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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
  • 50 Downloads

Abstract

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.

Keywords

Brazilian dairy microbiology Dairy metataxonomics Dairy microbial diversity Dairy core microbiota 

Notes

Acknowledgements

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)

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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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