Abstract
A total of 272 isolates of lactic acid bacteria (LAB) were isolated from 22 samples of naturally fermented milk products of Sikkim in India viz. dahi, soft-variety chhurpi, hard-variety chhurpi, mohi and philu, out of which, 68 LAB isolates were randomly grouped on the basis of phenotypic characteristics, and were identified by 16S rRNA gene sequence analysis. Leuconostoc mesenteroides was the most dominant genus, followed by Leuc. mesenteroides subsp. jonggajibkimchii, Lactococcus lactis subsp. cremoris, Lc. lactis, Lc. lactis subsp. hordniae, Lc. lactis subsp. tructae, Enterococcus faecalis, E. italicus and E. pseudoavium. LAB strains were tested for probiotics attributes by in vitro and genetic screening, based on marker genes. LAB strains showed tolerance to pH 3.0, bile salt, resistance to lysozyme and β-galactosidase activity. Enterococcus faecalis YS4-11 and YS4-14 and Lactococcus lactis subsp. cremoris SC3 showed more than 85% of hydrophobicity. Genes clp L and tdc encoding for low pH tolerance, agu A and Ir1516 encoding for bile tolerance, LBA1446 gene encoding for BSH activity, map A, apf, mub 1 and msa encoding for mucosal binding property were detected. Gene mesY for bacteriocin production was detected only in Leuconostoc spp. Based on the in vitro and genetic screening of probiotic attributes, Leuc. mesenteroides; Leuc. mesenteroides subsp. jonggajibkimchii and Lc. lactis subsp. cremoris were tentatively selected for possible probiotic candidates.
Similar content being viewed by others
Data availability
The sequences of 16S rRNA sequencing were deposited at GeneBank-NCBI under the accession number: MK290329–MK290372, MK574836–MK574857, MK583513, MK720122 and MK796023.
References
Abriouel H, Pérez Montoro B, Casimiro-Soriguer CS, Pérez Pulido AJ, Knapp CW et al (2017) Insight into potential probiotic markers predicted in Lactobacillus pentosus MP-10 genome sequence. Front Microbiol 8:891. https://doi.org/10.3389/fmicb.2017.00891
Adebola OO, Corcoran O, Morgan WA (2020) Prebiotics may alter bile salt hydrolase activity: possible implications for cholesterol metabolism. PharmaNutrition 12:100182. https://doi.org/10.1016/j.phanu.2020.100182
Alegría Á, Szczesny P, Mayo B, Bardowski J, Kowalczyk M (2012) Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and independent approaches. Appl Environ Microbiol 78(6):1890–1898
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Al-Zahrani K, Allam R, Amasha R, Jastaniah S, Aly M (2019) Isolation and identification of Lactobacillus plantarum KM5 from camel milk for β-galactosidase production. J Pharma Biol Sci 14(2):27–35
Angelescu IR, Zamfir M, Stancu MM, Grosu-Tudor SS (2019) Identification and probiotic properties of lactobacilli isolated from two different fermented beverages. Ann Microbiol 69:1557–1565
Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72:5734–5741
Ataseve MA, Ataseve M (2018) Some quality properties of Kurut, a traditional dairy product in Turkey. Manas J Agric Vet Life Sci 8:68–74
Balouiri M, Sadiki M, Ibnsouda SK (2016) Methods for in vitro evaluating antimicrobial activity: a review. J Pharm Anal 6(2):71–79
Bao Q, Yu J, Liu W, Qing M, Wang W et al (2012) Predominant lactic acid bacteria in traditional fermented yak milk products in the Sichuan Province of China. Dairy Sci Technol 92(3):309–319
Besrour-Aouam N, Mohedano ML, Fhoula I, Zarour K, Najjari A et al (2019) Different modes of regulation of the expression of dextransucrase in Leuconostoc lactis AVin and Lactobacillus sakei MN1. Front Microbiol 10:959. https://doi.org/10.3389/fmicb.2019.00959
