl. Food Res. 4, 100588 (2024).

    Google Scholar 

11. Marco, M. L. & Tachon, S. Environmental factors influencing the efficacy of probiotic bacteria. Curr. Opin. Biotechnol. 24, 207–213 (2013).

    Google Scholar 

12. Yulandi, A., Suwanto, A., Waturangi, D. E. & Wahyudi, A. T. Shotgun metagenomic analysis reveals new insights into bacterial community profiles in Tempeh. BMC Res. Notes 13, 1–7 (2020).

    Google Scholar 

13. He, M.H. & Howell, K.S. Vitamin-B₁₂ enrichment in Tempeh by co-culture with Propionibacterium freudenreichii during fermentation. Preprint at https://doi.org/10.1101/2022.11.06.515253 (2022).

14. Yarlina, V. P., Andoyo, R., Djali, M. & Lani, M. N. Metagenomic analysis for indigenous microbial diversity in soaking process of making Tempeh Jack Beans (Canavalia Ensiformis). Curr. Res. Nutr. Food Sci. 10, 620–632 (2022).

    Google Scholar 

15. Butowski, C. F., Dixit, Y., Reis, M. M. & Mu, C. Metatranscriptomics for understanding the microbiome in food and nutrition science. Metabolites 15, https://doi.org/10.3390/metabo15030185. (2025).

16. Kustyawati, M. E., Murhadi, S., Rizal, S. & Astuti, P. “Vitamin B₁₂ production in soybean fermentation for Tempeh. AIMS Agric. Food 5, 262–271 (2020).

    Google Scholar 

17. Ríos-Covián, D. et al. Intestinal short chain fatty acids and their link with diet and human health. Front. Microbiol. 7, 1–9 (2016).

    Google Scholar 

18. Wicaksono, W. A. et al. Traditionally produced Tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced Tempeh. Food Res. Int. 196, 115030 (2024).

    Google Scholar 

19. Astuti, T., Sitompul, M. & Faadhilanisyah, A. Tempeh consumption patterns in Indonesian family and contribution to nutritional adequacy. AcTion Aceh Nutr. J. 8, 518 (2023).

    Google Scholar 

20. Nout, M. J. R. & Kiers, J. L. Tempe fermentation, innovation and functionality: update into the third millenium. J. Appl. Microbiol. 98, 789–805 (2005).

    Google Scholar 

21. Barus, T., Giovania, G. & Lay, B. W. Lactic Acid Bacteria from Tempeh and their ability to acidify soybeans in Tempeh fermentation. Microbiol. Indones. 14, 149–155 (2020).

    Google Scholar 

22. Nurmilah, S. et al. Exploring microbial dynamics and metabolomic profiling of isoflavone transformation in black and yellow soybean tempe for sustainable functional foods. Food Chem. Mol. Sci. 11, 100279 (2025).

    Google Scholar 

23. Yarlina, V. P., Nabilah, F., Djali, M., Andoyo, R. & Lani, M. N. Mold characterization in ‘RAPRIMA’ Tempeh yeast from LIPI and over-fermented Koro Pedang (Jack Beans) Tempeh. Food Res. 7, 125–132 (2023).

    Google Scholar 

24. Samson, R. A. et al. Phylogeny, identification and nomenclature of the genus Aspergillus. Stud. Mycol. 78, 141–173 (2014).

    Google Scholar 

25. Efriwati, A., Suwanto, A., Rahayu, G. & Nuraida, L. “Population dynamics of yeasts and Lactic Acid Bacteria (LAB) during tempeh production,” HAYATI J. Biosci. 20, 57–64 (2013).

26. Seumahu, C. A., Suwanto, A., Rusmana, I. & Solihin, D. D. Bacterial and fungal communities in tempeh as reveal by amplified ribosomal intergenic sequence analysis. HAYATI J. Biosci. 20, 65–71 (2013).

    Google Scholar 

27. Watanabe, F., Yabuta, Y., Bito, T. & Teng, F. Vitamin B₁₂-containing plant food sources for vegetarians. Nutrients 6, 1861–1873 (2014).

    Google Scholar 

28. Watanabe, F. Vitamin B₁₂ sources and bioavailability. Exp. Biol. Med. 232, 1266–1274 (2007).

    Google Scholar 

29. Teoh, S.Q. et al. A review on health benefits and processing of Tempeh with outlines on its functional microbes. Futur. Foods 9, 100330 https://doi.org/10.1016/j.fufo.2024.100330 (2024).

