Analysis of kefir grains from different regions of the planet using high-throughput sequencing
https://doi.org/10.55959/MSU0137-0952-16-2022-77-4-266-272
Abstract
The taxonomic composition and spatial localization of yeast and bacteria in kefir grains (KG) obtained for study from different regions of the planet were investigated. The diversity of their microbiome has been demonstrated by high-throughput sequencing of bacterial 16S rRNA genes and the ITS1 region of the 18S-ITS1-5.8S-ITS2-28S complex of yeast rRNA. It has been established that the main representatives of the complex community of KG from different regions are lactic acid bacteria (LAB; lactobacilli, lactococci and Leuconostoc spp. in different ratios), and different types of yeast of the genus Kazachstania (family Saccharomycetaceae). Acetic acid bacteria and a small percentage of yeast Kluyveromyces marxianus were detected in the KG from Tibet, and yeast Pichia kluyveri was detected in the KG from Ossetia
About the Authors
F. Ding
Lomonosov Moscow State University, Shenzhen MSU-BIT University
China
China
Microbiology Department
1–12 Leninskie Gory, Moscow, 119234
No 299, Ruyi Road, Longgang District, Shenzhen, Guangdong, 518172
A. A. Krasilnikova
Lomonosov Moscow State University
Russian Federation
Russian Federation
Microbiology Department
1–12 Leninskie Gory, Moscow, 119234
M. R. Leontieva
Lomonosov Moscow State University
Russian Federation
Russian Federation
Microbiology Department
1–12 Leninskie Gory, Moscow, 119234
L. G. Stoyanova
Lomonosov Moscow State University
Russian Federation
Russian Federation
Microbiology Department
1–12 Leninskie Gory, Moscow, 119234
A. I. Netrusov
Lomonosov Moscow State University, High School of Economics
Russian Federation
Russian Federation
Microbiology Department,
1–12 Leninskie Gory, Moscow, 119234
Faculty of Biology and Biotechnology
20 Mjasnitskaja str., Moscow, 101000
References
1. Farag M.A., Jomaa S.A., El-Wahed A.A. The many faces of kefir fermented dairy products: quality characteristics, flavour chemistry, nutritional value, health benefits, and safety // Nutrients. 2020. Vol. 12. N 2. P. 346–359.
2. Nejati F., Junne S., Neubauer P. A big world in small grain: a review of natural milk Kefir starters // Microorganisms. 2020. Vol. 8. N 2: 192.
3. Khokhlacheva A.A., Egorova M.A., Kalinina A.N., Gradova N.B. Trophic patterns of functioning and microbial profile of an evolutionarily established associative culture of kefir grains // Microbiology. 2015. Vol. 84. N 4. P. 466–447.
4. Radhouani H., Goncalves C., Maia F.R., Oliveira J.M., Reis R.L. Biological performance of a promising kefiran-biopolymer with potential in regenerative medicine applications: a comparative study with hyaluronic acid // J. Mater. Sci. Mater. Med. 2018. Vol. 29. N 8: 124.
5. Kotova I.B., Cherdyntseva T.A., Netrusov A.I. Russian kefir grains microbial composition and its changes during production process // Advances in microbiology, infectious diseases and public health, vol. 932 / Ed. G. Donelli. Cham: Springer, 2016. P. 93–102.
6. Wang S.Y., Chen K.N., Lo Y.M., Chiang M.L., Chen H.C., Liu J.R., Chen M.J. Investigation of microorganisms involved in biosynthesis of the kefir grain // Food Microbiol. 2012. Vol. 3. N 2. P. 274–285.
7. Zajšek K., Kolar M., Goršek A. Characterisation of the exopolysaccharide kefiran produced by lactic acid bacteria entrapped within natural kefir grains // Int. J. Dairy Technol. 2011. Vol. 6. N 4. P. 544–548.
8. Diosma G., Romanin D.E., Rey-Burusco M.F., Londero A., Garrote G.L. Yeasts from kefir grains: isolation, identification, and probiotic characterization // World J. Microbiol. Biotechnol. 2014. Vol. 30. N 1. P. 43–53.
9. Zanirati D.F., Abatemarco M., Cicco Sandesb S.H., Nicolia J.R., Nunes A.C., Neumanna E. Selection of lactic acid bacteria from Brazilian kefir grains for potential use as starter or probiotic cultures // Anaеrobe. 2015. Vol. 3. N 2. P. 70–76.