Bezie A, Regasa H (2019) The role of starter culture and enzymes/rennet for fermented dairy products manufacture—a review. Nutr Food Sci Int J 9(2):555756. https://doi.org/10.19080/NFSIJ.2019.09.555756
Burgain J, Scher J, Francius G, Borges F, Corgneau M et al (2014) Lactic acid bacteria in dairy food: surface characterization and interactions with food matrix components. Adv Colloid Interface Sci 213:21–35
Choi SH (2016) Characterization of airag collected in Ulaanbaatar, Mongolia with emphasis on isolated lactic acid bacteria. J Anim Sci Technol 58:10. https://doi.org/10.1186/s40781-016-0090-8
Collins FWJ, Mesa-Pereira B, O’Connor PM, Rea MC, Hill C, Ross RP (2018) Reincarnation of bacteriocins from the Lactobacillus Pangenomic graveyard. Front Microbiol 9:1298. https://doi.org/10.3389/fmicb.2018.01298
Colombo M, Castilho NPA, Todorov SD, Nero LA (2018) Beneficial properties of lactic acid bacteria naturally present in dairy production. BMC Microbiol 18:219. https://doi.org/10.1186/s12866-018-1356-8
Daly AJ, Baetens JM, De Baets B (2018) Ecological diversity: measuring the unmeasurable. Mathematics 6:119. https://doi.org/10.3390/math6070119
Devi SM, Archer AC, Halami PM (2015) Screening, characterization and in vitro evaluation of probiotic properties among lactic acid bacteria through comparative analysis. Probiotics Antimicrob Proteins 7(3):181–192
Dewan S, Tamang JP (2006) Microbial and analytical characterization of Chhu, a traditional fermented milk product of the Sikkim Himalayas. J Sci Ind Res 65:747–752
Dewan S, Tamang JP (2007) Dominant lactic acid bacteria and their technological properties isolated from the Himalayan ethnic fermented milk products. Antonie Van Leeuwen 92:343–352
Feroze SM, Ray LIP, Singh KJ, Singh R (2019) Pastoral yak rearing system is changing with change in climate: an exploration of North Sikkim in Eastern Himalaya. Clim Change 157(3):483–498
Ghosh T, Beniwal A, Semwal A, Navani NK (2019) Mechanistic insights into probiotic properties of lactic acid bacteria associated with ethnic fermented dairy products. Front Microbiol 10:502. https://doi.org/10.3389/fmicb.2019.00502
Goel A, Halami PM, Tamang JP (2020) Genome analysis of Lactobacillus plantarum isolated from some Indian fermented foods for bacteriocin production and probiotic marker genes. Front Microbiol 11:40. https://doi.org/10.3389/fmicb.2020.00040
Gutiérrez-Cortés C, Suárez H, Buitrago G, Díaz-Moreno C (2017) Isolation and evaluation of the antagonist activity of lactic acid bacteria in raw cow milk. Agron Colomb 35(3):357–364
Hammer Ø, Harper DA, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Elect 4(1):9
Hayek S, Gyawali R, Aljaloud S, Krastanov A, Ibrahim S (2019) Cultivation media for lactic acid bacteria used in dairy products. J Dairy Res 86(4):490–502
Hickey CD, Sheehan JJ, Wilkinson MG, Auty MA (2015) Growth and location of bacterial colonies within dairy foods using microscopy techniques: a review. Front Microbiol 6:99. https://doi.org/10.3389/fmicb.2015.00099
Holst B, Glenting J, Holmstrøm K, Israelsen H, Vrang A et al (2019) Molecular switch controlling expression of the mannose-specific adhesin, msa in Lactobacillus plantarum. Appl Environ Microbiol 85(10):e02954-e3018. https://doi.org/10.1128/AEM.02954-18
Holzapfel WH, Wood BJ (2012) The genera of lactic acid bacteria, vol 2. Springer, New York
Horackova S, Vesela K, Klojdova I, Bercikova M, Plockova M (2020) Bile salt hydrolase activity, growth characteristics and surface properties in Lactobacillus acidophilus. Eur Food Res Technol 246:1627–1636
