Journal of Food Science and Technology

, Volume 56, Issue 12, pp 5326–5335 | Cite as

Finding a common core microbiota in two Brazilian dairies through culture and DNA metabarcoding studies

  • Diego Araújo Frazilio
  • Otávio Guilherme Gonçalves de Almeida
  • Fabian Camilo Niño-Arias
  • Elaine Cristina Pereira De MartinisEmail author
Original Article


Dairy foods are complex ecosystems composed of microorganisms from different origins that can affect flavor and safety of final products. The objective of this paper is to assess the in-house microbiota of two Brazilian dairies and to discuss the possible implications of the taxa determined for food protection. In total, 27 samples from dairies were cultured in selective (Baird Parker, de Man, Rogosa and Sharpe) and non-selective (Brain Heart Infusion) media, and the isolates were identified by Sanger sequencing. Moreover, metagenomic DNA was directly extracted from samples and the structure of the bacterial community was determined by massive DNA sequencing followed by bioinformatics analyses. The results showed the majority of isolates belonged to the group of lactic acid bacteria, but Enterobacteriaceae, Staphylococcacceae, Bacillaceae, Pseudomonadaceae and Moraxellaceae were also detected. From the reads obtained in metataxonomics analyses, a heatmap was constructed and the top 20 OTUs (operational taxonomic units) were determined. Besides, 12 most prevalent bacterial taxa were assigned to the core microbiota of the dairies evaluated, which included Thiomonas thermosulfata, Alkalibacillus salilacus, Pseudomonas clemancea, Erythrobacter aquimans, Tetragenococcus doogicus, Macrococcus brunensis, Pseudomonas ludensis, Streptococcus dentinousetti, Serratia entomophila, Vagococcus teuberi, Lactococcus fujiensis and Tolumonas auensis. In conclusion, the results reveal the presence of bacteria that may be related to spoilage and also foodborne diseases, in microbial niches that also present rare taxa, highlighting the importance to consider culture-independent results to evaluate and improve food safety.


Brazilian dairy microbiology Dairy metataxonomics Dairy microbial diversity Dairy core microbiota 



This work was supported by the São Paulo Research Foundation (FAPESP), Brazil (Grant # 2012-50507-1). O. G. G. Almeida is also grateful to FAPESP for a Ph.D. fellowship (Grant # 2017/13759-6). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES)—Finance Code 001. The authors are grateful to Émerson Santos, Ph.D. from Faculdade de Ciências Farmacêuticas de Ribeirão Preto for his excellent technical assistance with DNA sequencing.

Supplementary material

13197_2019_4003_MOESM1_ESM.xlsx (79 kb)
Supplementary material 1 (XLSX 78 kb)