10. Amorim F.G., Coitinho L.B., Dias A.T., Friques A.G.F., Monteiro B.L., de Rezende L.C.D., Pereira T.D.M.C., Campagnaro B.P., De Pauw E., Vasquez E.C., Quinton L. Identification of new bioactive peptides from Kefir milk through proteopeptidomics: bioprospection of antihypertensive molecules // Food Chem. 2019. Vol. 28. N 2. P. 109–119.
11. Cotârleț M., Vasile A.M., Cantaragiu A.M., Gaspar- Pintiliescu A., Crăciunescu O., Oancea A., Moraru A., Moraru I., Bahrim G.E. Colostrum-derived bioactive peptides obtained by fermentation with kefir grains enriched with selected yeasts // Ann. Univ. Dunarea Jos Galati Fascicle VI: Food Technol. 2019. Vol. 4. N 3. P. 54–68.
12. Ahmed Z., Wang Y., Ahmad A., Khan S. T., Nisa M., Ahmad H. Kefir and health: a contemporary perspective // Crit. Rev. Food Sci. Nutr. 2013. Vol. 5. N 3. P. 422–434.
13. Fadrosh D.W., Ma B., Gajer P., Sengamalay N., Ott S., Brotman R.M., Ravel J. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform // Microbiome. 2014. Vol. 24. N 2. P. 16–25.
14. Hugerth L.W., Wefer H.A., Lundin S., Jakobsson H.E., Lindberg M., Rodin S., Engstrand L., Andersson A.F. DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies // Appl. Environ. Microbiol. 2014. Vol. 80. N 16. P. 5116–5123.
15. Merkel A.Yu., Tarnovetskii I.Yu., Podosokorskaya O.A., Toshchakov S.V. Analysis of 16S rRNA primer systems for profiling of thermophilic microbial communities // Microbiology. 2019. Vol. 13. N 6. P. 671–680.
16. Bolyen E., Rideout J.R., Dillon M.R., et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 // Nat. Biotechnol. 2019. Vol. 37. N 8. P. 852–857.
17. Bokulich N.A., Mills D.A. Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities // Appl. Environ. Microbiol. 2013. Vol. 79. N 8. P. 2519–2526.
18. Willger S.D., Grim S.L., Dolben E.L., Shipunova A., Hampton T.H., Morrison H.G., Filkins L.M., O‘Toole G.A., Moulton L.A., Ashare A., Sogin M.L., Hogan D.A. Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis // Microbiome. 2014. Vol. 2. N 1: 40.
19. Edgar R.C. UPARSE: highly accurate OTU sequences from microbial amplicon reads // Nat. Methods. 2013. Vol. 10. N 10. P. 996–998. 20. Dannemiller K.C., Reeves D., Bibby K., Yamamoto N., Peccia J. Fungal high-throughput taxonomic identifi FHiTINGS) // J. Basic Microbiol. 2014. Vol. 5. N 4. P. 315–321.
20. Caporaso J.G., Kuczynski J., Stombaugh J., et al. QIIME allows analysis of high-throughput community sequencing data // Nat. Methods. 2010. Vol. 7. N 5. P. 335–336.
21. Jianzhong Z., Xiaoli L., Hanhu J., Mingsheng D. Analysis of the microflora in Tibetan kefir grains using denaturing gradient gel electrophoresis // Food Microbiol. 2009. Vol. 26. N 8. P. 770–775.
22. Gao J., Gu F., Abdella N. H., Ruan H., He G. Investigation on culturable microflora in Tibetan kefir grains from different areas of China // J. Food Sci. 2012. Vol. 77. N 8. P. 425–433.
23. Zheng Y., Lu Y., Wang J., Yang L., Pan C., Huang Y. Probiotic properties of Lactobacillus strains isolated from Tibetan Kefir grains // PLoS One. 2013. Vol. 8: e69868.
24. Lopitz-Otsoa F., Rementeria A., Elguezabala N., Garaizar J. Kefir: a simbiotic yeasts-bacteria community with alleged healthy capabilities // Rev. Iberoam. Micol. 2006. Vol. 23. N 1. P. 67–74.
Review
For citations:
Ding F., Krasilnikova A.A., Leontieva M.R., Stoyanova L.G., Netrusov A.I. Analysis of kefir grains from different regions of the planet using high-throughput sequencing. Vestnik Moskovskogo universiteta. Seriya 16. Biologiya. 2022;77(4):266-272. (In Russ.) https://doi.org/10.55959/MSU0137-0952-16-2022-77-4-266-272
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