185
Views
0
CrossRef citations to date
0
Altmetric
Review Article

Review on the NGS-based studies of microbiotas of artisanal and regional kinds of cheese with potential as functional foods: composition and functional analysis

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Article: 2361751 | Received 31 Mar 2024, Accepted 26 May 2024, Published online: 06 Jun 2024

References

  • Vargas-Ramella M, Pateiro M, Maggiolino A, et al. Buffalo milk as a source of probiotic functional products. Microorganisms. 2021;9(11):1. doi: 10.3390/microorganisms9112303.
  • Kontodimos I, Chatzimanoli E, Kasapidou E, et al. Characterization of bioactive compounds and element content in goat milk and cheese products. Biol Life Sci Forum. 2023;26:98.
  • Serra A, Conte G, Corrales-Retana L, et al. Nutraceutical and technological properties of buffalo and sheep cheese produced by the addition of kiwi juice as a coagulant. Foods. 2020;9(5):637. doi: 10.3390/foods9050637.
  • Ospanov A, Velyamov S, Makeeva R, Tlevlessova D., & Tastanova R. 2022. A study of the physico-chemical composition and technological properties of sheep and goat milk (ShGM) depending on the breed of the animal. Eureka: Life Sciences, (3), 29–38. https://doi.org/10.21303/2504-5695.2022.002606.
  • Ivanov, G.; Balabanova, M.; Ivanova, M.; Vlaseva, R.J.B.J.o.A.S. Comparative study of Bulgarian white brined cheese from cow and buffalo milk. Bulgarian Journal of Agricultural Science 2016; 22:643–646.
  • Neviani E, Bottari B, Lazzi C, et al. New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and parmigiano reggiano. Front Microbiol. 2013;4:36. doi: 10.3389/fmicb.2013.00036.
  • Zheng X, Shi X, Wang B. A review on the general cheese processing technology, flavor biochemical pathways and the influence of yeasts in cheese. Front Microbiol. 2021;12:703284. doi: 10.3389/fmicb.2021.703284.
  • Alegría Á, Szczesny P, Mayo B, et al. Biodiversity in oscypek, a traditional polish cheese, determined by culture-dependent and -independent approaches. Appl Environ Microbiol. 2012;78(6):1890–1898. doi: 10.1128/AEM.06081-11.
  • Parayre S, Falentin H, Madec M-N, et al. Easy DNA extraction method and optimisation of PCR-Temporal temperature gel electrophoresis to identify the predominant high and low GC-content bacteria from dairy products. J Microbiol Methods. 2007;69(3):431–441. doi: 10.1016/j.mimet.2007.02.011.
  • Martín-Platero AM, Valdivia E, Maqueda M, et al. Polyphasic approach to bacterial dynamics during the ripening of Spanish farmhouse cheese, using culture-dependent and -independent methods. Appl Environ Microbiol. 2008;74(18):5662–5673. doi: 10.1128/AEM.00418-08.
  • Babot JD, Hidalgo M, Argañaraz-Martínez E, et al. Fluorescence in situ hybridization for detection of classical propionibacteria with specific 16S rRNA-targeted probes and its application to enumeration in Gruyère cheese. Int J Food Microbiol. 2011;145(1):221–228. doi: 10.1016/j.ijfoodmicro.2010.12.024.
  • Cocolin L, Alessandria V, Dolci P, et al. Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int J Food Microbiol. 2013;167(1):29–43. doi: 10.1016/j.ijfoodmicro.2013.05.008.
  • De Filippis F, Parente E, Ercolini D. Recent past, present, and future of the food microbiome. Annu Rev Food Sci Technol. 2018;9:589–608.
  • Anastasiou R, Kazou M, Georgalaki M, et al. Omics approaches to assess flavor development in cheese. Foods. 2022;11(2):188. doi: 10.3390/foods11020188.
  • Franco-Duarte R, Černáková L, Kadam S, et al. Advances in chemical and biological methods to identify microorganisms—from past to present. Microorganisms. 2019;7(5):130. doi: 10.3390/microorganisms7050130.
  • Vataščinová T, Pipová M, Fraqueza MJR, et al. Short communication: antimicrobial potential of Lactobacillus plantarum strains isolated from Slovak raw sheep milk cheeses. J Dairy Sci. 2020;103(8):6900–6903. doi: 10.3168/jds.2019-17862.
  • Cailliez-Grimal C, Edima HC, Revol-Junelles AM, et al. Short communication: carnobacterium maltaromaticum: the only carnobacterium species in French ripened soft cheeses as revealed by polymerase chain reaction detection. J Dairy Sci. 2007;90(3):1133–1138. doi: 10.3168/jds.S0022-0302(07)71599-0.
