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De Filippis F, Valentino V, Yap M, Cabrera-Rubio R, Barcenilla C, Carlino N, Cobo-Díaz JF, Quijada NM, Calvete-Torre I, Ruas-Madiedo P, Sabater C, Sequino G, Pasolli E, Wagner M, Margolles A, Segata N, Álvarez-Ordóñez A, Cotter PD, Ercolini D. Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities. NPJ Biofilms Microbiomes 2024; 10:67. [PMID: 39095404 PMCID: PMC11297241 DOI: 10.1038/s41522-024-00541-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
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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Affiliation(s)
- Francesca De Filippis
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy
| | - Vincenzo Valentino
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Spain
| | - Coral Barcenilla
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | | | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Narciso Martín Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Giuseppina Sequino
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Edoardo Pasolli
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Danilo Ercolini
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy.
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Ritschard JS, Schuppler M. The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety. Foods 2024; 13:214. [PMID: 38254515 PMCID: PMC10814198 DOI: 10.3390/foods13020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.
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Affiliation(s)
| | - Markus Schuppler
- Laboratory of Food Microbiology, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland;
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Xu ZS, Ju T, Yang X, Gänzle M. A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities. Microorganisms 2023; 11:1575. [PMID: 37375077 DOI: 10.3390/microorganisms11061575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.
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Affiliation(s)
- Zhaohui S Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Xianqin Yang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada
| | - Michael Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Martin JGP, Cotter PD. Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity? Heliyon 2023; 9:e15110. [PMID: 37151695 PMCID: PMC10161367 DOI: 10.1016/j.heliyon.2023.e15110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The microbial diversity of artisanal cheeses has been ever more extensively explored over recent years. Many new studies have been particularly focused on the detection and identification of fungi associated with cheese rinds. This is not surprising given that the composition and abundance of fungi on the cheese surface can significantly contribute to desirable sensory qualities, while also contributing to defects, particularly during ripening, and risks associated with the production of mycotoxins. Here we critically review the impact of fungi on the quality of artisanal cheeses, as well as the risks associated with the presence of particular species or strains with specific phenotypes. Ultimately, we address the question; should fungi be predominantly considered villains when it comes to artisanal cheese safety or could their presence be better exploited by producers in order to generate innovative products with greater added value? Such discussions will be increasingly important from the perspective of the future commercialization and regulation of artisanal cheeses that frequently contain a high abundance of moulds.
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Affiliation(s)
- José Guilherme Prado Martin
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Corresponding author.
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland and VistaMilk, Ireland
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5
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Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities. mSystems 2023; 8:e0070122. [PMID: 36622155 PMCID: PMC9948695 DOI: 10.1128/msystems.00701-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.
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Martin JGP, Silva JMM, César ICDR, da Silva M, Santana SA, Veloso TGR, Silva JGE, Ferreira CLDLF, Leech J, Cotter PD. Seasonal variation in the Canastra cheese mycobiota. Front Microbiol 2023; 13:1076672. [PMID: 36817100 PMCID: PMC9936976 DOI: 10.3389/fmicb.2022.1076672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/28/2022] [Indexed: 02/05/2023] Open
Abstract
Canastra cheese is the most well-known artisanal cheese produced in Brazil. Although its production includes a step to remove fungi from the cheese surface, in recent years some cheesemakers have preserved the autochthonous fungi grown during ripening due to an interest in the sensory characteristics attributed to these microorganisms. In this work, the mycobiota of artisanal cheeses produced in the Canastra region was characterized based on ITS marker gene analysis. A total of 96 artisanal cheeses from 16 different farms across 9 cities were collected during two different periods (dry and wet seasons). The Canastra cheese mycobiota was significantly impacted by the season, the city of production and the farm but altitude did not affect the fungal community of the cheeses analyzed. Debaryomyces prosopidis was most abundant in the majority of samples across both seasons. During the wet season, Trichosporon asahii, Kluyveromyces lactis and Fusarium solani were the next most abundant species, followed by Torulaspora delbrueckii and Acremonium citrinum. These results highlight the importance of manufacturing practices and seasonality on the fungal composition of Canastra cheeses. These insights are particularly important in light of recent new regulation in Brazil, removing previous obstacles for surface fungi to persist on cheese. These new regulations will allow new approaches to cheese production, and ultimately, novel products.
