Metagenomic analysis and biodiversity of Lactic Acid Bacteria (LAB) on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Manguntungi B, Saputri DS, Mustopa AZ, Ekawati N, Afgani CA, Sari AP, Triratna L, Sukmarini L, Fatimah, Kusmiran A, Yanti S, Irawan S, Prasetyo MD, Fidien KA. 2020. Metagenomic analysis and biodiversity of Lactic Acid Bacteria (LAB) on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia. Biodiversitas 21: 3287-3293. Masin is a spontaneously fermented sauce from Sumbawa, West Nusa Tenggara Indonesia that is made of shrimp paste, chili, turmeric flower, and herbs mixed with some spices. This study aims to isolate Lactic Acid Bacteria (LAB) and analyze the metagenomic and biodiversity of its bacteria. Genome isolation for metagenomic analysis was using ZymoBIOMICSTM DNA Miniprep Kit. Sequencing analysis to identify LAB strain form masin was using 16S rRNA universal primer. Metagenomic analysis showed that relative abundance bacteria in masin for order taxon was Lactobacillales, the family taxon was Enteroccocaceae, and the genus was Tetragenoccocus. Six different groups were obtained from the phylogenetic tree analysis of 40 isolates found in masin. The representatives of each group taken were isolates number 2, 17, 11, 34, 28, and 5. Based on the results of sequencing analysis, the 6 isolates found in masin are Staphylococcus piscifermentans strain CIP103958 (Isolate Code 2), S. piscifermentans strain BULST54 (Isolate Code 17), S. piscifermentans strain SK03 (Isolate Code 11), S. piscifermentans strain ATCC 51136 (Isolate Code 34), S. piscifermentans strain PCM 2409 (Isolate Code 28) and S. piscifermentans strain PU-87 (Isolate Code 5). Through this research, it has been described a whole diversity of bacteria contained in masin, one of them is Lactic acid bacteria. The six LAB isolates that have been identified can be developed as starter candidates for masin production.
##plugins.themes.bootstrap3.article.details##
References
Azam M, Mohsin M, Ijaz H, Tulain UR, Ashraf MA, Fayyaz A, Abadeen Z, Kamran Q. 2017. Review: Lactic acid bacteria in traditional fermented Asian foods. Pak. J. Pharm. Sci. 30(5): 1803-1814.
Bintsis T. 2018. Review: Lactic acid bacteria: their applications in foods. Journal of Bacteriology & Mycology 6(2): 89 – 94.
Bjerke GA, Rudi K, Avershina E, Moen B, Blom H, Axelsson L. 2019. Exploring the Brine Microbiota of a Traditional Norwegian Fermented Fish Product (Rakfisk) from Six Different Producers during Two Consecutive Seasonal Productions. Foods 8(72), doi: 10.3390/foods8020072.
Bokulich NA, Subramanian SF, Faith JJ, Gavers D, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from illumina amplicon sequencing. Nat. Methods 10(1): 57-59.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7(5): 335-336.
Castellano P, Ibarreche MP, Massani MB, Fontana C, Vignolo GM. 2017. Review: Strategies for Pathogen Biocontrol Using Lactic Acid Bacteria and Their Metabolites: A Focus on Meat Ecosystems and Industrial Environments. Microorganisms 5(38), doi: 10.3390/microorganisms5030038.
Edgar RC, Haas BJ, Clemente JC, Quine C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16): 2194-2200.
Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10: 996-998.
Gevers D, Huys G, Swings J. 2001. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 205(1): 31-36.
Gupta S, Ravindra, Maurya PK, Parhi J, Sharma S, Chandravanshi S, Majumdar RK. 2018. Isolation and characterization of predominant bacteria, Staphylococcus piscifermentans associated with traditional fermented fish products of Northeast India. Int.J.Curr.Microbiol.App.Sci 7(5): 1758-1771.
Hajar S, Hamid THTA. 2013. Isolation of lactic acid bacteria strain Staphylococcus piscifermentans from Malaysian traditional fermented shrimp cincaluk. International Food Research Journal 20(1): 125-129.