  • Coton M, Berthier F, Coton E. Rapid identification of the three major species of dairy obligate heterofermenters Lactobacillus brevis, Lactobacillus fermentum and Lactobacillus parabuchneri by species-specific duplex PCR. FEMS Microbiol Lett. 2008;284(2):150–157. %J FEMS Microbiology Letters. doi: 10.1111/j.1574-6968.2008.01206.x.
  • Merchán AV, Ruiz-Moyano S, Hernández MV, et al. Characterization of autochthonal hafnia spp. strains isolated from Spanish soft raw ewe’s milk PDO cheeses to be used as adjunct culture. Int J Food Microbiol. 2022;373:109703. doi: 10.1016/j.ijfoodmicro.2022.109703.
  • Nurye M, Wolkero T. Identification of lactic acid bacteria in dairy products using culture-independent methods: a review. AJDFR. 2022;42:1–8. doi: 10.18805/ajdfr.DRF-277.
  • Quijada NM, Schmitz-Esser S, Zwirzitz B, et al. Austrian raw-milk hard-cheese ripening involves successional dynamics of non-inoculated bacteria and fungi. Foods. 2020;9(12):1851. doi: 10.3390/foods9121851.
  • Şahiner A, Çalışkan S, Halat E. Quantitative detection of late blowing agents C. tyrobutyricum, C. butyricum, and C. sporogenes in traditional Turkish cheese by multiplex real-time PCR. Food Anal Methods. 2023;16(4):781–786. doi: 10.1007/s12161-023-02454-z.
  • Tsirigoti E, Psomas E, Ekateriniadou LV, et al. Comparative qualitative and quantitative analysis of lactic acid bacteria by molecular methods in different Greek cheeses. J Dairy Res. 2022;89(4):449–452. doi: 10.1017/S0022029922000760.
  • Dimov SG. The controversial nature of some non-starter lactic acid bacteria actively participating in cheese ripening. BioTech. 2023;12(4):63. doi: 10.3390/biotech12040063.
  • Delannoy S, Hoffer C, Tran M-L, et al. High throughput qPCR analyses suggest that enterobacterales of French sheep and cow cheese rarely carry genes conferring resistances to critically important antibiotics for human medicine. Int J Food Microbiol. 2023;403:110303. doi: 10.1016/j.ijfoodmicro.2023.110303.
  • Siqueira JF, Rôças IN, Rosado AS. Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of endodontic infections. J Endod. 2005;31(11):775–782. doi: 10.1097/01.don.0000155221.33667.bb.
  • Rosenbaum V, Riesner D. Temperature-gradient gel electrophoresis: thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys Chem. 1987;26(2–3):235–246. doi: 10.1016/0301-4622(87)80026-1.
  • Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol. 1999;2(3):317–322. doi: 10.1016/s1369-5274(99)80055-1.
  • Orita M, Iwahana H, Kanazawa H, et al. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc Natl Acad Sci U S A. 1989;86(8):2766–2770. doi: 10.1073/pnas.86.8.2766.
  • Randazzo CL, Caggia C, Neviani E. Application of molecular approaches to study lactic acid bacteria in artisanal cheeses. J Microbiol Methods. 2009;78(1):1–9. doi: 10.1016/j.mimet.2009.04.001.
  • Ercolini D, Moschetti G, Blaiotta G, et al. The potential of a polyphasic PCR-DGGEApproach in evaluating microbial diversity of natural whey cultures for Water-Buffalo mozzarella cheese production: bias of culture-dependent and culture-independent analyses. Syst Appl Microbiol. 2001;24(4):610–617. doi: 10.1078/0723-2020-00076.
  • Dolci P, Zenato S, Pramotton R, et al. Cheese surface microbiota complexity: RT-PCR-DGGE, a tool for a detailed picture? Int J Food Microbiol. 2013;162(1):8–12. doi: 10.1016/j.ijfoodmicro.2012.12.009.
  • Preedy VR, Watson RR, Patel VB, et al. Handbook of cheese in health: production, nutrition and medical sciences. Wageningen Academic. 2023;515–530. doi: 10.3920/978-90-8686-766-0.
  • Gonçalves Dos Santos MTP, Benito MJ, Córdoba M, et al. Yeast community in traditional portuguese serpa cheese by culture-dependent and -independent DNA approaches. Int J Food Microbiol. 2017;262:63–70. doi: 10.1016/j.ijfoodmicro.2017.09.013.
  • Hajigholizadeh M, Mardani K, Moradi M, et al. Molecular detection, phylogenetic analysis, and antibacterial performance of lactic acid bacteria isolated from traditional cheeses, North-West Iran. Food Sci Nutr. 2020;8(11):6007–6013. doi: 10.1002/fsn3.1887.