  1. Afshari R, Pillidge CJ, Dias DA, Osborn AM, Gill H (2018) Cheesomics: the future pathway to understanding cheese flavour and quality. Crit Rev Food Sci Nutr. CrossRefPubMedGoogle Scholar
  2. Almeida OG, De Martinis ECP (2018) Bioinformatics tools to assess metagenomic data for applied microbiology. Appl Microbiol Biotechnol 103:69–82. CrossRefPubMedGoogle Scholar
  3. Arcuri EF, Sheikha AFE, Rychlik T, Piro-Métayer I, Montet D (2013) Determination of cheese origin by using 16S rDNA fingerprint of bacteria communities by PCR-DGGE: preliminary application to traditional Minas cheese. Food Control 30:1–6. CrossRefGoogle Scholar
  4. Arsène-Ploetze F, Koechler S, Marchal M et al (2010) Structure, function, and evolution of the Thiomonas spp. genome. PLoS Genet 6:2. CrossRefGoogle Scholar
  5. Bagge-Ravn D, Ng Y, Hjelm M, Christiansen JN, Johansen C, Gram L (2003) The microbial ecology of processing equipment in different fish industries—analysis of the microflora during processing and following cleaning and disinfection. Int J Food Microbiol 87:239–250. CrossRefPubMedGoogle Scholar
  6. Bokulich NA, Mills DA (2013) Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants. Appl Environ Microbiol 79(17):5214–5223. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Brasil (2008) IPHAN—Instituto do Patrimônio Histórico e Artístico Nacional Modo Artesanal de Fazer Queijo de Minas nas Regiões do Serro, da Serra da Canastra e do Salitre.*%3Adef%24%3B52g0_%5B3y3p600001n%5D8%3Am209#>. Process: 01450.012192/2006-65. Accessed 17 March 2019
  8. Calasso M, Ercolini D, Mancini L, Stellato G, Minervini F, Di Cagno R, De Angelis M, Gobbetti M (2016) Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at same dairy plant. Food Microbiol 54:115–126. CrossRefGoogle Scholar
  9. Coppola S, Blaiotta G, Ercolini D, Moschetti G (2001) Molecular evaluation of microbial diversity occurring in different types of Mozzarella cheese. J Appl Microbiol 90(3):414–420. CrossRefPubMedGoogle Scholar
  10. Dalmasso A, Del Rio MDS, Civera T, Pattono D, Cardazzo B, Bottero MT (2016) Characterization of microbiota in Plaisentif cheese by high-throughput sequencing. Food Sci Technol 69:490–496. CrossRefGoogle Scholar
  11. De Fillipis F, La Storia A, Stellato G, Gatti M, Ercolini D (2014) A selected core microbiome drives the early stages of three popular Italian cheese manufactures. PLoS ONE 6:1–12. CrossRefGoogle Scholar
  12. De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M (2014) Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese. Appl Environ Microbiol 80(19):6243–6255. CrossRefPubMedPubMedCentralGoogle Scholar
  13. Delgado S, Rachid CT, Fernandez E, Rychilk T, Alegria A, Peixoto RS, Mayo B (2013) Diversity of thermophilic bacteria in raw, pasteurized and selectively cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing. Food Microbiol 80(19):6243–6255. CrossRefGoogle Scholar
  14. Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Berdugo M, Campbell CD, Singh BK (2016) Microbial diversity drives multifunctionality in terrestrial ecossystems. Nat Commun 7:10541. CrossRefPubMedPubMedCentralGoogle Scholar
  15. Ercolini D (2013) High-throughput sequencing and metagenomics: steps ahead in the culture-independent of food microbial ecology. Appl Environ Microbiol 79(10):3148–3155. CrossRefPubMedPubMedCentralGoogle Scholar
  16. Fischer-Romero C, Tindall BJ, Jüttner F (1996) Tolumonas auensis a toluene-producing bacterium from anoxic sediments of a freshwater lake. Int J Syst Bacteriol 46:183–188. CrossRefPubMedGoogle Scholar
  17. Gobbetti M, Di Cagno R, Calasso M, Neviani E, Fox PF, De Angelis M (2018) Drivers that establish and assembly the lactic acid bacteria biota in cheeses. Trends Food Sci Technol 78:244–254. CrossRefGoogle Scholar
  18. Hill TCJ, Walsh KA, Harris A, Moffet BF (2006) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43:1–11. CrossRefGoogle Scholar
  19. Kamimura BA, De Filippis F, Sant’Ana AS, Ercolini D (2019) Large-scale mapping of microbial diversity in artisanal Brazilian cheeses. Food Microbiol 80:40–49. CrossRefPubMedGoogle Scholar
  20. Kumari S, Sarkar PK (2016) Bacillus cereus hazard and control in industrial dairy processing environment. Food Control 69:20–29. CrossRefGoogle Scholar