Lahiri DK, Schnabel B. 1993. DNA isolation by a rapid method from human blood samples: effects of MgCl2, EDTA, storage time, and temperature on DNA yield and quality. Biochem. Genet. 31(7-8): 321-328.
Lavefve L, Marasini D, Carbonero F. 2019. Microbial Ecology of Fermented Vegetables and Non Alcoholic Drinks and Current Knowledge on Their Impact on Human Health, pp. 147-185. In Toldra F (ed.), Advances in Food and Nutrition Research, vol. 87. Academic Press, Oxford, U.K.
Linares DM, Gomez C, Renes E, Fresno JM, Tornadijo ME, Ross RP, Stanton C. 2017. Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods. Front. Microbiol. 8:846 doi: 10.3389/fmicb.2017.00846.
Mago? T, Salzberg SL. 2011 FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21): 2957-2963.
Majumdar RK, Roy D, Bejjanki S, Bhaskar N. 2016. Chemical and microbial properties of shidal, a traditional fermented fish of Northeast India. J. Food Sci. Technol. 53(1): 401-410.
Manguntungi B, Saputri, DS, Afgani CA, Mustopa AZ, Fatimah, Kusmiran A. 2020. Biodiversity of Enterobacteriaceae on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia. Biodiversitas 21: 1001-1006.
Mekadim C, Killer J, Mrázek J, Bunešová V, Pechar R, Hroncová Z, Vlková E. 2018. Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales. Arch. Microbiol. 200(10): 1427–1437.
Mohania D, Nagpal R, Kumar M, Bhardwaj A, Yadav M, Jain S, Marotta F, Singh V, Parkash O, Yadav H. 2008. Molecular approaches for identification and characterization of lactic acid bacteria. J. Dig. Dis. 9(4): 190-198.
Mokoena MP, Mutanda T, Olaniran AO. 2016. Perspectives on the probiotic potential of lactic acid bacteria from African traditional fermentedfoods and beverages. Food Nutr. Res. 60:1, doi: 10.3402/fnr.v60.29630.
Muryany I, Salwany I, Ghazali AR, Hing HL, Fadilah, N. 2017. Identification and characterization of the Lactic Acid Bacteria isolated from Malaysian fermented fish (Pekasam). International Food Research Journal 24(2): 868-875.
Nga TT, Tra DX, Ha LT. 2017. Isolation Of Halophilic Lactic Bacteria Tetragenococcus Halophilus From Vietnamese Fish Sauce. Vietnam Journal of Science and Technology 55: 186-194.
Ouobaa LII, Mbozoc ABV, Anyogud A, Obiohaa PI, Sawadogoe HL, Sutherlanda JP, Jespersenf L, Ghoddusia HB. 2019. Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements. International Journal of Food Microbiology 311. doi: 10.1016/j.ijfoodmicro.2019.108356.
Pessione E and Cirrincione S. 2016. Review: Bioactive Molecules Released in Food by Lactic Acid Bacteria: Encrypted Peptides and Biogenic Amines. Front. Microbiol. 7:876. doi: 10.3389/fmicb.2016.00876.
Putra TF, Suprapto H, Tjahjaningsih W, Pramono H. 2018. The antagonistic activity of lactic acid bacteria isolated from peda, an Indonesian traditional fermented fish. Asean-Fen International Fisheries Symposium – 2017 IOP Publishing IOP Conf. Series: Earth and Environmental Science 012060 doi:10.1088/1755-1315/137/1/012060.
Quast C, Pruesse E, Yilmas P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41: 590-596.
Reuter G. 1985. Elective and selective media for lactic acid bacteria. Int. Journal of Food Microbiology 2: 55-68.
Silva VP, Pareira OG, Leandro ES, Da Silva TC, Ribeiro KG, Mantovani HC, Santos SA. 2016. Effects of lactic acid bacteria with bacteriocinogenicpotential on the fermentation profile and chemical composition of alfalfa silage in tropical conditions. J. Dairy Sci. 99:1895–1902.