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Affiliation(s)
- José Guilherme Prado Martin
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil,*Correspondence: José Guilherme Prado Martin,
| | - João Marcos Maia Silva
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Isabel Cristina da Rocha César
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Meiriele da Silva
- Laboratory of Mycorrhizae (LAMIC), Department of Microbiology, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | - Samara Aparecida Santana
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Tomás Gomes Reis Veloso
- Laboratory of Mycorrhizae (LAMIC), Department of Microbiology, Universidade Federal de Viçosa (UFV), Viçosa, Brazil
| | | | | | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland,APC Microbiome Ireland and VistaMilk, Fermoy, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland,APC Microbiome Ireland and VistaMilk, Fermoy, Ireland
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Woods DF, Kozak IM, O'Gara F. Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36099016 DOI: 10.1099/mic.0.001238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genus Halomonas was identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernica B1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated that H. hibernica B1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover, H. hibernica exhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.
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Affiliation(s)
- David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Iwona M Kozak
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Synthesis and Solid State Pharmaceutical Centre, University College Cork, Cork, Ireland
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8
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Raymond-Fleury A, Lessard MH, Chamberland J, Pouliot Y, Dugat-Bony E, Turgeon SL, St-Gelais D, Labrie S. Analysis of Microbiota Persistence in Quebec's Terroir Cheese Using a Metabarcoding Approach. Microorganisms 2022; 10:microorganisms10071381. [PMID: 35889100 PMCID: PMC9316450 DOI: 10.3390/microorganisms10071381] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental short amplicon sequencing, or metabarcoding, is commonly used to characterize the bacterial and fungal microbiota of cheese. Comparisons between different metabarcoding studies are complicated by the use of different gene markers. Here, we systematically compare different metabarcoding molecular targets using V3–V4 and V6–V8 regions of the bacterial 16S rDNA and fungal ITS1 and ITS2 regions. Taxonomic profiles varied depending on the molecular markers used. Based on data quality and detection capacity of the markers toward microorganisms usually associated with the dairy environment, the ribosomal regions V3–V4 and ITS2 were selected and further used to evaluate variability in the microbial ecosystem of terroir cheeses from the province of Quebec in Canada. Both fungal and bacterial ecosystem profiles were described for 32 different ready-to-eat bloomy-, washed- and natural-rind specialty cheese varieties. Among them, 15 were studied over two different production years. Using the Bray–Curtis dissimilarity index as an indicator of microbial shifts, we found that most variations could be explained by either a voluntary change in starter or ripening culture composition, or by changes in the cheesemaking technology. Overall, our results suggest the persistence of the microbiota between the two years studied—these data aid understanding of cheese microbiota composition and persistence during cheese ripening.
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Affiliation(s)
- Annick Raymond-Fleury
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
| | - Marie-Hélène Lessard
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
| | - Julien Chamberland
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
| | - Yves Pouliot
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
| | - Eric Dugat-Bony
- UMR SayFood, INRAE, AgroParisTech, Université Paris-Saclay, Avenue Lucien Brétignières, 78850 Thiverval-Grignon, France;
| | - Sylvie L. Turgeon
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
| | - Daniel St-Gelais
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Center, 3600 Casavant Boulevard West, Saint-Hyacinthe, QC J2S 8E3, Canada
| | - Steve Labrie
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l’Agriculture, Quebec City, QC G1V 0A6, Canada; (A.R.-F.); (M.-H.L.); (J.C.); (Y.P.); (S.L.T.); (D.S.-G.)
- Correspondence:
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Lacorte GA, Cruvinel LA, de Paula Ávila M, Dias MF, de Abreu Pereira A, Nascimento AMA, de Melo Franco BDG. Investigating the influence of Food Safety Management Systems (FSMS) on microbial diversity of Canastra cheeses and their processing environments. Food Microbiol 2022; 105:104023. [DOI: 10.1016/j.fm.2022.104023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
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10
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Quijada NM, Dzieciol M, Schmitz-Esser S, Wagner M, Selberherr E. Metatranscriptomic Analyses Unravel Dynamic Changes in the Microbial and Metabolic Transcriptional Profiles in Artisanal Austrian Hard-Cheeses During Ripening. Front Microbiol 2022; 13:813480. [PMID: 35300479 PMCID: PMC8921697 DOI: 10.3389/fmicb.2022.813480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/02/2022] [Indexed: 11/30/2022] Open
Abstract
Vorarlberger Bergkäse (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows' raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30 days of ripening) and after (90 days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30 days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.
