Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities
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| Název: | Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities |
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| Autoři: | De Filippis, Francesca, Ercolini, Danilo, Cotter, Paul D., Álvarez-Ordóñez, Avelino, Segata, Nicola, Margolles, Abelardo, Wagner, Martin, Pasolli, Edoardo, Sequino, Giuseppina, Sabater, Carlos, Ruas-Madiedo, Patricia, Calvete-Torre, Inés, Quijada, Narciso Martín, Cobo-Díaz, José F, Carlino, Niccolò, Barcenilla, Coral, Cabrera-Rubio, Raul, Valentino, Vincenzo, Yap, Min |
| Přispěvatelé: | Tecnologia de los Alimentos, Facultad de Veterinaria, European Commission, Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| Zdroj: | NPJ Biofilms Microbiomes BULERIA. Repositorio Institucional de la Universidad de León Universidad de León Digital.CSIC. Repositorio Institucional del CSIC Consejo Superior de Investigaciones Científicas (CSIC) npj Biofilms and Microbiomes, Vol 10, Iss 1, Pp 1-16 (2024) |
| Informace o vydavateli: | Springer Science and Business Media LLC, 2024. |
| Rok vydání: | 2024 |
| Témata: | 0301 basic medicine, 3309 Tecnología de Los Alimentos, Tecnología de los alimentos, Article, Microbial ecology, 03 medical and health sciences, microbiomes, Cheese, Humans, Dairy industry, 2. Zero hunger, metagenomics, 0303 health sciences, Bacteria, Metagenomes, Probiotics, Microbiota, QR100-130, Europe, Dairying, probiotics, dairy industry, Food Microbiology, Metagenome, Microbiome, Metagenomics, Cheese microbiology, Dairying methods, Metagenomics methods, Bacteria genetics classification isolation & purification, 2414 Microbiología |
| Popis: | The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators’ hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin. |
| Druh dokumentu: | Article Other literature type |
| Popis souboru: | application/pdf |
| Jazyk: | English |
| ISSN: | 2055-5008 |
| DOI: | 10.1038/s41522-024-00541-5 |
| DOI: | 10.13039/501100000780 |
| Přístupová URL adresa: | https://pubmed.ncbi.nlm.nih.gov/39095404 https://www.nature.com/articles/s41522-024-00541-5 https://hdl.handle.net/10612/24354 http://hdl.handle.net/10261/366019 https://api.elsevier.com/content/abstract/scopus_id/85200273002 https://doaj.org/article/560467437ad349f4b7e293a24673f140 https://hdl.handle.net/11588/967705 https://hdl.handle.net/10612/24354 https://phaidra.vetmeduni.ac.at/o:3530 https://doi.org/10.1038/s41522-024-00541-5 |
| Rights: | CC BY CC BY NC ND |
| Přístupové číslo: | edsair.doi.dedup.....06dd9c693e9bd1b99b6af2e8b1bfc34e |
| Databáze: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstrakt: | The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators’ hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin. |
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| ISSN: | 20555008 |
| DOI: | 10.1038/s41522-024-00541-5 |