Ibrahim AH (2018) Enhancement of β-galactosidase activity of lactic acid bacteria in fermented camel milk. Emir J Food Agric 30(4):256–267
Ingty T (2021) Pastoralism in the highest peaks: role of the traditional grazing systems in maintaining biodiversity and ecosystem function in the alpine Himalaya. PLoS ONE 16(1):e0245221. https://doi.org/10.1371/journal.pone.0245221
Jatmiko YD, Howarth G, Barton MD (2017) Assessment of probiotic properties of lactic acid bacteria isolated from Indonesian naturally fermented milk. AIP Conf Proc 1908:050008. https://doi.org/10.1063/1.5012732
Jiang Y, Li N, Wang Q, Liu Z, Lee YK et al (2020) Microbial diversity and volatile profile of traditional fermented yak milk. J Dairy Sci 103(1):87–97
Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P et al (2019) Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Com 10:5029. https://doi.org/10.1038/s41467-019-13036-1
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J System Evo Microbiol 62:716–721
Kolev P, Rocha-Mendoza D, Ruiz-Ramírez S, Ortega-Anaya J, Jiménez-Flores R, García-Cano I (2021) Screening and characterization of β-galactosidase activity in lactic acid bacteria for the valorization of acid whey. JDS Commun. https://doi.org/10.3168/jdsc.2021-0145
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley, New York, pp 115–175
Maged S, Masalam B, Bahieldin A, Alharbi MG, Al-Masaudi S et al (2018) Isolation, molecular characterization and probiotic potential of lactic acid bacteria in Saudi raw and fermented milk. Evid Based Complement Altern Med 7970463:12. https://doi.org/10.1155/2018/7970463
Mattiello S, Caroprese M, Matteo CG, Fortina R, Martini A et al (2018) Typical dairy products in Africa from local animal resources. Ital J Anim Sci 17(3):740–754
Motey GA, Owusu-Kwarteng J, Obiri-Danso K, Ofori LA, Ellis WO et al (2021) In vitro properties of potential probiotic lactic acid bacteria originating from Ghanaian indigenous fermented milk products. World J Microbiol Biotechnol 37:52. https://doi.org/10.1007/s11274-021-03013-6
Mulaw G, Tessema TS, Muleta D, Tesfaye A (2019) In vitro evaluation of probiotic properties of lactic acid bacteria isolated from some traditionally fermented Ethiopian food products. Int J Microbiol. https://doi.org/10.1155/2019/7179514
Nithya V, Halami PM (2013) Evaluation of probiotic characteristics of Bacillus species isolated from different food sources. Ann Microbiol 63(1):129–137
Nostro A, Cannatelli MA, Crisafi G, Musolino AD, Procopio F et al (2004) Modifications of hydrophobicity, in vitro adherence and cellular aggregation of Streptococcus mutans by Helichrysum italicum extract. Lett Appl Microbiol 38(5):423–427
Oki K, Dugersuren J, Demberel S, Watanabe K (2014) Pyrosequencing analysis of the microbial diversity of Airag, Khoormog and Tarag, traditional fermented dairy products of Mongolia. Biosci Microbio Food Health 33(2):53–64
Parker M, Zobrist S, Donahue C, Edick C, Mansen K et al (2018) Naturally fermented milk from northern Senegal: bacterial community composition and probiotic enrichment with Lactobacillus rhamnosus. Front Microbiol 9:2218. https://doi.org/10.3389/fmicb.2018.02218
Polak-Berecka M, Waśko A, Paduch R, Skrzypek T, Sroka-Bartnicka A (2014) The effect of cell surface components on adhesion ability of Lactobacillus rhamnosus. Antonie Van Leeuwen 106(4):751–762
Pradhan P, Tamang JP (2019) Phenotypic and genotypic identification of bacteria isolated from traditionally prepared dry starters of the Eastern Himalayas. Front Microbiol 10:2526. https://doi.org/10.3389/fmicb.2019.02526