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Affiliation(s)
- Narciso Martín Quijada
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Monika Dzieciol
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Martin Wagner
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Evelyne Selberherr
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
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Dimov SG, Gyurova A, Zagorchev L, Dimitrov T, Georgieva-Miteva D, Peykov S. NGS-Based Metagenomic Study of Four Traditional Bulgarian Green Cheeses from Tcherni Vit. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Sun L, D’Amico DJ. Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese. mSystems 2021; 6:e0083021. [PMID: 34581601 PMCID: PMC8547439 DOI: 10.1128/msystems.00830-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/09/2021] [Indexed: 12/21/2022] Open
Abstract
Prior to the advent of milk pasteurization and the use of defined-strain starter cultures, the production and ripening of cheese relied on the introduction and growth of adventitious microbes from the environment. This study characterized microbial community structures throughout a traditional farmstead cheese production continuum and evaluated the role of the environment in microbial transfer. In total, 118 samples (e.g., raw milk, cheese, and environmental surfaces) were collected from milk harvesting through cheese ripening. Microbial communities were characterized based on amplicon sequencing of bacterial 16S rRNA and fungal internal transcribed spacer genes using the Illumina MiSeq platform. Results indicated that the environment in each processing room harbored unique microbial ecosystems and consistently contributed microbes to milk, curd, and cheese. The diverse microbial composition of milk was initially attributed to milker hands and cow teats and then changed substantially following overnight ripening in a wooden vat to one dominated by lactic acid bacteria, including Lactococcus lactis, Lactobacillus, and Leuconostoc, as well as fungi such as Exophiala, Kluyveromyces, and Candida. Additional microbial contributions were attributed to processing tools, but the composition of the cheese paste remained relatively stable over 60 days of ripening. In contrast, rind communities that were largely influenced by direct contact with bamboo aging mats showed a distinct succession pattern compared to the interior sections. Overall, these findings highlight the critical role of traditional tools and practices in shaping the microbial composition of cheese and broaden our understanding of processing environments as important sources of microbes in food. IMPORTANCE Throughout the 20th century, especially in the United States, sanitation practices, pasteurization of milk, and the use of commercial defined-strain starter cultures have enhanced the safety and consistency of cheese. However, these practices can reduce cheese microbial diversity. The rapid growth of the artisanal cheese industry in the United States has renewed interest in recapturing the diversity of dairy products and the microbes involved in their production. Here, we demonstrate the essential role of the environment, including the use of wooden tools and cheesemaking equipment, as sources of dominant microbes that shape the fermentation and ripening processes of a traditional farmstead cheese produced without the addition of starter cultures or direct inoculation of any other bacteria or fungi. These data enrich our understanding of the microbial interactions between products and the environment and identify taxa that contribute to the microbial diversity of cheese and cheese production.
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Affiliation(s)
- Lang Sun
- Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA
| | - Dennis J. D’Amico
- Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA
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13
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Gérard A, El-Hajjaji S, Burteau S, Fall PA, Pirard B, Taminiau B, Daube G, Sindic M. Study of the microbial diversity of a panel of Belgian artisanal cheeses associated with challenge studies for Listeria monocytogenes. Food Microbiol 2021; 100:103861. [PMID: 34416961 DOI: 10.1016/j.fm.2021.103861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/05/2021] [Accepted: 06/13/2021] [Indexed: 12/29/2022]
Abstract
High throughput sequencing could become a powerful tool in food safety. This study was the first to investigate artisanal cheeses from Belgium (31 batches) using metagenetics, in relation to Listeria monocytogenes growth data acquired during a previous project. Five cheese types were considered, namely unripened acid-curd cheeses, smear- and mold-ripened soft cheeses, and Gouda-type and Saint-Paulin-type cheeses. Each batch was analyzed in triplicate the first and the last days of storage at 8 °C. Globally, 2697 OTUs belonging to 277 genera and to 15 phyla were identified. Lactococcus was dominant in all types, but Streptococcus was co-dominant in smear-ripened soft cheeses and Saint-Paulin-type cheeses. The dominant population was not always associated with added starter cultures. Bacterial richness and diversity were significantly higher in both types of soft cheeses than in other categories, including particular genera like Prevotella, Faecalibacterium and Hafnia-Obesumbacterium in mold-ripened cheeses and Brevibacterium, Brachybacterium, Microbacterium, Bacteroides, Corynebacterium, Marinilactibacillus, Fusobacterium, Halomonas and Psychrobacter in smear-ripened soft cheeses. A strong correlation was observed between no growth of L. monocytogenes in a smear-ripened cheese and the presence of an unknown Fusobacterium (relative abundance around 10%). This in silico correlation should be confirmed by further experiments in vitro and in situ.