  21. Lacerda ICA, Gomes FCO, Borelli BM, Faria CLL Jr, Franco GR, Mourão MM, Morais PB, Rosa CA (2011) Identification of the bacterial community responsible for traditional fermentation during sour cassava starch, cachaça and minas cheese production using culture-independent 16S rRNA gene sequence analysis. Braz J Microbiol 42(2):650–657. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Lahti L, Shetty S, Blake T, Salojarvi J (2018) Microbiome R package, version 1.2.1. Accessed 12 Aug 2018
  23. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175Google Scholar
  24. MacFadyen AC, Fisher EA, Costa B, Cullen C, Paterson GKP (2018) Genome analysis of methicillin resistance in Macrococcus caseolyticus from dairy cattle in England and Wales. Microb Genom 4:1–8. CrossRefGoogle Scholar
  25. Marchand S, Block J, Jonghe V, Coorevits A, Heyndrickx ML, Herman L (2012) Biofilm formation in milk production and processing environments; influence on milk quality and safety. Compr Rev Food Sci Food Saf 11(2):133–147. CrossRefGoogle Scholar
  26. Marino M, Innocente N, Maifreni M, Mounier J, Cobo-Díaz JF, Coton E, Carraro L, Cardazzo B (2017) Diversity within Italian cheesemaking brine-associated bacterial communities evidenced by massive parallel 16S rRNA gene tag sequencing. Front Microbiol 9(1020):1–12. CrossRefGoogle Scholar
  27. Martins MCF, Freitas R, Deuvaux JC, Eller MR, Nero LA, Carvalho AF (2018) Bacterial diversity of artisanal cheese from the Amazonian region of Brazil during the dry and rainy seasons. Food Res Int 108:295–300. CrossRefPubMedGoogle Scholar
  28. McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible Interactive analysis and graphics of microbiome census data. PLoS ONE 8:1–11. CrossRefGoogle Scholar
  29. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2018) Community ecology package, version 2.5-2. Accessed 12 Aug 2018
  30. Oxaran V, Dittmann KK, Lee SHI, Chaul LT, Oliveira CAF, Corassin CH, Alves VF, De Martinis ECP, Gram L (2018) Behavior of foodborne pathogens Listeria monocytogenes and Staphylococcus aureus in mixed-species biofilms exposed to biocides. Appl Environ Microbiol 68:16–23. CrossRefGoogle Scholar
  31. Sant’Anna FM, Wetzels SU, Sandes SHC, Figueiredo RC, Sales GA, Figueiredo NC, Cantini A, Schmitz ES, Mann E, Wagner M, Souza MR (2019) Microbial shifts in Minas artisanal cheeses from the Serra do Salitre region of Minas Gerais, Brazil throughout ripening time. Food Microbiol. CrossRefPubMedGoogle Scholar
  32. Stellato G, De Filippis F, La Storia A, Ercolini D (2015) Coexistence of lactic acid bacteria and potential spoilage microbiota in a dairy processing environment. Appl Environ Microbiol 81(22):7893–7904. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Trmčić A, Chauhan K, Kent DJ, Ralyea RD, Martin NH, Boor KJ, Wiedmann M (2016) Coliform detection in cheese is associated with specific cheese characteristics, but no association was found with pathogen detection. J Dairy Sci 99(8):6105–6120. CrossRefPubMedGoogle Scholar
  34. USDA United States Department of Agriculture (2017) Brazil: dairy and products annual. USDA Foreign Agricultural Service. Gain Report number BR1719. Accessed 29 Nov 2018
  35. Wullschleger S, Jans C, Seifert C, Baumgartner S, Lacroix C, Bonfoh B, Stevens MJA, Meile L (2018) Vagococcus teuberi sp. isolated from the Malian artisanal sour milk fènè. Syst Appl Microbiol 41(2):65–72. CrossRefPubMedGoogle Scholar
  36. Zheng Q, Lin W, Liu Y, Chen C, Jiao N (2016) A comparison of 14 Erythrobacter genomes provides insights into the genomic divergence and scattered distribution of phototrophs. Front Microbiol. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Association of Food Scientists & Technologists (India) 2019

Authors and Affiliations

  • Diego Araújo Frazilio
    • 1
  • Otávio Guilherme Gonçalves de Almeida
    • 1
  • Fabian Camilo Niño-Arias
    • 1
  • Elaine Cristina Pereira De Martinis
    • 1
    Email author
  1. 1.Faculdade de Ciências Farmacêuticas de Ribeirão PretoUniversidade de São PauloRibeirão PrêtoBrazil

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