Speranza et al. 2017. Autochthonous lactic acid bacteria with probiotic aptitudes as startercultures for fish-based products. Food Microbiology 65: 244-253.
Subagiyo, Margino S, Triyanto, Setyati WA. 2015. Pengaruh pH, suhu dan salinitas terhadap pertumbuhan dan produksi asam organik bakteri asam laktat yang diisolasi dari intestinum udang penaeid. Ilmu Kelautan 20(4): 187-194.
Tanasupawat S, Hashimoto Y, Ezaki T, Kozaki M, Komagata K. 1992. Staphylococcus piscifermentans sp. nov., from Fermented Fish in Thailand. International Journal of Systematic Bacteriology 42(4): 577-581.
Woraprayote W, Malila Y, Sorapukdee S, Swetwiwathana A, Benjakul S, Visessanguan W. 2016. Bacteriocins from lactic acid bacteria and their applications in meat and meat products. Meat Sci. 120: 118-132.
Zhang J, Wang X, Huo D, Li W, Hu Q, Xu C, Liu S, Li C. 2016. Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food. Scientific Reports 6 DOI: 10.1038/srep32524
Zhao CC and Eun JB. 2020. Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product. Food Research International 131: 109030
Bintsis T. 2018. Review: Lactic acid bacteria: their applications in foods. Journal of Bacteriology & Mycology 6(2): 89 – 94.
Bjerke GA, Rudi K, Avershina E, Moen B, Blom H, Axelsson L. 2019. Exploring the Brine Microbiota of a Traditional Norwegian Fermented Fish Product (Rakfisk) from Six Different Producers during Two Consecutive Seasonal Productions. Foods 8(72), doi: 10.3390/foods8020072.
Bokulich NA, Subramanian SF, Faith JJ, Gavers D, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from illumina amplicon sequencing. Nat. Methods 10(1): 57-59.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7(5): 335-336.
Castellano P, Ibarreche MP, Massani MB, Fontana C, Vignolo GM. 2017. Review: Strategies for Pathogen Biocontrol Using Lactic Acid Bacteria and Their Metabolites: A Focus on Meat Ecosystems and Industrial Environments. Microorganisms 5(38), doi: 10.3390/microorganisms5030038.
Edgar RC, Haas BJ, Clemente JC, Quine C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16): 2194-2200.
Edgar RC. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10: 996-998.
Gevers D, Huys G, Swings J. 2001. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 205(1): 31-36.
Gupta S, Ravindra, Maurya PK, Parhi J, Sharma S, Chandravanshi S, Majumdar RK. 2018. Isolation and characterization of predominant bacteria, Staphylococcus piscifermentans associated with traditional fermented fish products of Northeast India. Int.J.Curr.Microbiol.App.Sci 7(5): 1758-1771.
Hajar S, Hamid THTA. 2013. Isolation of lactic acid bacteria strain Staphylococcus piscifermentans from Malaysian traditional fermented shrimp cincaluk. International Food Research Journal 20(1): 125-129.
Lahiri DK, Schnabel B. 1993. DNA isolation by a rapid method from human blood samples: effects of MgCl2, EDTA, storage time, and temperature on DNA yield and quality. Biochem. Genet. 31(7-8): 321-328.
Lavefve L, Marasini D, Carbonero F. 2019. Microbial Ecology of Fermented Vegetables and Non Alcoholic Drinks and Current Knowledge on Their Impact on Human Health, pp. 147-185. In Toldra F (ed.), Advances in Food and Nutrition Research, vol. 87. Academic Press, Oxford, U.K.
Linares DM, Gomez C, Renes E, Fresno JM, Tornadijo ME, Ross RP, Stanton C. 2017. Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods. Front. Microbiol. 8:846 doi: 10.3389/fmicb.2017.00846.
Mago? T, Salzberg SL. 2011 FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21): 2957-2963.
Majumdar RK, Roy D, Bejjanki S, Bhaskar N. 2016. Chemical and microbial properties of shidal, a traditional fermented fish of Northeast India. J. Food Sci. Technol. 53(1): 401-410.