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Affiliation(s)
- Amaury Gérard
- Laboratory of Quality and Safety of Agro-Food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium.
| | - Soundous El-Hajjaji
- Laboratory of Quality and Safety of Agro-Food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
| | - Sophie Burteau
- Genalyse Partner sa, rue Hayeneux, 62, 4040, Herstal, Belgium
| | | | - Barbara Pirard
- Faculty of Veterinary Medicine, Food Science Department, FARAH, University of Liège, Sart-Tilman, B43b, 4000, Liège, Belgium
| | - Bernard Taminiau
- Faculty of Veterinary Medicine, Food Science Department, FARAH, University of Liège, Sart-Tilman, B43b, 4000, Liège, Belgium
| | - Georges Daube
- Faculty of Veterinary Medicine, Food Science Department, FARAH, University of Liège, Sart-Tilman, B43b, 4000, Liège, Belgium
| | - Marianne Sindic
- Laboratory of Quality and Safety of Agro-Food Products, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030, Gembloux, Belgium
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14
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Wadhawan K, Steinberger A, Rankin S, Suen G, Czuprynski C. Characterizing the microbiota of wooden boards used for cheese ripening. JDS COMMUNICATIONS 2021; 2:171-176. [PMID: 36338451 PMCID: PMC9623629 DOI: 10.3168/jdsc.2020-0014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/20/2021] [Indexed: 11/23/2022]
Abstract
The phyla Actinobacteria, Firmicutes, and Proteobacteria dominated the microbiota of the boards. The boards displayed differences in both diversity and richness. We identified 288 total operational taxonomic units (OTU), with 7 OTU forming a core microbiota across all boards. The boards appeared to select for salt- and cold-tolerant bacteria.
Wooden boards are commonly used for aging artisan cheeses. Although considered critical to the development of desired flavors and aromas, knowledge about the microbial communities associated with these boards is limited. To begin to address this need, we performed a 16S ribosomal RNA analysis of the bacterial communities present on the surface and within 5 wooden boards used for cheese ripening that were obtained from 3 cheese-processing facilities. The 5 boards were dominated by bacteria in the phyla Actinobacteria, Firmicutes, and Proteobacteria and displayed differences in both diversity and richness. Analysis of these boards also identified significant board-to-board variation. A total of 288 operational taxonomic units were identified across all samples, with 7 operational taxonomic units forming a core microbiota across all boards. Taken together, these data reflect the cheese-ripening environment, which appears to select for salt- and cold-tolerant bacteria.
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Affiliation(s)
- K. Wadhawan
- Department of Pathobiological Sciences, University of Wisconsin, Madison 53706
| | - A.J. Steinberger
- Department of Bacteriology, University of Wisconsin, Madison 53706
| | - S.A. Rankin
- Department of Food Science, University of Wisconsin, Madison 53706
| | - G. Suen
- Department of Bacteriology, University of Wisconsin, Madison 53706
- Food Research Institute, University of Wisconsin, Madison 53706
| | - C.J. Czuprynski
- Department of Pathobiological Sciences, University of Wisconsin, Madison 53706
- Food Research Institute, University of Wisconsin, Madison 53706
- Corresponding author
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15
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Michailidou S, Pavlou E, Pasentsis K, Rhoades J, Likotrafiti E, Argiriou A. Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding. Food Microbiol 2021; 99:103836. [PMID: 34119120 DOI: 10.1016/j.fm.2021.103836] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/14/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023]
Abstract
Greece is a country possessing many cheese products granted with a PDO (Protected Designation of Origin) certificate, with high exporting activities. In this study, we analyzed six popular cheese PDO products purchased from different industries to assess their microbial communities using amplicon metabarcoding analysis. To this end, using Next Generation Sequencing technology, we sequenced the 16S rRNA gene and the ITS spacer for prokaryotes and fungi, respectively. Alpha diversity indices revealed higher bacterial species richness for some cheeses (Kopanisti, Batzos) and poor for others (Feta, Galotiri). Kopanisti, together with Kalathaki and Anevato, also presented increased species diversity concerning fungal populations. Results showed that lactic acid bacteria (LAB) prevailed the bacterial populations in all samples (Lactococcus, Lactobacillus, Streptococcus, Leuconostoc), whereas for fungi, members of the Saccharomycetaceae, Dipodascaceae and Debaryomycetaceae families prevailed the fungal populations. Several other genera were identified that make up each product's microbiome leading to the creation of the unique organoleptic attributes of Greek PDO cheeses. However, the identified species could not be directly linked to certain cheese types, assuming that starter and adjunct cultures, combined with the raw material used during production greatly impact the microbial communities in cheeses. Our data, produced for the first time for six Greek PDO cheeses, can be exploited in the process of creating a core microbial signature within each cheese type, supporting the Greek brand name and valorizing cheese products.