30. Şanlier, N., Gökcen, B. B. & Sezgin, A. C. Health benefits of fermented foods. Crit. Rev. Food Sci. Nutr. 59, 506–527 (2019).

    Google Scholar 

31. Handoyo, T. & Morita, N. Structural and functional properties of fermented soybean (Tempeh) by using Rhizopus oligosporus. Int. J. Food Prop. 9, 347–355 (2006).

    Google Scholar 

32. Pangastuti, A. et al. Metagenomic analysis of microbial community in over-fermented Tempeh. Biodiversitas 20, 1106–1114 (2019).

    Google Scholar 

33. Ridhowati, S., Lestari, S. D., Rendi, M. & Rachmawati, S. H. “Characterization of physicochemical properties and enzymatic digestibility of lotus (Nelumbo nucifera) Tempeh through different methods. Food Res. 7, 42–52 (2023).

    Google Scholar 

34. Fusco, W. et al. Short-chain fatty-acid-producing bacteria: key components of the human gut microbiota. Nutrients 15, https://doi.org/10.3390/nu15092211 (2023).

35. Puspitojati, E., Indrati, R., Cahyanto, M. N. & Marsono, Y. Formation of ACE-inhibitory peptides during fermentation of jack bean tempe inoculated by usar Hibiscus tiliaceus leaves starter. IOP Conf. Ser. Earth Environ. Sci. 292, 0–8 (2019).

    Google Scholar 

36. Purwandari, F. A., Fogliano, V. & Capuano, E. Tempeh fermentation improves the nutritional and functional characteristics of Jack beans (Canavalia ensiformis (L.) DC). Food Funct. 15, 3680–3691 (2024).

    Google Scholar 

37. Chao, S.H. et al. Microbial diversity analysis of fermented mung beans (Lu-Doh-Huang) by using pyrosequencing and culture methods. PLoS ONE 8, https://doi.org/10.1371/journal.pone.0063816 (2013).

38. Kiers, J.L. Effects of fermented soya bean on digestion, absorption and diarrhoea 110 (Wageningen Universiteit, 2001).

39. Monika, S. avitri, Kumar, V., Kumari, A., Angmo, K. & Bhalla, T. C. “Isolation and characterization of Lactic Acid Bacteria from traditional pickles of Himachal Pradesh, India. J. Food Sci. Technol. 54, 1945–1952 (2017).

    Google Scholar 

40. Barus, T. et al. Genetic diversity of Klebsiella spp. isolated from tempe based on enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). HAYATI J. Biosci. 20, 171–176 (2013).

    Google Scholar 

41. Kuligowski, M., Pawłowska, K. & Jasińska-kuligowska, I. Isoflavone composition, polyphenols content and antioxidative activity of soybean seeds during Tempeh fermentation. CyTA J. Food 15, 27–33 (2017).

    Google Scholar 

42. Kwon, D. Y., Daily, J. W., Kim, H. J. & Park, S. Antidiabetic effects of fermented soybean products on type 2 diabetes. Nutr. Res. 30, 1–13 (2010).

    Google Scholar 

43. Messina, M. Soy and health update: evaluation of the clinical and epidemiologic literature. Nutrients 8, https://doi.org/10.3390/nu8120754 (2016).

44. Javed, Z. et al. Genistein as a regulator of signaling pathways and microRNAs in different types of cancers. Cancer Cell Int. 21, 1–12 (2021).

    Google Scholar 

45. Naeem, H. et al. Anticancer perspectives of genistein: a comprehensive review. Int. J. Food Prop. 26, 3305–3341 (2023).

    Google Scholar 

46. Messina, M. Insights gained from 20 years of soy research. J. Nutr. 140, 2289–2295 (2010).

    Google Scholar 

47. Mackay, G. M. et al. Tryptophan metabolism and oxidative stress in patients with chronic brain injury. Eur. J. Neurol. 13, 30–42 (2006).

    Google Scholar 

48. Szerszunowicz, I. & Kozicki, S. “Plant-derived proteins and peptides as potential immunomodulators. Molecules 29, https://doi.org/10.3390/molecules29010209 (2024).

49. Granato, D. et al. Functional foods: product development, technological trends, efficacy testing, and safety. Annu. Rev. Food Sci. Technol. 11, 93–118 (2020).

    Google Scholar 

50. Frias, J., Young, S. S., Martínez-Villaluenga, C., De Mejia, E. G. & Vidal-Valverde, C. Immunoreactivity and amino acid content of fermented soybean products. J. Agric. Food Chem. 56, 99–105 (2008).

