Novel Insights into the isolation and in vitro probiotic characterization of Weissella confusa from Navara Rice in Kerala, India
Article Main
Abstract
Fermented foods are important reservoirs of probiotic lactic acid bacteria (LAB), which confer health benefits by modulating gut microbiota. Navara, a medicinal rice from Kerala, India, valued in Ayurveda, is an underexplored source of these bacteria. This study aimed to isolate, identify, and conduct the first in-vitro probiotic characterization of LAB from fermented Navara rice. A bacterial isolate was obtained on MRS agar and identified via 16S rRNA gene sequencing as Weissella confusa strain PK18202456.1. Its probiotic potential was evaluated using standard in vitro assays. The isolate demonstrated strong antagonistic activity against enteric pathogens (e.g., 12 mm zone vs. MRSA), robust coaggregation (76.67% with E. coli), and high cell-surface hydrophobicity (93.92% at 4 h). It survived simulated gastrointestinal stress, tolerating pH 3.0 and 0.3% bile salts, and exhibited bile salt hydrolase activity (22.7 ± 2.5 mm zone). Antibiotic profiling showed susceptibility to ampicillin, tetracycline, erythromycin, and clindamycin, with resistance to vancomycin and gentamicin. This work provides the first evidence for the isolation and comprehensive probiotic characterization of a Weissella confusa strain from Navara rice, establishing it as a promising candidate for future functional food applications.
Article Details
Article Details
Keywords
Antibiotic, Bacteria, Health Navara , Probiotic, Rice
References
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Archer, A. C. & Halami, P. M. (2015). Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products. Applied Microbiology and Biotechnology, 99(19), 8113-8123. https://doi.org/10.1007/s00253-015-6679-x
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Bora, S. S., Keot, J., Das, S., Sarma, K. & Barooah, M. (2016). Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India. 3 Biotech, 6(2), 153. https://doi.org/10.1007/s13205-016-0471-1
Choi, J. S., Kim, J. W., Cho, H. R., Kim, K. Y., Lee, J. K., Sohn, J. H. & Ku, S. K. (2014). Laxative effects of fermented rice extract in rats with loperamide‑induced constipation. Experimental and Therapeutic Medicine, 8(6), 1847-1854. https://doi.org/10.3892/etm.2014.2030
Chunguang, S. & Dapeng, L. (2008). Research on enriched L-lactic acid fermented black rice beverage and its fermentation process. J. Heilongjiang August First Land Reclamation University, 3.,
Dashkevicz, M. P. & Feighner, S. D. (1989). Development of a differential medium for bile salt hydrolase-active Lactobacillus spp. Applied and Environmental Microbiology, 55(1), 11-16. https://doi.org/10.1128/aem.55.1.11-16.1989
Fairfax, M. R., Lephart, P. R. & Salimnia, H. (2014). Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic. Frontiers in Microbiology, 5, 254. https://doi.org/10.3389/fmicb.2014.00254
Fessard, A. & Remize, F. (2017). Why are Weissella spp. not used as commercial starter cultures for food fermentation? Fermentation, 3(3), 38. https://doi.org/10.3390/fermentation3030038
Hamon, E., Horvatovich, P., Izquierdo, E., Bringel, F., Marchioni, E., Aoudé-Werner, D. & Ennahar, S. (2011). Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiology, 11(1), 63. https://doi.org/10.1186/1471-2180-11-63
Han, Q., Kong, B., Chen, Q., Sun, F. & Zhang, H. (2017). In vitro comparison of probiotic properties of lactic acid bacteria isolated from Harbin dry sausages and selected probiotics. Journal of Functional Foods, 32, 391-400. https://doi.org/10.1016/j.jff.2017.03.020
Huang, X., Hu, D., Zhang, W., Cai, J., Zhou, H., Ye, X., . . . Xia, X. (2025). The priority effect of microbial community on the initiation of Chinese rice wine fermentation and flavor formation. Food Bioscience, 106771. https://doi.org/10.1016/j.fbio.2025.106771
Jeyagowri, N., Parahitiyawa, N., Jeyatilake, S., Ranadheera, S. & Madhujith, T. (2015). Study on isolation of potentially probiotic Lactobacillus species from fermented rice.