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Affiliation(s)
- Sofia Michailidou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece.
| | - Eleftherios Pavlou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece
| | - Konstantinos Pasentsis
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece
| | - Jonathan Rhoades
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400, Thessaloniki, Greece
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Science and Technology, International Hellenic University, 57400, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Center for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, P.O. Box 60361, GR-57001, Greece; Department of Food Science and Nutrition, University of the Aegean, Myrina, 81400, Lemnos, Greece
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16
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De Filippis F, Valentino V, Alvarez-Ordóñez A, Cotter PD, Ercolini D. Environmental microbiome mapping as a strategy to improve quality and safety in the food industry. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Mayo B, Rodríguez J, Vázquez L, Flórez AB. Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety. Foods 2021; 10:602. [PMID: 33809159 PMCID: PMC8000492 DOI: 10.3390/foods10030602] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (J.R.); (L.V.); (A.B.F.)
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18
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Johnson J, Curtin C, Waite-Cusic J. The Cheese Production Facility Microbiome Exhibits Temporal and Spatial Variability. Front Microbiol 2021; 12:644828. [PMID: 33767682 PMCID: PMC7985343 DOI: 10.3389/fmicb.2021.644828] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 01/04/2023] Open
Abstract
A primary goal of modern cheese manufacturing is consistent product quality. One aspect of product quality that remains poorly understood is the variability of microbial subpopulations due to temporal or facility changes within cheese production environments. Therefore, our aim was to quantify this variability by measuring day-day and facility-facility changes in the cheese facility microbiome. In-process product (i.e., milk and cheese) and food-contact surfaces were sampled over the course of three production days at three cheese manufacturing facilities. Microbial communities were characterized using 16S rRNA metabarcoding and by plating on selective growth media. Each facility produced near-identical Cheddar cheese recipes on near-identical processing equipment during the time of sampling. Each facility also used a common pool of Lactococcus starter cultures which were rotated daily as groups of 4-5 strains and selected independently at each facility. Diversity analysis revealed significant facility-facility and day-day differences at each sample location. Facility differences were greatest on the food contact surfaces (i.e., draining-matting conveyor belts), explaining between 25 and 41% of the variance. Conversely, daily differences within each facility explained a greater proportion of the variance in the milk (20% vs. 12%) and cheese (29% vs. 20%). Further investigation into the sources of these differences revealed the involvement of several industrially relevant bacteria, including lactobacilli, which play a central role in flavor and texture development during Cheddar cheese ripening. Additionally, Streptococcus was found to contribute notably to differences observed in milk samples, whereas Acinetobacter, Streptococcus, Lactococcus, Exiguobacterium, and Enterobacteriaceae contributed notably to differences on the food contact surfaces. Facility differences in the cheese were overwhelmingly attributed to the rotation of Lactococcus starter cultures, thus highlighting circumstances where daily microbial shifts could be misinterpreted and emphasizing the importance of repeated sampling over time. The outcomes of this work highlight the complexity of the cheese facility microbiome and demonstrate daily and facility-facility microbial variations which might impact cheese product quality.