  • Kaufmann M. Pulsed-Field Gel Electrophoresis. In: Woodford, N., Johnson, A.P. (eds) Molecular Bacteriology. Methods in Molecular Medicine™ Humana Press: 1998;15:33–50. doi: 10.1385/0-89603-498-4:33.
  • Vernile A, Giammanco G, Spano G, et al. Genotypic characterization of lactic acid bacteria isolated from traditional pecorino siciliano cheese. Dairy Sci Technol. 2008;88(6):619–629. Technology doi: 10.1051/dst:2008009.
  • Ercolini D, Mauriello G, Blaiotta G, et al. PCR–DGGE fingerprints of microbial succession during a manufacture of traditional water buffalo Mozzarella cheese. J Appl Microbiol. 2004;96(2):263–270. doi: 10.1046/j.1365-2672.2003.02146.x.
  • V Wintzingerode F, Göbel UB, Stackebrandt E, et al. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev. 1997;21(3):213–229. doi: 10.1111/j.1574-6976.1997.tb00351.x.
  • Jany J-L, Barbier G. Culture-independent methods for identifying microbial communities in cheese. Food Microbiol. 2008;25(7):839–848. doi: 10.1016/j.fm.2008.06.003.
  • Teuber M. The genus lactococcus. In: Wood, B.J.B., Holzapfel, W.H. (eds), The Genera of Lactic Acid Bacteria. The Lactic Acid Bacteria, vol 2. Boston, MA: Springer: 1995; pp. 173–234. doi: 10.1007/978-1-4615-5817-0_6.
  • von Wright A. Genus lactococcus. In: Vinderola G, Ouwehand A, Salminen S, von Wright A, editors. Lactic acid bacteria. Boca Raton, FL: CRC; 2019. p. 33–46.
  • Caro I, Quinto EJ, Fuentes L, et al. Characterization of Lactococcus strains isolated from artisanal Oaxaca cheese. LWT. 2020;122:109041. doi: 10.1016/j.lwt.2020.109041.
  • Mangia NP, Fancello F, Deiana P. Microbiological characterization using combined culture dependent and independent approaches of casizolu pasta filata cheese. J Appl Microbiol. 2016;120(2):329–345. doi: 10.1111/jam.13001.
  • Dimov SG. The unusual microbiota of the traditional Bulgarian dairy product Krokmach – a pilot metagenomics study. Int J Dairy Tech. 2022;75(1):139–149. doi: 10.1111/1471-0307.12809.
  • Psoni L, Kotzamanidis C, Yiangou M, et al. Genotypic and phenotypic diversity of Lactococcus lactis isolates from batzos, a Greek PDO raw goat milk cheese. Int J Food Microbiol. 2007;114(2):211–220. doi: 10.1016/j.ijfoodmicro.2006.09.020.
  • Odamaki T, Yonezawa S, Kitahara M, et al. Novel multiplex polymerase chain reaction primer set for identification of Lactococcus species. Lett Appl Microbiol. 2011;52(5):491–496. %. doi: 10.1111/j.1472-765X.2011.03028.x.
  • Biolcati F, Andrighetto C, Bottero MT, et al. Microbial characterization of an artisanal production of Robiola di Roccaverano cheese. J Dairy Sci. 2020;103(5):4056–4067. doi: 10.3168/jds.2019-17451.
  • Fortina MG, Ricci G, Acquati A, et al. Genetic characterization of some lactic acid bacteria occurring in an artisanal protected denomination origin (PDO) Italian cheese, the Toma piemontese. Food Microbiol. 2003;20(4):397–404. doi: 10.1016/S0740-0020(02)00149-1.
  • Morea M, Baruzzi F, Cocconcelli P. Molecular and physiological characterization of dominant bacterial populations in traditional Mozzarella cheese processing. J Appl Microbiol. 1999;87(4):574–582. doi: 10.1046/j.1365-2672.1999.00855.x.
  • Hardie J, Whiley R. Classification and overview of the genera Streptococcus and enterococcus. J Appl Microbio. 1997;83(S1):1S–11S. doi: 10.1046/j.1365-2672.83.s1.1.x.
  • Delorme C, Abraham A-L, Renault P, et al. Genomics of Streptococcus salivarius, a major human commensal. Infect Genet Evol. 2015;33:381–392. doi: 10.1016/j.meegid.2014.10.001.
  • Alexandraki V, Kazou M, Blom J, et al. Comparative genomics of Streptococcus thermophilus support important traits concerning the evolution, biology and technological properties of the species. Front Microbiol. 2019;10:2916. doi: 10.3389/fmicb.2019.02916.