Manguntungi B, Saputri, DS, Afgani CA, Mustopa AZ, Fatimah, Kusmiran A. 2020. Biodiversity of Enterobacteriaceae on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia. Biodiversitas 21: 1001-1006.
Mekadim C, Killer J, Mrázek J, Bunešová V, Pechar R, Hroncová Z, Vlková E. 2018. Evaluation of the infB and rpsB gene fragments as genetic markers intended for identification and phylogenetic analysis of particular representatives of the order Lactobacillales. Arch. Microbiol. 200(10): 1427–1437.
Mohania D, Nagpal R, Kumar M, Bhardwaj A, Yadav M, Jain S, Marotta F, Singh V, Parkash O, Yadav H. 2008. Molecular approaches for identification and characterization of lactic acid bacteria. J. Dig. Dis. 9(4): 190-198.
Mokoena MP, Mutanda T, Olaniran AO. 2016. Perspectives on the probiotic potential of lactic acid bacteria from African traditional fermentedfoods and beverages. Food Nutr. Res. 60:1, doi: 10.3402/fnr.v60.29630.
Muryany I, Salwany I, Ghazali AR, Hing HL, Fadilah, N. 2017. Identification and characterization of the Lactic Acid Bacteria isolated from Malaysian fermented fish (Pekasam). International Food Research Journal 24(2): 868-875.
Nga TT, Tra DX, Ha LT. 2017. Isolation Of Halophilic Lactic Bacteria Tetragenococcus Halophilus From Vietnamese Fish Sauce. Vietnam Journal of Science and Technology 55: 186-194.
Ouobaa LII, Mbozoc ABV, Anyogud A, Obiohaa PI, Sawadogoe HL, Sutherlanda JP, Jespersenf L, Ghoddusia HB. 2019. Environmental heterogeneity of Staphylococcus species from alkaline fermented foods and associated toxins and antimicrobial resistance genetic elements. International Journal of Food Microbiology 311. doi: 10.1016/j.ijfoodmicro.2019.108356.
Pessione E and Cirrincione S. 2016. Review: Bioactive Molecules Released in Food by Lactic Acid Bacteria: Encrypted Peptides and Biogenic Amines. Front. Microbiol. 7:876. doi: 10.3389/fmicb.2016.00876.
Putra TF, Suprapto H, Tjahjaningsih W, Pramono H. 2018. The antagonistic activity of lactic acid bacteria isolated from peda, an Indonesian traditional fermented fish. Asean-Fen International Fisheries Symposium – 2017 IOP Publishing IOP Conf. Series: Earth and Environmental Science 012060 doi:10.1088/1755-1315/137/1/012060.
Quast C, Pruesse E, Yilmas P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41: 590-596.
Reuter G. 1985. Elective and selective media for lactic acid bacteria. Int. Journal of Food Microbiology 2: 55-68.
Silva VP, Pareira OG, Leandro ES, Da Silva TC, Ribeiro KG, Mantovani HC, Santos SA. 2016. Effects of lactic acid bacteria with bacteriocinogenicpotential on the fermentation profile and chemical composition of alfalfa silage in tropical conditions. J. Dairy Sci. 99:1895–1902.
Speranza et al. 2017. Autochthonous lactic acid bacteria with probiotic aptitudes as startercultures for fish-based products. Food Microbiology 65: 244-253.
Subagiyo, Margino S, Triyanto, Setyati WA. 2015. Pengaruh pH, suhu dan salinitas terhadap pertumbuhan dan produksi asam organik bakteri asam laktat yang diisolasi dari intestinum udang penaeid. Ilmu Kelautan 20(4): 187-194.
Tanasupawat S, Hashimoto Y, Ezaki T, Kozaki M, Komagata K. 1992. Staphylococcus piscifermentans sp. nov., from Fermented Fish in Thailand. International Journal of Systematic Bacteriology 42(4): 577-581.
Woraprayote W, Malila Y, Sorapukdee S, Swetwiwathana A, Benjakul S, Visessanguan W. 2016. Bacteriocins from lactic acid bacteria and their applications in meat and meat products. Meat Sci. 120: 118-132.