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Affiliation(s)
- Jared Johnson
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, United States
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19
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Pellegrino L, Hogenboom JA, Rosi V, D’Incecco P. Evaluating the Authenticity of the Raw-Milk Cheese Fontina (PDO) with Respect to Similar Cheeses. Foods 2021; 10:foods10020350. [PMID: 33562236 PMCID: PMC7915116 DOI: 10.3390/foods10020350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 01/29/2023] Open
Abstract
The implementation of quality assurance schemes for the assessment of PDO food authenticity is an issue involving manufacturers, traders, retailers and consumers. In this respect, reliable analytical methods are needed to integrate paper-trailing information. The feasibility of distinguishing the Italian Fontina PDO cheese from the generic Fontal cheese was preliminarily evaluated on a set of commercial samples by measuring selected parameters (pH, alkaline phosphatase activity, content of copper, volatiles, extent of proteolysis) related to the different manufacturing processes. The relative profile of free amino acids proved to be a promising tool. A new set of 41 samples of Fontina PDO cheese was collected at representative dairies within the recognized production area and analyzed for free amino acids. A chemometric model of Fontina PDO cheese was built based on the mean content and standard deviation of 15 free amino acids. On this basis, all of the PDO samples were correctly identified, whereas all of the Fontal cheeses were recognized as different cheeses.
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20
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Zwirzitz B, Wetzels SU, Dixon ED, Fleischmann S, Selberherr E, Thalguter S, Quijada NM, Dzieciol M, Wagner M, Stessl B. Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events. Front Microbiol 2021; 12:632935. [PMID: 33613505 PMCID: PMC7892895 DOI: 10.3389/fmicb.2021.632935] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/13/2021] [Indexed: 12/27/2022] Open
Abstract
A large part of foodborne outbreaks related to Listeria monocytogenes are linked to meat and meat products. Especially, recontamination of meat products and deli-meat during slicing, packaging, and repackaging is in the focus of food authorities. In that regard, L. monocytogenes persistence in multi-species biofilms is one major issue, since they survive elaborate cleaning and disinfection measures. Here, we analyzed the microbial community structure throughout a meat processing facility using a combination of high-throughput full-length 16S ribosomal RNA (rRNA) gene sequencing and traditional microbiological methods. Samples were taken at different stages during meat cutting as well as from multiple sites throughout the facility environment to capture the product and the environmental associated microbiota co-occurring with Listeria spp. and L. monocytogenes. The listeria testing revealed a widely disseminated contamination (50%; 88 of 176 samples were positive for Listeria spp. and 13.6%; 24 of 176 samples were positive for L. monocytogenes). The pulsed-field gel electrophoresis (PFGE) typing evidenced 14 heterogeneous L. monocytogenes profiles with PCR-serogroup 1/2a, 3a as most dominant. PFGE type MA3-17 contributed to the resilient microbiota of the facility environment and was related to environmental persistence. The core in-house microbiota consisted mainly of the genera Acinetobacter, Pseudomonas, Psychrobacter (Proteobacteria), Anaerobacillus, Bacillus (Firmicutes), and Chryseobacterium (Bacteroidota). While the overall microbial community structure clearly differed between product and environmental samples, we were able to discern correlation patterns regarding the presence/absence of Listeria spp. in both sample groups. Specifically, our longitudinal analysis revealed association of Listeria spp. with known biofilm-producing Pseudomonas, Acinetobacter, and Janthinobacterium species on the meat samples. Similar patterns were also observed on the surface, indicating dispersal of microorganisms from this multispecies biofilm. Our data provided a better understanding of the built environment microbiome in the meat processing context and promoted more effective options for targeted disinfection in the analyzed facility.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Stefanie U. Wetzels
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Emmanuel D. Dixon
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Svenja Fleischmann
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Sarah Thalguter
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Narciso M. Quijada
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Monika Dzieciol
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Austrian Competence Center for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Beatrix Stessl
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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21
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Morandi S, Battelli G, Silvetti T, Tringali S, Nunziata L, Villa A, Acquistapace A, Brasca M. Impact of salting and ripening temperatures on late blowing defect in Valtellina Casera PDO cheese. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107508] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Sawada K, Koyano H, Yamamoto N, Yamada T. The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds. Sci Rep 2021; 11:1791. [PMID: 33469050 PMCID: PMC7815776 DOI: 10.1038/s41598-021-81105-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/04/2021] [Indexed: 01/02/2023] Open
Abstract
The microbial community during fermented vegetable production has a large impact on the quality of the final products. Lactic acid bacteria have been well-studied in such processes, but knowledge about the roles of non-lactic acid bacteria is limited. This study aimed to provide useful knowledge about the relationships between the microbiota, including non-lactic acid bacteria, and metabolites in commercial pickle production by investigating Japanese pickles fermented in rice-bran. The samples were provided by six manufacturers, divided into two groups depending on the production conditions. The microbiological content of these samples was investigated by high-throughput sequencing, and metabolites were assessed by liquid chromatography-mass spectrometry and enzymatic assay. The data suggest that Halomonas, halophilic Gram-negative bacteria, can increase glutamic acid content during the pickling process under selective conditions for bacterial growth. In contrast, in less selective conditions, the microbiota consumed glutamic acid. Our results indicate that the glutamic acid content in fermented pickle is influenced by the microbiota, rather than by externally added glutamic acid. Our data suggest that both lactic acid bacteria and non-lactic acid bacteria are positive key factors in the mechanism of commercial vegetable fermentation and affect the quality of pickles.