    Google Scholar 

51. Danial, A. M., Peng, K. S. & Long, K. Enrichment of Mung Bean with L-DOPA, GABA, essential amino acids via controlled biofermentation strategy. Int. J. Biotechnol. Wellness Ind. 4, 114–122 (2016).

    Google Scholar 

52. Bahar, A. & Witono, Y. Process optimization of Tempeh protein isolate from Soybean (Glycine max Merr) and Cowpea (Vigna unguiculata) mixture. Int. J. Adv. Sci. Eng. Inf. Technol. 5, 139–143 (2015).

    Google Scholar 

53. Leblanc, J. G. et al. B-Group vitamin production by Lactic Acid Bacteria – current knowledge and potential applications. J. Appl. Microbiol. 111, 1297–1309 (2011).

    Google Scholar 

54. Masuda, M. et al. Production potency of folate, Vitamin B₁₂, and thiamine by Lactic Acid Bacteria isolated from Japanese pickles. Biosci. Biotechnol. Biochem. 76, 2061–2067 (2012).

    Google Scholar 

55. Egounlety, M. & Aworh, O. Effect of soaking, dehulling, cooking and fermentation with Rhizopus oligosporus on the oligosaccharides, trypsin inhibitor, phytic acid and tannins of soybean (GlycinemaxMerr.), cowpea (Vigna unguiculata L. Walp) and ground bean (Macrotyloma geocarpa Ha. J. Food Eng. 56, 249–254 (2003).

    Google Scholar 

56. Narad, P. & Kirthanashri, S. V. Introduction to Omics. in Omics approaches, technologies and applications: integrative approaches for understanding OMICS data 1–10 (Springer Nature Singapore, 2018).

57. Yoshii, H. et al. Antihypertensive effect of ACE inhibitory oligopeptides from chicken egg yolks. Comp. Biochem. Physiol. C Pharmacol. Toxicol. Endocrinol. 128, 27–33 (2001).

    Google Scholar 

58. Diana, M., Quílez, J. & Rafecas, M. Gamma-aminobutyric acid as a bioactive compound in foods: a review. J. Funct. Foods 10, 407–420 (2014).

    Google Scholar 

59. Nkhata, S.G., Ayua, E., Kamau, E.H. & Shingiro, J.B. Fermentation and germination improve nutritional value of cereals and legumes through activation of endogenous enzymes. Food Sci. Nutr. 6, 2446–2458 (2018) .

60. Steinkraus, K. H. Fermentations in world food processing. Compr. Rev. Food Sci. Food Saf. 1, 23–32 (2002).

    Google Scholar 

61. Sumathy, J. “A study on the enterobacteriaceae pathogen klebsiella pneumoniae isolated from sewage and drinking water environment. IOSR J. Biotechnol. Biochem. 4, 1–5 (2018).

    Google Scholar 

62. Cui, Y., Miao, K., Niyaphorn, S. & Qu, X. Production of gamma-aminobutyric acid from Lactic Acid Bacteria: a systematic review. Int. J. Mol. Sci. 21, 1–21 (2020).

    Google Scholar 

63. Moa, H. et al. “Effect of soybean processing on content and bioaccessibility of folate, vitamin B₁₂ and isoflavones in tofu and tempe. Food Chem. 141, 2418–2425 (2013).

    Google Scholar 

64. Teixeira-Guedes, C., Sánchez-Moya, T., Pereira-Wilson, C., Ros-Berruezo, G. & López-Nicolás, R. In vitro modulation of gut microbiota and metabolism by cooked cowpea and black bean. Foods 9, https://doi.org/10.3390/foods9070861 (2020).

65. Poernomo, A. T. Isnaeni, and Purwanto, “Aktivitas Invitro Enzim Fibrinolitik Ekstrak Tempe Hasil Fermentasi Rhizopus Oligosporus ATCC 6010 Pada Substrat Kedelai Hitam. Berk. Ilm. Kim. Farm. 4, 18–24 (2014).

    Google Scholar 

66. Gibbs, B. F., Zougman, A., Masse, R. & Mulligan, C. Production and characterization of bioactive peptides from soy hydrolysate and soy-fermented food. Food Res. Int. 37, 123–131 (2004).

    Google Scholar 

67. Barus, T., Suwanto, A. & Agustina, W. Metagenomic analysis of bacterial diversity in tempe using terminal restriction fragment length polymorphism (T-RFLP) Technique. Biota 15, 80–273 (2010).