Kamboj, K., Vasquez, A. & Balada-Llasat, J.-M. (2015). Identification and significance of Weissella species infections. Frontiers in Microbiology, 6, 1204. https://doi.org/10.3389/fmicb.2015.01204
Kirtzalidou, E., Pramateftaki, P., Kotsou, M. & Kyriacou, A. (2011). Screening for lactobacilli with probiotic properties in the infant gut microbiota. Anaerobe, 17(6), 440-443. https://doi.org/10.1016/j.anaerobe.2011.05.007
Ko, H. I., Jeong, C. H., Hong, S. W., Eun, J.-B. & Kim, T.-W. (2022). Optimizing conditions in the acid tolerance test for potential probiotics using response surface methodology. Microbiology Spectrum, 10(4), e01625-01622. https://doi.org/10.1128/spectrum.01625-22
Koll P, Mändar R, Smidt I, Hütt P, Truusalu K. (2010). Screening and evaluation of human intestinal lactobacilli for the development of novel gastrointestinal probiotics. Curr. Microbiol., 61(6): 560-566, doi: 10.1007/ s00284-010-9653-y
Lee, K. W., Park, J. Y., Jeong, H. R., Heo, H. J., Han, N. S. & Kim, J. H. (2012). Probiotic properties of Weissella strains isolated from human faeces. Anaerobe, 18(1), 96-102. https://doi.org/10.1016/j.anaerobe.2011.12.015
Lu, Z. H., Peng, H. H., Cao, W., Tatsumi, E. & Li, L. T. (2008). Isolation, characterization and identification of lactic acid bacteria and yeasts from sour Mifen, a traditional fermented rice noodle from China. Journal of Applied Microbiology, 105(3), 893-903. https://doi.org/10.1111/j.1365-2672.2008.03814.x
Mercado‐Monroy, J., Falfán‐Cortés, R. N., Muñóz‐Pérez, V. M., Gómez‐Aldapa, C. A. & Castro‐Rosas, J. (2025). Probiotics as modulators of intestinal barrier integrity and immune homeostasis: a comprehensive review. Journal of the Science of Food and Agriculture, https://doi.org/10.1002/jsfa.70168
Mohammed, E. A. H., Ahmed, A. E. M., Kovács, B. & Pál, K. (2025). The significance of probiotics in aquaculture: a review of research trend and latest scientific findings. Antibiotics, 14(3), 242. https://doi.org/10.3390/antibiotics14030242
Nath, S., Paul, P., Roy, R., Bhattacharjee, S. & Deb, B. (2019). Isolation and identification of metal-tolerant and antibiotic-resistant bacteria from soil samples of Cachar district of Assam, India. SN Applied Sciences, 1(7), 727. https://doi.org/10.1007/s42452-019-0762-3
Nath, S., Sikidar, J., Roy, M. & Deb, B. (2020). In vitro screening of probiotic properties of Lactobacillus plantarum isolated from fermented milk product. Food Quality and Safety, 4(4), 213-223. https://doi.org/10.1093/fqsafe/fyaa026
Nostro, A., Cannatelli, M., Crisafi, G., Musolino, A., Procopio, F. & Alonzo, V. (2004). Modifications of hydrophobicity, in vitro adherence and cellular aggregation of Streptococcus mutans by Helichrysum italicum extract. Letters in Applied Microbiology, 38(5), 423-427. https://doi.org/10.1111/j.1472-765X.2004.01509.x
Oh, A., Daliri, E. B.-M. & Oh, D. H. (2018). Screening for potential probiotic bacteria from Korean fermented soybean paste: In vitro and Caenorhabditis elegans model testing. Lwt, 88, 132-138. https://doi.org/10.1016/j.lwt.2017.10.007
Pan, W.-H., Li, P.-L. & Liu, Z. (2006). The correlation between surface hydrophobicity and adherence of Bifidobacterium strains from centenarians’ faeces. Anaerobe, 12(3), 148-152. https://doi.org/10.1016/j.anaerobe.2006.03.001
Patel, A., Prajapati, J., Holst, O. & Ljungh, A. (2014). Determining probiotic potential of exopolysaccharide producing lactic acid bacteria isolated from vegetables and traditional Indian fermented food products. Food Bioscience, 5, 27-33. https://doi.org/10.1016/j.fbio.2013.10.002
Quattrini, M., Korcari, D., Ricci, G. & Fortina, M. G. (2020). A polyphasic approach to characterize Weissella cibaria and Weissella confusa strains. Journal of Applied Microbiology, 128(2), 500-512. https://doi.org/10.1111/jam.14483
Ray, M., Ghosh, K., Singh, S. & Mondal, K. C. (2016). Folk to functional: an explorative overview of rice-based fermented foods and beverages in India. Journal of Ethnic Foods, 3(1), 5-18. https://doi.org/10.1016/j.jef.2016.02.002
Ray, R. C. & Swain, M. R. (2013). Indigenous fermented foods and beverages of Odisha, India: an overview. Indigenous Fermented foods of South Asia, 1-6.