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Affiliation(s)
- Kazunori Sawada
- Corporate Strategy Office, Gurunavi, Inc., Toho Hibiya Building, 1-2-2 Yurakucho, Chiyoda-ku, Tokyo, 100-0006, Japan
| | - Hitoshi Koyano
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Nozomi Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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23
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Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi. Foods 2020; 9:foods9121851. [PMID: 33322552 PMCID: PMC7763656 DOI: 10.3390/foods9121851] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Cheese ripening involves successional changes of the rind microbial composition that harbors a key role on the quality and safety of the final products. In this study, we analyzed the evolution of the rind microbiota (bacteria and fungi) throughout the ripening of Austrian Vorarlberger Bergkäse (VB), an artisanal surface-ripened cheese, by using quantitative and qualitative approaches. The real-time quantitative PCR results revealed that bacteria were more abundant than fungi in VB rinds throughout ripening, although both kingdoms were abundant along the process. The qualitative investigation was performed by high-throughput gene-targeted (amplicon) sequencing. The results showed dynamic changes of the rind microbiota throughout ripening. In the fresh products, VB rinds were dominated by Staphylococcus equorum and Candida. At early ripening times (14–30 days) Psychrobacter and Debaryomyces flourished, although their high abundance was limited to these time points. At the latest ripening times (90–160 days), VB rinds were dominated by S. equorum, Brevibacterium, Corynebacterium, and Scopulariopsis. Strong correlations were shown for specific bacteria and fungi linked to specific ripening periods. This study deepens our understanding of VB ripening and highlights different bacteria and fungi associated to specific ripening periods which may influence the organoleptic properties of the final products.
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24
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The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes. PLoS One 2020; 15:e0233945. [PMID: 32701964 PMCID: PMC7377500 DOI: 10.1371/journal.pone.0233945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
The survival of Listeria (L.) monocytogenes in foods and food production environments (FPE) is dependent on several genes that increase tolerance to stressors; this includes competing with intrinsic bacteria. We aimed to uncover genes that are differentially expressed (DE) in L. monocytogenes sequence type (ST) 121 strain 6179 when co-cultured with cheese rind bacteria. L. monocytogenes was cultivated in broth or on plates with either a Psychrobacter or Brevibacterium isolate from cheese rinds. RNA was extracted from co-cultures in broth after two or 12 hours and from plates after 24 and 72 hours. Broth co-cultivations with Brevibacterium or Psychrobacter yielded up to 392 and 601 DE genes, while plate co-cultivations significantly affected the expression of up to 190 and 485 L. monocytogenes genes, respectively. Notably, the transcription of virulence genes encoding the Listeria adhesion protein and Listeriolysin O were induced during plate and broth co-cultivations. The expression of several systems under the control of the global stress gene regulator, σB, increased during co-cultivation. A cobalamin-dependent gene cluster, responsible for the catabolism of ethanolamine and 1,2-propanediol, was upregulated in both broth and plate co-cultures conditions. Finally, a small non-coding (nc)RNA, Rli47, was induced after 72 hours of co-cultivation on plates and accounted for 50-90% of the total reads mapped to L. monocytogenes. A recent study has shown that Rli47 may contribute to L. monocytogenes stress survival by slowing growth during stress conditions through the suppression of branch-chained amino acid biosynthesis. We hypothesize that Rli47 may have an impactful role in the response of L. monocytogenes to co-cultivation by regulating a complex network of metabolic and virulence mechanisms.