Pradhan P, Tamang JP (2021) Probiotic properties of lactic acid bacteria isolated from traditionally prepared dry starters of the Eastern Himalayas. World J Microbiol Biotechnol 37:7. https://doi.org/10.1007/s11274-020-02975-3
Rai R (2020) Diversity of lactic acid bacteria and their probiotic properties in some naturally fermented milk products of Sikkim. PhD Thesis, Sikkim University, Gangtok, India
Rai R, Shangpliang HNJ, Tamang JP (2016) Naturally fermented milk products of the Eastern Himalayas. J Ethnic Foods 3:270–275
Refay RM, Abushady HM, Amer SA, Mailam MA (2020) Determination of bacteriocin-encoding genes of lactic acid bacteria isolated from traditional dairy products of Luxor province, Egypt. Future J Pharm Sci 6:22. https://doi.org/10.1186/s43094-020-00031-3
Reuben RC, Roy PC, Sarkar SL, Rubayet Ul Alam ASM, Jahid IK (2020) Characterization and evaluation of lactic acid bacteria from indigenous raw milk for potential probiotic properties. J Dairy Sci 103(2):1223–1237
Rezac S, Kok CR, Heermann M, Hutkins R (2018) Fermented foods as a dietary source of live organisms. Front Microbiol 9:1785. https://doi.org/10.3389/fmicb.2018.01785
Ridlon JM, Harris SC, Bhowmik S, Kang DJ, Hylemon PB (2016) Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes 7(1):22–39
Ruvalcaba-Gómez JM, Delgado-Macuil RJ, Zelaya-Molina LX, Maya-Lucas O, Ruesga-Gutiérrez E et al (2021) Bacterial succession through the artisanal process and seasonal effects defining bacterial communities of raw-milk Adobera cheese revealed by high throughput DNA sequencing. Microorganisms 9:24. https://doi.org/10.3390/microorganisms9010024
Sagheddu V, Guidesi E, Galletti S, Elli M (2019) Selection and characterization criteria of probiotics intended for human use from the past to the future. Food Sci Nutr Studies 3:73. https://doi.org/10.22158/fsns.v3n2p73
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425
Schmitz A, Riesner D (2006) Purification of nuclei acids by selective precipitation with polyethylene glycol 6000. Anal Biochem 354(2):311–313
Shangpliang HNK, Tamang JP (2021) Phenotypic and genotypic characterizations of lactic acid bacteria isolated from exotic naturally fermented milk (cow and yak) products of Arunachal Pradesh, India. Int Dairy J 118:105038. https://doi.org/10.1016/j.idairyj.2021.105038
Shangpliang HNJ, Sharma S, Rai R, Tamang JP (2017) Some technological properties of lactic acid bacteria isolated from Dahi and Datshi, naturally fermented milk products of Bhutan. Front Microbiol 8:116. https://doi.org/10.3389/fmicb.2017.00116
Shangpliang HNJ, Rai R, Keisam S, Jeyaram K, Tamang JP (2018) Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing. Sci Rep 8(1):1532. https://doi.org/10.1038/s41598-018-19524-6
Sharma BR, Halami PM, Tamang JP (2021) Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods. Food Sci Biotechnol. https://doi.org/10.1007/s10068-021-00986-w
Singh TP, Kaur G, Malik RK, Schillinger U, Guigas C et al (2012) Characterization of intestinal Lactobacillus reuteri strains as potential probiotics. Probiotics Antimicro Proteins 4:47–58. https://doi.org/10.1007/s12602-012-9090-2
Tamang JP, Dewan S, Thapa S, Olasupo NA, Schillinger U et al (2000) Identification and enzymatic profiles of the predominant lactic acid bacteria isolated from soft-variety chhurpi, a traditional cheese typical of the Sikkim Himalayas. Food Biotechnol 14(1–2):99–112
Tamang JP, Okumiya K, Kosaka Y (2010) Cultural adaptation of the Himalayan ethnic foods with special reference to Sikkim, Arunachal Pradesh and Ladakh. Himal Study Monogr 11:177–185