Zhang J, Wang X, Huo D, Li W, Hu Q, Xu C, Liu S, Li C. 2016. Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food. Scientific Reports 6 DOI: 10.1038/srep32524
Zhao CC and Eun JB. 2020. Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product. Food Research International 131: 109030
Most read articles by the same author(s)
- KHADIJAH ALLIYA FIDIEN, BASO MANGUNTUNGI, LINDA SUKMARINI, APON ZAENAL MUSTOPA, LITA TRIRATNA, FATIMAH, KUSDIANAWATI, Diversity analysis, identification, and bioprospecting of Lactic Acid Bacteria (LAB) isolated from Sumbawa horse milk , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 6 (2021)
- ALMANDO GERALDI, CHIA CHAY TAY, NI’MATUZAHROH, FATIMAH, WAN NURHAYATI WAN HANAFI , Unraveling the bacterial diversity of Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 9 (2021)
- KUSDIANAWATI, APON Z. MUSTOPA, FATIMAH, BUGI R. BUDIARTO, Genetic diversity of lactic acid bacteria isolated from Sumbawa horse milk, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 7 (2020)
- FAUZIYAH, APON Z. MUSTOPA, FATIMAH, ANNA I. S. PURWIYANTO, ROZIRWAN, FITRI AGUSTRIANI, WIKE A.E. PUTRI, Morphometric variation of the horseshoe crab Tachypleus gigas (Xiphosura: Limulidae) from the Banyuasin estuarine of South Sumatra, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 11 (2021)
- NI’MATUZAHROH NI’MATUZAHROH, SILVIA KURNIA SARI, IRINE PUSPA NINGRUM, APRILLA DILA PUSFITA, LISA MARJAYANDARI, NASTITI TRIKURNIADEWI, SYAHRIAR NUR MAULANA MALIK IBRAHIM, FATIMAH FATIMAH, TRI NURHARIYATI, TINI SURTININGSIH, HANIF YULIANI, The potential of indigenous bacteria from oil sludge for biosurfactant production using hydrolysate of agricultural waste , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 5 (2019)
- BASO MANGUNTUNGI, DINAR S. SAPUTRI, CHAIRUL A. AFGANI, APON Z. MUSTOPA, FATIMAH, AMIRIN KUSMIRAN, Biodiversity of Enterobacteriaceae on masin (fermented sauce) from Sumbawa, West Nusa Tenggara, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 3 (2020)
- ARIDO YUGOVELMAN AHADDIN, SRI BUDIARTI, A. ZAENAL MUSTOPA, HUDA S. DARUSMAN, LITA TRIRATNA, Short Communication: Acute toxicity study of plantaricin from Lactobacillus plantarum S34 and its antibacterial activity , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 1 (2021)
- FARAH AISYAH NAFIDIASTRI, RIZKY DANANG SUSETYO, TRI NURHARIYATI, AGUS SUPRIYANTO, ALMANDO GERALDI, NI’MATUZAHROH, FATIMAH, SALAMUN, Biosurfactant activity of indigenous Bacillus sp. ES4.3 isolated from endemic breeding sites of dengue hemorrhagic fever vector in Surabaya, East Java, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 12 (2021)
- MUSTOFA HELMI EFFENDI, HAYYUN DURROTUL FARIDAH, FRESHINDY MARISSA WIBISONO, FRESHINTA JELLIA WIBISONO, NABILATUN NISA, FATIMAH, EMMANUEL NNABUIKE UGBO, Detection of virulence factor encoding genes on Escherichia coli isolated from broiler chicken in Blitar District, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 23 No. 7 (2022)
- APON ZAENAL MUSTOPA, INES FERDIANA PUSPITASARI, FATIMAH FATIMAH, LITA TRIRATNA, GINA KARTINA, Genetic diversity of mastitis cow’s milk bacteria based on RAPD-PCR , Biodiversitas Journal of Biological Diversity: Vol. 19 No. 5 (2018)