Shangpliang, H., Sharma, S., Rai, R. & Tamang, J. P. (2017). Some technological properties of lactic acid bacteria isolated from Dahi and Datshi, naturally fermented milk products of Bhutan. Frontiers in Microbiology, 8, 116. https://doi.org/10.3389/fmicb.2017.00116
Sharma, S., Kandasamy, S., Kavitake, D. & Shetty, P. H. (2018). Probiotic characterization and antioxidant properties of Weissella confusa KR780676, isolated from an Indian fermented food. Lwt, 97, 53-60. https://doi.org/10.1016/j.lwt.2018.06.033
Shukla, S. & Goyal, A. (2011). 16S rRNA‐Based Identification of a Glucan‐Hyperproducing Weissella confusa. Enzyme Research, 2011(1), 250842. https://doi.org/10.4061/2011/250842
Singh, A., Thakur, S., Lakharwal, P., Dhar, P. & Nath, P. C. (2025). Diversity of microorganism towards ethnic fermented food products and beverage. In Ethnic and Indigenous Food Technologies: Role in Climate and Health Resilience, (pp. 447-469): Springer. https://doi.org/10.1007/978-981-96-9286-6_22
Song, Y.-R., Jeong, D.-Y., Cha, Y.-S. & Baik, S.-H. (2013). Exopolysaccharide produced by Pediococcus acidilactici M76 isolated from the Korean traditional rice wine, makgeolli. Journal of Microbiology and Biotechnology, 23(5), 681-688. https://doi.org/10.4014/jmb.1301.01032
Tenea, G. N. & Lara, M. I. (2019). Antimicrobial compounds produced by Weissella confusa Cys2-2 strain inhibit Gram-negative bacteria growth. CyTA-Journal of Food, 17(1), 105-111. https://doi.org/10.1080/19476337.2018.1561520
Xu, H., Jeong, H., Lee, H. & Ahn, J. (2009). Assessment of cell surface properties and adhesion potential of selected probiotic strains. Letters in Applied Microbiology, 49(4), 434-442. https://doi.org/10.1111/j.1472-765X.2009.02684.x
Yumnam, H., Nath, S., Chakraborty, P. & Sharma, I. (2025). Assessment of potential probiotic lactic acid bacteria in rice-based fermented products of Southern Assam, Northeast India. Frontiers in Microbiology, 16, 1536593. https://doi.org/10.3389/fmicb.2025.1536593
Ahmadova, A., Todorov, S. D., Choiset, Y., Rabesona, H., Zadi, T. M., Kuliyev, A., . . . Haertlé, T. (2013). Evaluation of antimicrobial activity, probiotic properties and safety of wild strain Enterococcus faecium AQ71 isolated from Azerbaijani Motal cheese. Food Control, 30(2), 631-641. https://doi.org/10.1016/j.foodcont.2012.08.009
Angmo, K., Kumari, A. & Bhalla, T. C. (2016). Probiotic characterization of lactic acid bacteria isolated from fermented foods and beverage of Ladakh. LWT-food Science and Technology, 66, 428-435. https://doi.org/10.1016/j.lwt.2015.10.057
Archer, A. C. & Halami, P. M. (2015). Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products. Applied Microbiology and Biotechnology, 99(19), 8113-8123. https://doi.org/10.1007/s00253-015-6679-x
Baccer, R., Kirby, M., Sherris, J. & Turek, M. (1966). Antibiotic susceptibility testing by standard single disc diffusion method. Am. J. Clin. Pathol, 45, 493-496. https://pubmed.ncbi.nlm.nih.gov/5325707/
Bora, S. S., Keot, J., Das, S., Sarma, K. & Barooah, M. (2016). Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India. 3 Biotech, 6(2), 153. https://doi.org/10.1007/s13205-016-0471-1
Choi, J. S., Kim, J. W., Cho, H. R., Kim, K. Y., Lee, J. K., Sohn, J. H. & Ku, S. K. (2014). Laxative effects of fermented rice extract in rats with loperamide‑induced constipation. Experimental and Therapeutic Medicine, 8(6), 1847-1854. https://doi.org/10.3892/etm.2014.2030
Chunguang, S. & Dapeng, L. (2008). Research on enriched L-lactic acid fermented black rice beverage and its fermentation process. J. Heilongjiang August First Land Reclamation University, 3.,
Dashkevicz, M. P. & Feighner, S. D. (1989). Development of a differential medium for bile salt hydrolase-active Lactobacillus spp. Applied and Environmental Microbiology, 55(1), 11-16. https://doi.org/10.1128/aem.55.1.11-16.1989