  • Vanatkova Z, Okenkova E, Bunkova L, et al. Molecular diagnostic of Streptococcus thermophilus. Ecol Chem Eng A. 2009;16:1627–1635.
  • Arcuri EF, El Sheikha AF, Rychlik T, et al. Determination of cheese origin by using 16S rDNA fingerprinting of bacteria communities by PCR–DGGE: preliminary application to traditional minas cheese. Food Control. 2013;30(1):1–6. doi: 10.1016/j.foodcont.2012.07.007.
  • Morandi S, Brasca M. Safety aspects, genetic diversity and technological characterisation of wild-type Streptococcus thermophilus strains isolated from North Italian traditional cheeses. Food Control. 2012;23(1):203–209. doi: 10.1016/j.foodcont.2011.07.011.
  • Andrighetto C, Borney F, Barmaz A, et al. Genetic diversity of Streptococcus thermophilus strains isolated from Italian traditional cheeses. Int Dairy J. 2002;12(2–3):141–144. doi: 10.1016/S0958-6946(01)00134-0.
  • Pacini F, Cariolato D, Andrighetto C, et al. Occurrence of Streptococcus macedonicus in Italian cheeses. FEMS Microbiol Lett. 2006;261(1):69–73. doi: 10.1111/j.1574-6968.2006.00330.x.
  • Zheng J, Wittouck S, Salvetti E, et al. A taxonomic note on the genus lactobacillus: description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae. Int J Syst Evol Microbiol. 2020;70(4):2782–2858. doi: 10.1099/ijsem.0.004107.
  • Salvetti E, Torriani S, Felis GEJP. The genus lactobacillus: a taxonomic update. Probiotics Antimicrob Proteins. 2012;4(4):217–226. proteins, a doi: 10.1007/s12602-012-9117-8.
  • Beresford TP, Fitzsimons NA, Brennan NL, et al. Recent advances in cheese microbiology. Int Dairy J. 2001;11(4–7):259–274. doi: 10.1016/S0958-6946(01)00056-5.
  • Huang C-H, Li S-W, Huang L, et al. Identification and classification for the Lactobacillus casei group. Front Microbiol. 2018;9:1974. doi: 10.3389/fmicb.2018.01974.
  • Antonsson M, Molin G, Ardö Y. Lactobacillus strains isolated from danbo cheese as adjunct cultures in a cheese model system. Int J Food Microbiol. 2003;85(1–2):159–169. doi: 10.1016/S0168-1605(02)00536-6.
  • Sánchez I, Seseña S, Poveda JM, et al. Phenotypic and genotypic characterization of lactobacilli isolated from Spanish goat cheeses. Int J Food Microbiol. 2005;102(3):355–362. doi: 10.1016/j.ijfoodmicro.2004.11.041.
  • Bautista-Gallego J, Alessandria V, Fontana M, et al. Diversity and functional characterization of lactobacillus spp. isolated throughout the ripening of a hard cheese. Int J Food Microbiol. 2014;181:60–66. doi: 10.1016/j.ijfoodmicro.2014.04.020.
  • Ehsani A, Mahmoudi R, Hashemi M, et al. Identification of lactobacillus species isolated from traditional cheeses of west Azerbaijan. Iran-J-Med-Microbiol. 2014;8:38–43.
  • Giraffa G, Andrighetto C, Antonello C, et al. Genotypic and phenotypic diversity of Lactobacillus delbrueckii subsp. lactis strains of dairy origin. Int J Food Microbiol. 2004;91(2):129–139. doi: 10.1016/S0168-1605(03)00368-4.
  • Henri-Dubernet S, Desmasures N, Guéguen MJLL. Culture-dependent and culture-independent methods for molecular analysis of the diversity of lactobacilli in “camembert de normandie” cheese. Dairy Sci Technol. 2004;84:179–189.
  • Bergey DH, Whitman WB, De Vos P, et al. Bergey’s manual of systematic bacteriology. The Firmicutes. 2nd ed. Vol. 3. Springer; 2009.
  • Haakensen M, Dobson CM, Deneer H, et al. Real-time PCR detection of bacteria belonging to the firmicutes phylum. Int J Food Microbiol. 2008;125(3):236–241. doi: 10.1016/j.ijfoodmicro.2008.04.002.
  • Beskrovnaya P, Fakih D, Morneau I, et al. No endospore formation confirmed in members of the phylum proteobacteria. Appl Environ Microbiol. 2021;87(5):e02312–02320. doi: 10.1128/AEM.02312-20.