68. Astawan, M., Mardhiyyah, Y. S. & Wijaya, C. H. Potential of bioactive components in tempe for the treatment of obesity. J. Gizi dan Pangan 13, 79–86 (2018). pp.

    Google Scholar 

69. Duliński, R. & Starzyńska-Janiszewska, A. “Content and in vitro bioavailability of selected B vitamins and myo-inositol in spelt wheat (Triticum spelta L.) subjected to solid-state fermentation. J. Food Nutr. Res. 59, 1–6 (2020).

    Google Scholar 

70. Maryati, Y., Susilowati, A., Melanie, H. & Lotulung, P.D. Fermentation of soybean (Glycine max (L.) Merr.) using mix inocula of Rhizopus sp. and Saccharomyces cerevisiae for an alternative source of folic acid. IOP Conf. Ser. Mater. Sci. Eng. 536, https://doi.org/10.1088/1757-899X/536/1/012124. (2019).

71. Agustina, R.K., Dieny, E.F. & Rustanti, N. Antioxidant activity and soluble protein content of tempeh gembus hydrolysate. Hiroshima J. Med. Sci. 67, 1–7 (2018).

72. Wang, R. et al. Preparation of bioactive peptides with antidiabetic, antihypertensive, and antioxidant activities and identification of α-glucosidase inhibitory peptides from soy protein. Food Sci. Nutr. 7, 1848–1856 (2019).

    Google Scholar 

73. Sybesma, W., Starrenburg, M., Tijsseling, L., Hoefnagel, M. H. N. & Hugenholtz, J. Effects of cultivation conditions on folate production by Lactic Acid Bacteria. Appl. Environ. Microbiol. 69, 4542–4548 (2003).

    Google Scholar 

74. Rizal, S., Murhadi, M., Kustyawati, M. E. & Hasanudin, U. Growth optimization of saccharomyces cerevisiae and rhizopus oligosporus during fermentation to produce Tempeh with high β-glucan content. Biodiversitas 21, 2667–2673 (2020).

    Google Scholar 

75. Prativi, M. B. N. et al. “Metabolite changes in Indonesian Tempe production from raw soybeans to over-fermented Tempe. Metabolites 13, 300 (2023).

    Google Scholar 

76. Rong, P. et al. Untargeted metabolomics analysis of non-volatile metabolites and dynamic changes of antioxidant capacity in Douchi with edible mushroom. Food Chem. 431, 137066 (2024).

    Google Scholar 

77. Mei Feng, X., Ostenfeld Larsen, T. & Schnürer, J. Production of volatile compounds by Rhizopus oligosporus during soybean and barley Tempeh fermentation. Int. J. Food Microbiol. 113, 133–141 (2007).

    Google Scholar 

78. Kadar, A. D., Astawan, M., Putri, S. P. & Fukusaki, E. Metabolomics-based study of the effect of raw materials on the end product of tempe—an Indonesian fermented soybean. Metabolites 10, 1–11 (2020).

    Google Scholar 

79. Panchaud, A., Affolter, M. & Kussmann, M. Mass spectrometry for nutritional peptidomics: how to analyze food bioactives and their health effects. J. Proteomics 75, 3546–3559 (2012).

    Google Scholar 

80. Nemec, A. et al. Taxonomy of haemolytic and/or proteolytic strains of the genus Acinetobacter with the proposal of Acinetobacter courvalinii sp. Nov. (genomic species 14 sensu Bouvet and Jeanjean), Acinetobacter dispersus sp. nov. (genomic species 17), Acinetobacter modes,”. Int. J. Syst. Evol. Microbiol. 66, 1673–1685 (2016).

    Google Scholar 

81. Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. “dRep : a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).

82. Prakash, J. et al. Analysis of meta-transcriptomics and identification of genes linked to bioactive peptides and vitamins in Indonesian tempe. Food Res. Int. 202, 115757 (2025).

    Google Scholar 

83. Akinyemi, O. Integrated multi-omics approach to investigate the microbiome of Tempeh, a traditional Indonesian fermented food. (2024).

84. Kuczynski, J. et al. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr. Protoc. Bioinform. 36, https://doi.org/10.1002/0471250953.bi1007s36 (2011).

85. Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007).

    Google Scholar 

86. Yulandi, Y., Suwanto, A., Waturangi, D.E. & Wahyudi, A.T. Shotgun metagenomic analysis reveals new insights into bacterial community profiles in Tempeh. BMC Res. 13, https://doi.org/10.1186/s13104-020-05406-6 (2020).

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