Fairfax, M. R., Lephart, P. R. & Salimnia, H. (2014). Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic. Frontiers in Microbiology, 5, 254. https://doi.org/10.3389/fmicb.2014.00254
Fessard, A. & Remize, F. (2017). Why are Weissella spp. not used as commercial starter cultures for food fermentation? Fermentation, 3(3), 38. https://doi.org/10.3390/fermentation3030038
Hamon, E., Horvatovich, P., Izquierdo, E., Bringel, F., Marchioni, E., Aoudé-Werner, D. & Ennahar, S. (2011). Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance. BMC Microbiology, 11(1), 63. https://doi.org/10.1186/1471-2180-11-63
Han, Q., Kong, B., Chen, Q., Sun, F. & Zhang, H. (2017). In vitro comparison of probiotic properties of lactic acid bacteria isolated from Harbin dry sausages and selected probiotics. Journal of Functional Foods, 32, 391-400. https://doi.org/10.1016/j.jff.2017.03.020
Huang, X., Hu, D., Zhang, W., Cai, J., Zhou, H., Ye, X., . . . Xia, X. (2025). The priority effect of microbial community on the initiation of Chinese rice wine fermentation and flavor formation. Food Bioscience, 106771. https://doi.org/10.1016/j.fbio.2025.106771
Jeyagowri, N., Parahitiyawa, N., Jeyatilake, S., Ranadheera, S. & Madhujith, T. (2015). Study on isolation of potentially probiotic Lactobacillus species from fermented rice.
Kamboj, K., Vasquez, A. & Balada-Llasat, J.-M. (2015). Identification and significance of Weissella species infections. Frontiers in Microbiology, 6, 1204. https://doi.org/10.3389/fmicb.2015.01204
Kirtzalidou, E., Pramateftaki, P., Kotsou, M. & Kyriacou, A. (2011). Screening for lactobacilli with probiotic properties in the infant gut microbiota. Anaerobe, 17(6), 440-443. https://doi.org/10.1016/j.anaerobe.2011.05.007
Ko, H. I., Jeong, C. H., Hong, S. W., Eun, J.-B. & Kim, T.-W. (2022). Optimizing conditions in the acid tolerance test for potential probiotics using response surface methodology. Microbiology Spectrum, 10(4), e01625-01622. https://doi.org/10.1128/spectrum.01625-22
Koll P, Mändar R, Smidt I, Hütt P, Truusalu K. (2010). Screening and evaluation of human intestinal lactobacilli for the development of novel gastrointestinal probiotics. Curr. Microbiol., 61(6): 560-566, doi: 10.1007/ s00284-010-9653-y
Lee, K. W., Park, J. Y., Jeong, H. R., Heo, H. J., Han, N. S. & Kim, J. H. (2012). Probiotic properties of Weissella strains isolated from human faeces. Anaerobe, 18(1), 96-102. https://doi.org/10.1016/j.anaerobe.2011.12.015
Lu, Z. H., Peng, H. H., Cao, W., Tatsumi, E. & Li, L. T. (2008). Isolation, characterization and identification of lactic acid bacteria and yeasts from sour Mifen, a traditional fermented rice noodle from China. Journal of Applied Microbiology, 105(3), 893-903. https://doi.org/10.1111/j.1365-2672.2008.03814.x
Mercado‐Monroy, J., Falfán‐Cortés, R. N., Muñóz‐Pérez, V. M., Gómez‐Aldapa, C. A. & Castro‐Rosas, J. (2025). Probiotics as modulators of intestinal barrier integrity and immune homeostasis: a comprehensive review. Journal of the Science of Food and Agriculture, https://doi.org/10.1002/jsfa.70168
Mohammed, E. A. H., Ahmed, A. E. M., Kovács, B. & Pál, K. (2025). The significance of probiotics in aquaculture: a review of research trend and latest scientific findings. Antibiotics, 14(3), 242. https://doi.org/10.3390/antibiotics14030242
Nath, S., Paul, P., Roy, R., Bhattacharjee, S. & Deb, B. (2019). Isolation and identification of metal-tolerant and antibiotic-resistant bacteria from soil samples of Cachar district of Assam, India. SN Applied Sciences, 1(7), 727. https://doi.org/10.1007/s42452-019-0762-3
Nath, S., Sikidar, J., Roy, M. & Deb, B. (2020). In vitro screening of probiotic properties of Lactobacillus plantarum isolated from fermented milk product. Food Quality and Safety, 4(4), 213-223. https://doi.org/10.1093/fqsafe/fyaa026