  • Le Bourhis A-G, Saunier K, Doré J, et al. Development and validation of PCR primers to assess the diversity of clostridium spp. in cheese by temporal temperature gradient gel electrophoresis. Appl Environ Microbiol. 2005;71(1):29–38. doi: 10.1128/AEM.71.1.29-38.2005.
  • Klijn N, Nieuwenhof FF, Hoolwerf JD, et al. Identification of Clostridium tyrobutyricum as the causative agent of late blowing in cheese by species-specific PCR amplification. Appl Environ Microbiol. 1995;61(8):2919–2924. doi: 10.1128/aem.61.8.2919-2924.1995.
  • Brändle J, Fraberger V, Berta J, et al. Butyric acid producing clostridia in cheese – towards the completion of knowledge by means of an amalgamate of methodologies. Int Dairy J. 2018;86:86–95. doi: 10.1016/j.idairyj.2018.07.008.
  • Borelli B, Lacerda I, Brandão L, et al. Identification of Staphylococcus spp. isolated during the ripening process of a traditional minas cheese. Arq Bras Med Vet e Zootec. 2011;63:481–487.
  • Silva MP, Carvalho AF, Andretta M, et al. Presence and growth prediction of Staphylococcus spp. and Staphylococcus aureus in minas Frescal cheese, a soft fresh cheese produced in Brazil. J Dairy Sci. 2021;104(12):12312–12320. doi: 10.3168/jds.2021-20633.
  • Hoppe-Seyler TS, Jaeger B, Bockelmann W, et al. Molecular identification and differentiation of Staphylococcus species and strains of cheese origin. Syst Appl Microbiol. 2004;27(2):211–218. doi: 10.1078/072320204322881835.
  • Stackebrandt E, Murray R, Trüper H, et al. Proteobacteria classis nov., a name for the phylogenetic taxon that includes the “purple bacteria and their relatives”. Int J Syst Bacteriol. 1988;38(3):321–325. doi: 10.1099/00207713-38-3-321.
  • Woese C. Bacterial evolution. Clin Microbiol Rev. 1987;51(2):221–271. doi: 10.1128/MMBR.51.2.221-271.1987.
  • Rizzatti G, Lopetuso LR, Gibiino G, et al. Proteobacteria: a common factor in human diseases. Biomed Res Int. 2017;2017:9351507–9351507. doi: 10.1155/2017/9351507.
  • Guzzon R, Carafa I, Tuohy K, et al. Exploring the microbiota of the red-brown defect in smear-ripened cheese by 454-pyrosequencing and its prevention using different cleaning systems. Food Microbiol. 2017;62:160–168. doi: 10.1016/j.fm.2016.10.018.
  • Korena K, Krzyzankova M, Florianova M, et al. Microbial succession in the cheese ripening process—competition of the starter cultures and the microbiota of the cheese plant environment. Microorganisms. 2023;11(7):11–1735. doi: 10.3390/microorganisms11071735.
  • Pasquale ID, Calasso M, Mancini L, et al. Causal relationship between microbial ecology dynamics and proteolysis during manufacture and ripening of protected designation of origin (PDO) cheese canestrato pugliese. Appl Environ Microbiol. 2014;80(14):4085–4094. doi: 10.1128/AEM.00757-14.
  • Van Hoorde K, Heyndrickx M, Vandamme P, et al. Influence of pasteurization, brining conditions and production environment on the microbiota of artisan Gouda-type cheeses. Food Microbiol. 2010;27(3):425–433. doi: 10.1016/j.fm.2009.12.001.
  • Ozturkoglu Budak S, Figge MJ, Houbraken J, et al. The diversity and evolution of microbiota in traditional Turkish divle cave cheese during ripening. Int Dairy J. 2016;58:50–53. doi: 10.1016/j.idairyj.2015.09.011.
  • Mounier J, Monnet C, Jacques N, et al. Assessment of the microbial diversity at the surface of livarot cheese using culture-dependent and independent approaches. Int J Food Microbiol. 2009;133(1–2):31–37. doi: 10.1016/j.ijfoodmicro.2009.04.020.
  • Nogarol C, Acutis PL, Bianchi DM, et al. Molecular characterization of Pseudomonas fluorescens isolates involved in the italian “blue mozzarella” event. J Food Prot. 2013;76(3):500–504. doi: 10.4315/0362-028X.JFP-12-312.
  • Tornadijo ME, García MC, Fresno JM, et al. Study of enterobacteriaceae during the manufacture and ripening of San simón cheese. Food Microbiol. 2001;18(5):499–509. doi: 10.1006/fmic.2001.0423.