Tamang JP, Holzapfel WH, Watanabe K (2016) Diversity of microorganisms in global fermented foods and beverages. Front Microbiol 7:377. https://doi.org/10.3389/fmicb.2016.00377
Tamang JP, Cotter P, Endo A, Han NS, Kort R et al (2020) Fermented foods in a global age: east meets west. Compr Rev Food Sci Food Safe 19:184–217. https://doi.org/10.1111/1541-4337.12520
Tamang JP, Jeyaram K, Rai AK, Mukherjee PK (2021) Diversity of beneficial microorganisms and their functionalities in community-specific ethnic fermented foods of the Eastern Himalayas. Food Res Int 148:110633. https://doi.org/10.1016/j.foodres.2021.110633
Teneva-Angelova T, Balabanova T, Boyanova P, Beshkova D (2018) Traditional Balkan fermented milk products. Engineer Life Sci 18:807–819
Thapa N, Tamang JP (2020) Ethnic fermented foods and beverages of Sikkim and Darjeeling Hills (Gorkhaland Territorial Administration). In: Tamang JP (ed) Ethnic fermented foods and alcoholic beverages of India: science history and culture. Springer, Singapore, pp 479–537
Turpin W, Humblot C, Guyot JP (2011) Genetic screening of functional properties of lactic acid bacteria in a fermented pearl millet slurry and in the metagenome of fermented starchy foods. Appl Environ Microbiol 77(24):8722–8734
Turpin W, Humbolt C, Noordine ML, Thomas M, Guyot JP (2012) Lactobacillaceae and cell adhesion: genomic and functional screening. PLoS ONE. https://doi.org/10.1371/journal.pone.0038034
Vinderola CG, Reinheimer JA (2003) Lactic acid starter and probiotic bacteria: a comparative “in vitro” study of probiotic characteristics and biological barrier resistance. Food Res Int 36(9–10):895–904
Wang D, Liu W, Ren Y, De L, Zhang D et al (2016) Isolation and identification of lactic acid bacteria from traditional dairy products in Baotou and Bayannur of midwestern Inner Mongolia and q-PCR analysis of predominant species. Food Sci Animal Res 36(4):499–507
Wirawati CU, Sudarwanto MB, Lukman DW, Wientarsih I, Srihanto EA (2019) Diversity of lactic acid bacteria in dadih produced by either back-slopping or spontaneous fermentation from two different regions of West Sumatra, Indonesia. Vet World 12(6):823–829
Yadav R, Puniya AK, Shukla P (2016) Probiotic properties of Lactobacillus plantarum RYPR1 from an indigenous fermented beverage Raabadi. Front Microbiol 7:1683. https://doi.org/10.3389/fmicb.2016.01683
Ying AN, Adachi Y, Ogawa Y (2004) Classification of lactic acid bacteria isolated from chigee and mare milk collected in Inner Mongolia. Anim Sci J 75:245–252
Yue F, Shi J, Tang J (2009) Simultaneous phylogeny reconstruction and multiple sequence alignment. BMC Bioinform 10(Suppl 1):S11. https://doi.org/10.1186/1471-2105-10-S1-S11
Zago M, Fornasari ME, Carminati D, Burns P, Suàrez V et al (2011) Characterization and probiotic potential of Lactobacillus plantarum strains isolated from cheeses. Food Microbiol 28(5):1033–1040
Acknowledgements
Authors are gratefully to Department of Biotechnology (DBT), Govt. of India for financial support.
Author information
Authors and Affiliations
Contributions
RR has done the major experimental parts. JPT has supervised the experiments and and finalised the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Rai, R., Tamang, J.P. In vitro and genetic screening of probiotic properties of lactic acid bacteria isolated from naturally fermented cow-milk and yak-milk products of Sikkim, India. World J Microbiol Biotechnol 38, 25 (2022). https://doi.org/10.1007/s11274-021-03215-y
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11274-021-03215-y