Nostro, A., Cannatelli, M., Crisafi, G., Musolino, A., Procopio, F. & Alonzo, V. (2004). Modifications of hydrophobicity, in vitro adherence and cellular aggregation of Streptococcus mutans by Helichrysum italicum extract. Letters in Applied Microbiology, 38(5), 423-427. https://doi.org/10.1111/j.1472-765X.2004.01509.x
Oh, A., Daliri, E. B.-M. & Oh, D. H. (2018). Screening for potential probiotic bacteria from Korean fermented soybean paste: In vitro and Caenorhabditis elegans model testing. Lwt, 88, 132-138. https://doi.org/10.1016/j.lwt.2017.10.007
Pan, W.-H., Li, P.-L. & Liu, Z. (2006). The correlation between surface hydrophobicity and adherence of Bifidobacterium strains from centenarians’ faeces. Anaerobe, 12(3), 148-152. https://doi.org/10.1016/j.anaerobe.2006.03.001
Patel, A., Prajapati, J., Holst, O. & Ljungh, A. (2014). Determining probiotic potential of exopolysaccharide producing lactic acid bacteria isolated from vegetables and traditional Indian fermented food products. Food Bioscience, 5, 27-33. https://doi.org/10.1016/j.fbio.2013.10.002
Quattrini, M., Korcari, D., Ricci, G. & Fortina, M. G. (2020). A polyphasic approach to characterize Weissella cibaria and Weissella confusa strains. Journal of Applied Microbiology, 128(2), 500-512. https://doi.org/10.1111/jam.14483
Ray, M., Ghosh, K., Singh, S. & Mondal, K. C. (2016). Folk to functional: an explorative overview of rice-based fermented foods and beverages in India. Journal of Ethnic Foods, 3(1), 5-18. https://doi.org/10.1016/j.jef.2016.02.002
Ray, R. C. & Swain, M. R. (2013). Indigenous fermented foods and beverages of Odisha, India: an overview. Indigenous Fermented foods of South Asia, 1-6.
Shangpliang, H., Sharma, S., Rai, R. & Tamang, J. P. (2017). Some technological properties of lactic acid bacteria isolated from Dahi and Datshi, naturally fermented milk products of Bhutan. Frontiers in Microbiology, 8, 116. https://doi.org/10.3389/fmicb.2017.00116
Sharma, S., Kandasamy, S., Kavitake, D. & Shetty, P. H. (2018). Probiotic characterization and antioxidant properties of Weissella confusa KR780676, isolated from an Indian fermented food. Lwt, 97, 53-60. https://doi.org/10.1016/j.lwt.2018.06.033
Shukla, S. & Goyal, A. (2011). 16S rRNA‐Based Identification of a Glucan‐Hyperproducing Weissella confusa. Enzyme Research, 2011(1), 250842. https://doi.org/10.4061/2011/250842
Singh, A., Thakur, S., Lakharwal, P., Dhar, P. & Nath, P. C. (2025). Diversity of microorganism towards ethnic fermented food products and beverage. In Ethnic and Indigenous Food Technologies: Role in Climate and Health Resilience, (pp. 447-469): Springer. https://doi.org/10.1007/978-981-96-9286-6_22
Song, Y.-R., Jeong, D.-Y., Cha, Y.-S. & Baik, S.-H. (2013). Exopolysaccharide produced by Pediococcus acidilactici M76 isolated from the Korean traditional rice wine, makgeolli. Journal of Microbiology and Biotechnology, 23(5), 681-688. https://doi.org/10.4014/jmb.1301.01032
Tenea, G. N. & Lara, M. I. (2019). Antimicrobial compounds produced by Weissella confusa Cys2-2 strain inhibit Gram-negative bacteria growth. CyTA-Journal of Food, 17(1), 105-111. https://doi.org/10.1080/19476337.2018.1561520
Xu, H., Jeong, H., Lee, H. & Ahn, J. (2009). Assessment of cell surface properties and adhesion potential of selected probiotic strains. Letters in Applied Microbiology, 49(4), 434-442. https://doi.org/10.1111/j.1472-765X.2009.02684.x
Yumnam, H., Nath, S., Chakraborty, P. & Sharma, I. (2025). Assessment of potential probiotic lactic acid bacteria in rice-based fermented products of Southern Assam, Northeast India. Frontiers in Microbiology, 16, 1536593. https://doi.org/10.3389/fmicb.2025.1536593
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Novel Insights into the isolation and in vitro probiotic characterization of Weissella confusa from Navara Rice in Kerala, India. (2026). Journal of Applied and Natural Science, 18(1), 364-375. https://doi.org/10.31018/jans.v18i1.7247