  • Morales P, Fernández-García E, Nuñez M. Caseinolysis in cheese by enterobacteriaceae strains of dairy origin. Lett Appl Microbiol. 2003;37(5):410–414. doi: 10.1046/j.1472-765X.2003.01422.x.
  • Amaresan N, Kumar MS, Annapurna K, Kumar K, Sankaranarayanan A, editors. Beneficial microbes in agro-ecology: bacteria and fungi. Cambridge, MA: Academic Press; 2020.
  • Anandan R, Dharumadurai D, Manogaran GP. An introduction to actinobacteria. In: Actinobacteria-basics and biotechnological applications. London: IntechOpen; 2016.
  • Barka Essaid A, Vatsa P, Sanchez L, et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev. 2015;80(1):1–43. doi: 10.1128/mmbr.00019-15.
  • Denis C, Irlinger F. Safety assessment of dairy microorganisms: aerobic coryneform bacteria isolated from the surface of smear-ripened cheeses. Int J Food Microbiol. 2008;126(3):311–315. doi: 10.1016/j.ijfoodmicro.2007.08.018.
  • Hanifian S. Behavior of Mycobacterium avium paratuberculosis in Lighvan cheese tracked by propidium monoazide qPCR and culture. LWT. 2020;133:109886. doi: 10.1016/j.lwt.2020.109886.
  • Ikonomopoulos J, Pavlik I, Bartos M, et al. Detection of Mycobacterium avium subsp. paratuberculosis in retail cheeses from Greece and the Czech Republic. Appl Environ Microbiol. 2005;71(12):8934–8936. doi: 10.1128/AEM.71.12.8934-8936.2005.
  • Galiero A, Fratini F, Mataragka A, et al. Detection of mycobacterium avium subsp. paratuberculosis in cheeses from small ruminants in Tuscany. Int J Food Microbiol. 2016;217:195–199. doi: 10.1016/j.ijfoodmicro.2015.10.029.
  • Clark DL, Jr, Anderson JL, Koziczkowski JJ, et al. Detection of Mycobacterium avium subspecies paratuberculosis genetic components in retail cheese curds purchased in Wisconsin and Minnesota by PCR. Mol Cell Probes. 2006;20(3–4):197–202. doi: 10.1016/j.mcp.2005.12.006.
  • Garrido-Cardenas JA, Manzano-Agugliaro F. The metagenomics worldwide research. Curr Genet. 2017;63(5):819–829. doi: 10.1007/s00294-017-0693-8.
  • Goussarov G, Mysara M, Vandamme P, et al. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologi Open. 2022;11:e1298.
  • Tucker, T.; Marra, M.; Friedman, J.M.J.T.A.J.o.H.G. Massively parallel sequencing: the next big thing in genetic medicine. The American Journal of Human Genetics 2009;85:142–154. doi: 10.1016/j.ajhg.2009.06.022.
  • Hu T, Chitnis N, Monos D, et al. Next-generation sequencing technologies: an overview. Hum Immunol. 2021;82(11):801–811. doi: 10.1016/j.humimm.2021.02.012.
  • Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53–59. doi: 10.1038/nature07517.
  • Rothberg JM, Leamon J. The development and impact of 454 sequencing. Nat Biotechnol. 2008;26(10):1117–1124. doi: 10.1038/nbt1485.
  • Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475(7356):348–352. doi: 10.1038/nature10242.
  • Logsdon GA, Vollger MR, Eichler, E G. Long-read human genome sequencing and its applications. Nat Rev Genet. 2020;21(10):597–614. doi: 10.1038/s41576-020-0236-x.
  • Levene MJ, Korlach J, Turner SW, et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science. 2003;299(5607):682–686. doi: 10.1126/science.1079700.
  • Miga KH, Koren S, Rhie A, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020;585(7823):79–84. doi: 10.1038/s41586-020-2547-7.
  • McCombie WR, McPherson JD, Mardis ER. Next-generation sequencing technologies. Cold Spring Harb Perspect Med. 2019;9(11):a036798. PMID: 30478097; PMCID: PMC6824406 doi: 10.1101/cshperspect.a036798.
  • Mayo B, Rodríguez J, Vázquez L, et al. Microbial interactions within the cheese ecosystem and their application to improve quality and safety. Foods. 2021;10(3):602. doi: 10.3390/foods10030602.
  • Zotta T, Ricciardi A, Condelli N, et al. Nutrition. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Food Sci Nutr. 2022;62:3898–3912.
  • Tilocca B, Costanzo N, Morittu VM, et al. Milk microbiota: characterization methods and role in cheese production. J Proteomics. 2020;210:103534. doi: 10.1016/j.jprot.2019.103534.
