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Alexa EA, Cobo-Díaz JF, Renes E, O Callaghan TF, Kilcawley K, Mannion D, Skibinska I, Ruiz L, Margolles A, Fernández-Gómez P, Alvarez-Molina A, Puente-Gómez P, Crispie F, López M, Prieto M, Cotter PD, Alvarez-Ordóñez A. The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits. Microbiome 2024; 12:78. [PMID: 38678226 PMCID: PMC11055350 DOI: 10.1186/s40168-024-01790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. RESULTS Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. CONCLUSION Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.
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Affiliation(s)
- Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Erica Renes
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Tom F O Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, T12 Y337, Ireland
| | | | - David Mannion
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
| | | | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | | | | | - Paula Puente-Gómez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.
- Institute of Food Science and Technology, Universidad de León, León, Spain.
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McCarthy WP, Srinivas M, Danaher M, Connor CO, Callaghan TFO, van Sinderen D, Kenny J, Tobin JT. Isolation and identification of chlorate-reducing Hafnia sp. from milk. Microbiology (Reading) 2023; 169:001347. [PMID: 37450378 PMCID: PMC10433419 DOI: 10.1099/mic.0.001347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/31/2023] [Indexed: 07/18/2023]
Abstract
Chlorate has become a concern in the food and beverage sector, related to chlorine sanitizers in industrial food production and water treatment. It is of particular concern to regulatory bodies due to the negative health effects of chlorate exposure. This study investigated the fate of chlorate in raw milk and isolated bacterial strains of interest responsible for chlorate breakdown. Unpasteurized milk was demonstrated to have a chlorate-reducing capacity, breaking down enriched chlorate to undetectable levels in 11 days. Further enrichment and isolation using conditions specific to chlorate-reducing bacteria successfully isolated three distinct strains of Hafnia paralvei. Chlorate-reducing bacteria were observed to grow in a chlorate-enriched medium with lactate as an electron donor. All isolated strains were demonstrated to reduce chlorate in liquid medium; however, the exact mechanism of chlorate degradation was not definitively identified in this study.
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Affiliation(s)
- William P. McCarthy
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7, Ireland
| | - Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Martin Danaher
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Christine O. Connor
- School of Food Science and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7, Ireland
| | - Tom F. O. Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - John Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- VistaMilk Science Foundation Ireland Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
| | - John T. Tobin
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- VistaMilk Science Foundation Ireland Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
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Magan JB, O Callaghan TF, Kelly AL, McCarthy NA. Compositional and functional properties of milk and dairy products derived from cows fed pasture or concentrate-based diets. Compr Rev Food Sci Food Saf 2021; 20:2769-2800. [PMID: 33949109 DOI: 10.1111/1541-4337.12751] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/24/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022]
Abstract
Worldwide milk production is predominantly founded on indoor, high-concentrate feeding systems, whereas pasture-based feeding systems are most common in New Zealand and Ireland but have received greater attention recently in countries utilizing conventional systems. Consumer interest in 'pasture-fed' dairy products has also increased, arising from environmental, ethical, and nutritional concerns. A substantial body of research exists describing the effect of different feeding strategies on the composition of milk, with several recent studies focusing on the comparison of pasture- and concentrate-based feeding regimes. Significant variation is typically observed in the gross composition of milk produced from different supplemental feeds, but various changes in the discrete composition of macromolecular components in milk have also been associated with dietary influence, particularly in relation to the fatty acid profile. Changes in milk composition have also been shown to have implications for milk and dairy product processability, functionality and sensory properties. Methods to determine the traceability of dairy products or verify marketing claims such as 'pasture-fed' have also been established, based on compositional variation due to diet. This review explores the effects of feed types on milk composition and quality, along with the ultimate effect of diet-induced changes on milk and dairy product functionality, with particular emphasis placed on pasture- and concentrate-based feeding systems.
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Affiliation(s)
- Jonathan B Magan
- Food Chemistry and Technology, Teagasc Food Research Centre, Cork, Ireland.,School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Tom F O Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Alan L Kelly
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Noel A McCarthy
- Food Chemistry and Technology, Teagasc Food Research Centre, Cork, Ireland
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