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Metataxonomics contributes to unravel the microbiota of a Brazilian dairy

Published online by Cambridge University Press:  04 September 2020

Diego Araújo Frazilio ,
Otávio Guilherme Gonçalves de Almeida ,
Carlos Augusto Fernandes de Oliveira ,
Sarah Hwa In Lee ,
Carlos Humberto Corassin ,
Virgínia Farias Alves  and
Elaine Cristina Pereira De Martinis
Diego Araújo Frazilio
Affiliation:
Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
Otávio Guilherme Gonçalves de Almeida
Affiliation:
Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
Carlos Augusto Fernandes de Oliveira
Affiliation:
Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
Sarah Hwa In Lee
Affiliation:
Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
Carlos Humberto Corassin
Affiliation:
Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
Virgínia Farias Alves
Affiliation:
Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
Elaine Cristina Pereira De Martinis*
Affiliation:
Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
*
Author for correspondence: Elaine Cristina Pereira De Martinis, Email: edemarti@usp.br
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Abstract

For this research communication, 90 samples of a Brazilian dairy were combined into four groups (raw material, final product, food-contact and non-food contact surfaces) and analyzed by metataxonomics based on 16S rRNA gene sequencing. The results showed high alpha-diversity indexes for final product and non-food contact surfaces but, overall, beta-diversity indexes were low. The samples were separated in two main clusters, and the core microbiota was composed by Macrococcus, Alkaliphilus, Vagococcus, Lactobacillus, Marinilactibacillus, Streptococcus, Lysinibacillus, Staphylococcus, Clostridium, Halomonas, Lactococcus, Enterococcus, Bacillus and Psychrobacter. These results highlight that rare taxa occur in dairies, and this may aid the development of strategies for food protection.

Keywords

dairy microbiotalactic acid bacteriafood metataxonomicscheese microbiomemilk microbiome
Type
Research Article
Information
Journal of Dairy Research , Volume 87 , Issue 3 , August 2020 , pp. 360 - 363
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of Hannah Dairy Research Foundation.

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References

Deetae, P, Bonnarme, P, Spinnler, HE and Helinck, S (2007) Production of volatile aroma compounds by bacterial strains isolated from different surface-ripened French cheeses. Applied Microbiology and Biotechnology 76, 1161–1171.10.1007/s00253-007-1095-5CrossRefGoogle ScholarPubMed
Delcenserie, V, Taminiau, B, Delhale, L, Nezer, C, Doyen, P, Crevecoeur, S, Roussey, D, Korsak, N and Daube, G (2014) Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomics analysis. Journal of Dairy Science 97, 6046–6056.10.3168/jds.2014-8225CrossRefGoogle Scholar
Dittmann, KK, Chaul, L, Lee, SY, Corassin, CH, Oliveira, CAF, De Martinis, ECP, Alves, VF, Gram, L and Oxaran, V (2017) Staphylococcus aureus in some Brazilian dairy industries: changes of contamination and diversity. Frontiers in Microbiology 8, 2049.10.3389/fmicb.2017.02049CrossRefGoogle ScholarPubMed
Ercolini, D (2013) High-throughput sequencing and metagenomics: steps ahead in the culture-independent of food microbial ecology. Applied and Environmental Microbiology 79, 3148–3155.10.1128/AEM.00256-13CrossRefGoogle Scholar
Gopal, N, Hill, C, Ross, PR, Beresford, TP, Fenelon, MA and Cotter, PD (2015) The prevalence and control of Bacillus and related spore-forming bacteria in the dairy industry. Frontiers in Microbiology 6, 1418.10.3389/fmicb.2015.01418CrossRefGoogle ScholarPubMed
Ishikawa, M, Nakajima, K, Yanagi, M, Yamamoto, Y and Yamasato, K (2003) Marinilactibacillus psychrotolerans gen. nov., sp. nov., a halophilic and alkaliphilic marine lactic acid bacterium isolated from marine organisms in temperate and subtropical areas of Japan. International Journal of Systematic and Evolutionary Microbiology 53, 711–720.10.1099/ijs.0.02446-0CrossRefGoogle ScholarPubMed
Kamimura, BA, De Filippis, F, Sant'Ana, AS and Ercolini, D (2019) Large-scale mapping of microbial diversity in artisanal Brazilian cheeses. Food Microbiology 80, 40–49.10.1016/j.fm.2018.12.014CrossRefGoogle ScholarPubMed
Lahti, L, Shetty, S, Blake, T and Salojarvi, J (2018) 2012–2017 Microbiome R package, version 1.2.1. Available at http://microbiome.github.io/microbiome (Accessed 12 August 2018).Google Scholar
Li, N, Wang, Y, You, C, Ren, J, Chen, W, Zheng, H and Liu, Z (2018) Variation in raw milk microbiota throughout 12 months and the impact of weather conditions. Scientific Reports 8, 2371.CrossRefGoogle ScholarPubMed
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 and Wagner, H (2018) Community Ecology Package version 25 2.Google Scholar
Olm, R, West, PT, Brooks, B, Firek, BA, Baker, R, Morowitz, MJ and Banfield, JF (2019) Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital room. Microbiome 7, 26.10.1186/s40168-019-0638-1CrossRefGoogle Scholar
Shade, A and Handelsman, J (2012) Beyond the Venn diagram: the hunt for a core microbiome. Environmental Microbiology 14, 4–12.10.1111/j.1462-2920.2011.02585.xCrossRefGoogle Scholar
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