  • Dimov SG, Gyurova A, Zagorchev L, et al. NGS-Based metagenomic study of four traditional Bulgarian green cheeses from Tcherni Vit. LWT. 2021;152:112278. doi: 10.1016/j.lwt.2021.112278.
  • Castellanos-Rozo J, Pérez Pulido R, Grande MJ, et al. Analysis of the bacterial diversity of paipa cheese (a traditional raw cow’s milk cheese from Colombia) by high-throughput sequencing. Microorganisms. 2020;8(2):218. doi: 10.3390/microorganisms8020218.
  • Kamilari E, Anagnostopoulos DA, Papademas P, et al. Characterizing halloumi cheese’s bacterial communities through metagenomic analysis. LWT. 2020;126:109298. doi: 10.1016/j.lwt.2020.109298.
  • Papademas P, Aspri M, Mariou M, et al. Conventional and omics approaches shed light on Halitzia cheese, a long-forgotten white-brined cheese from Cyprus. Int Dairy J. 2019;98:72–83. doi: 10.1016/j.idairyj.2019.06.010.
  • Zheng X, Liu F, Shi X, et al. Dynamic correlations between microbiota succession and flavor development involved in the ripening of Kazak artisanal cheese. Food Res Int. 2018;105:733–742. doi: 10.1016/j.foodres.2017.12.007.
  • Marino M, Dubsky de Wittenau G, Saccà E, et al. Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese. Food Microbiol. 2019;79:123–131. doi: 10.1016/j.fm.2018.12.007.
  • Ribani A, Schiavo G, Utzeri VJ, et al. Application of next generation semiconductor based sequencing for species identification in dairy products. Food Chem. 2018;246:90–98. doi: 10.1016/j.foodchem.2017.11.006.
  • Gezginc Y, Karabekmez-Erdem T, Tatar HD, et al. Metagenomics and volatile profile of Turkish artisanal Tulum cheese microbiota. Food Biosci. 2022;45:101497. doi: 10.1016/j.fbio.2021.101497.
  • Güley Z, Fallico V, Cabrera-Rubio R, et al. Diversity of the microbiota of traditional izmir tulum and izmir brined tulum cheeses and selection of potential probiotics. Foods. 2023;12(18):3482. doi: 10.3390/foods12183482.
  • Ceugniez A, Taminiau B, Coucheney F, et al. Fungal diversity of “Tomme d’Orchies” cheese during the ripening process as revealed by a metagenomic study. Int J Food Microbiol. 2017;258:89–93. doi: 10.1016/j.ijfoodmicro.2017.07.015.
  • O’Sullivan Daniel J, Cotter Paul D, O’Sullivan O, et al. Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese. Appl Environ Microbiol. 2015;81(7):2525–2533. doi: 10.1128/AEM.04054-14.
  • Quigley L, O’Sullivan O, Beresford Tom P, et al. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl Environ Microbiol. 2012;78(16):5717–5723. doi: 10.1128/AEM.00918-12.
  • Aldrete-Tapia A, Escobar-Ramírez CM, Tamplin ML, et al. Characterization of bacterial communities in Mexican artisanal raw milk “Bola de Ocosingo” cheese by high-throughput sequencing. Front Microbiol. 2018;9:2598. doi: 10.3389/fmicb.2018.02598.
  • Jin H, Mo L, Pan L, et al. Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses. J Dairy Sci. 2018;101(8):6885–6896. doi: 10.3168/jds.2018-14403.
  • Li J, Zheng Y, Xu H, et al. Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses. BMC Microbiol. 2017;17(1):13. doi: 10.1186/s12866-016-0911-4.
  • Planý M, Sitarčík J, Pavlović J, et al. Evaluation of bacterial consortia associated with dairy fermentation by ribosomal RNA (rrn) operon metabarcoding strategy using MinION device. Food Biosci. 2023;51:102308. doi: 10.1016/j.fbio.2022.102308.
  • Catozzi C, Ceciliani F, Lecchi C, et al. Short communication: milkmicrobiota profiling on water buffalo with full-length 16S rRNA using nanopore sequencing. J Dairy Sci. 2020;103(3):2693–2700. doi: 10.3168/jds.2019-17359.
  • Yang C, You L, Kwok L-Y, et al. Strain-level multiomics analysis reveals significant variation in cheeses from different regions. LWT. 2021;151:112043. doi: 10.1016/j.lwt.2021.112043.
  • Papadimitriou K, Venieraki A, Tsigkrimani M, et al. Whole-genome sequence data of the proteolytic and bacteriocin producing strain Enterococcus faecalis PK23 isolated from the traditional Halitzia cheese produced in Cyprus. Data Brief. 2021;38:107437. doi: 10.1016/j.dib.2021.107437.
  • Ruppitsch W, Nisic A, Hyden P, et al. Genetic diversity of Leuconostoc mesenteroides isolates from traditional montenegrin brine cheese. Microorganisms. 2021;9(8):1612. doi: 10.3390/microorganisms9081612.
  • Alexandraki V, Kazou M, Pot B, et al. Whole-genome sequence data and analysis of Lactobacillus delbrueckii subsp. lactis ACA-DC 178 isolated from Greek kasseri cheese. Data Brief. 2019;25:104282. doi: 10.1016/j.dib.2019.104282.
  • Kazou M, Alexandraki V, Pot B, et al. Whole-genome sequence of the cheese isolate lactobacillus rennini ACA-DC 565. Genome Announc. 2017;5(5):e01579-16. doi: 10.1128/genomea.01579-16.
  • Suárez N, Weckx S, Minahk C, et al. Metagenomics-based approach for studying and selecting bioprotective strains from the bacterial community of artisanal cheeses. Int J Food Microbiol. 2020;335:108894. doi: 10.1016/j.ijfoodmicro.2020.108894.
  • Vermote L, Verce M, De Vuyst L, et al. Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process. Int Dairy J. 2018;87:44–53. doi: 10.1016/j.idairyj.2018.07.010.
  • Ianni A, Di Domenico M, Bennato F, et al. Metagenomic and volatile profiles of ripened cheese obtained from dairy ewes fed a dietary hemp seed supplementation. J Dairy Sci. 2020;103(7):5882–5892. doi: 10.3168/jds.2019-17954.
  • Pace NR, Stahl DA, Lane DJ, et al. The analysis of natural microbial opulations by ribosomal RNA sequences. In: Marshall KC, editor. Advances in microbial ecology. Vol. 9. Boston, MA: Springer; 1986. doi: 10.1007/978-1-4757-0611-6_1.
  • Alves L, Westmann CA, Lovate GL, et al. Metagenomic approaches for understanding new concepts in microbial science. Int J Genomics. 2018;2018:2312987–2312915. doi: 10.1155/2018/2312987.
  • Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol. 1998;5(10):R245–R249. doi: 10.1016/s1074-5521(98)90108-9.
  • Nelli A, Venardou B, Skoufos I, et al. An insight into goat cheese: the tales of artisanal and industrial gidotyri microbiota. Microorganisms. 2023;11(1):123. doi: 10.3390/microorganisms11010123.
  • Gérard A, El-Hajjaji S, Burteau S, et al. Study of the microbial diversity of a panel of Belgian artisanal cheeses associated with challenge studies for Listeria monocytogenes. Food Microbiol. 2021;100:103861. doi: 10.1016/j.fm.2021.103861.
  • Ruvalcaba-Gómez JM, Delgado-Macuil RJ, Zelaya-Molina LX, et al. Bacterial succession through the artisanal process and seasonal effects defining bacterial communities of raw-milk adobera cheese revealed by high throughput DNA sequencing. Microorganisms. 2021;9(1):24. doi: 10.3390/microorganisms9010024.
  • De Respinis S, Caminada A, Pianta E, et al. Fungal communities on alpine cheese rinds in Southern Switzerland. Bot Stud. 2023;64(1):6. doi: 10.1186/s40529-023-00371-2.
  • Ranjan R, Rani A, Metwally A, et al. Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun. 2016;469(4):967–977. doi: 10.1016/j.bbrc.2015.12.083.
  • Kim D-S, Choi S-H, Kim D-W, et al. Genome sequence of Lactobacillus cypricasei KCTC 13900. J Bacteriol. 2011;193(18):5053–5054. doi: 10.1128/jb.05659-11.
  • Stefanovic E, Casey A, Cotter P, et al. Draft genome sequence of lactobacillus casei DPC6800, an isolate with the potential to diversify flavor in cheese. Genome Announc. 2016;4(2):e00063-16. doi: 10.1128/genomea.00063-16.
  • Bertuzzi AS, Guinane CM, Crispie F, et al. Genome sequence of Staphylococcus saprophyticus DPC5671, a strain isolated from cheddar cheese. Genome Announc. 2017;5(16):e00193-17. doi: 10.1128/genomea.00193-17.
  • D’Auria G, Džunkova M, Moya A, et al. Genome sequence of Lactobacillus plantarum 19L3, a strain proposed as a starter culture for Slovenská bryndza ovine cheese. Genome Announc. 2014;2(2):e00292-14. doi: 10.1128/genomea.00292-14.
  • Quick J, Loman NJ, Duraffour S, et al. Real-time, portable genome sequencing for ebola surveillance. Nature. 2016;530(7589):228–232. doi: 10.1038/nature16996.