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25
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McHugh AJ, Feehily C, Fenelon MA, Gleeson D, Hill C, Cotter PD. Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder. mSystems 2020; 5:e00226-20. [PMID: 32265313 PMCID: PMC7141888 DOI: 10.1128/msystems.00226-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Microorganisms from the environment can enter the dairy supply chain at multiple stages, including production, milk collection, and processing, with potential implications for quality and safety. The ability to track these microorganisms can be greatly enhanced by the use of high-throughput DNA sequencing (HTS). Here HTS, both 16S rRNA gene amplicon and shotgun metagenomic sequencing were applied to investigate the microbiomes of fresh mid- and late-lactation milk collected from farm bulk tanks, collection tankers, milk silos, skimmed milk silos, a cream silo, and powder samples to investigate the microbial changes throughout a skim milk powder manufacturing process. 16S rRNA gene analysis established that the microbiota of raw milks from farm bulk tanks and in collection tankers were very diverse but that psychrotrophic genera associated with spoilage, Pseudomonas and Acinetobacter, were present in all samples. Upon storage within the whole-milk silo at the processing facility, the species Pseudomonas fluorescens and Acinetobacter baumannii became dominant. The skimmed milk powder generated during the mid-lactation period had a microbial composition that was very different from that of raw milk; specifically, two thermophilic genera, Thermus and Geobacillus, were enriched. In contrast, the microbiota of skimmed milk powder generated from late-lactation milk more closely resembled that of the raw milk and was dominated by spoilage-associated psychrotrophic bacteria. This study demonstrates that the dairy microbiota can differ significantly across different sampling days. More specifically, HTS can be used to trace microbial species from raw milks through processing to final powdered products.IMPORTANCE Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.
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Affiliation(s)
- Aoife J McHugh
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Conor Feehily
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Mark A Fenelon
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Cork, Ireland
| | - David Gleeson
- Teagasc Animal and Grassland Research and Innovation Centre, Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
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26
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Anast JM, Dzieciol M, Schultz DL, Wagner M, Mann E, Schmitz-Esser S. Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment. Sci Rep 2019; 9:6164. [PMID: 30992535 PMCID: PMC6467879 DOI: 10.1038/s41598-019-42525-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/02/2019] [Indexed: 02/01/2023] Open
Abstract
The genus Brevibacterium harbors many members important for cheese ripening. We performed real-time quantitative PCR (qPCR) to determine the abundance of Brevibacterium on rinds of Vorarlberger Bergkäse, an Austrian artisanal washed-rind hard cheese, over 160 days of ripening. Our results show that Brevibacterium are abundant on Vorarlberger Bergkäse rinds throughout the ripening time. To elucidate the impact of Brevibacterium on cheese production, we analysed the genomes of three cheese rind isolates, L261, S111, and S22. L261 belongs to Brevibacterium aurantiacum, whereas S111 and S22 represent novel species within the genus Brevibacterium based on 16S rRNA gene similarity and average nucleotide identity. Our comparative genomic analysis showed that important cheese ripening enzymes are conserved among the genus Brevibacterium. Strain S22 harbors a 22 kb circular plasmid which encodes putative iron and hydroxymethylpyrimidine/thiamine transporters. Histamine formation in fermented foods can cause histamine intoxication. We revealed the presence of a putative metabolic pathway for histamine degradation. Growth experiments showed that the three Brevibacterium strains can utilize histamine as the sole carbon source. The capability to utilize histamine, possibly encoded by the putative histamine degradation pathway, highlights the importance of Brevibacterium as key cheese ripening cultures beyond their contribution to cheese flavor production.
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Affiliation(s)
- Justin M Anast
- Interdepartmental Microbiology Graduate Program Iowa State University, Ames, IA, USA.,Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Monika Dzieciol
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Dylan L Schultz
- Interdepartmetal Microbiology Undergraduate Program, Iowa State University, Ames, IA, USA
| | - Martin Wagner
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria.,Austrian Competence Center for Feed and Food Quality, Safety and Innovation (FFoQSI), Technopark C, 3430, Tulln, Austria
| | - Evelyne Mann
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stephan Schmitz-Esser
- Interdepartmental Microbiology Graduate Program Iowa State University, Ames, IA, USA. .,Department of Animal Science, Iowa State University, Ames, IA, USA.
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27
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Sant'Anna FM, Wetzels SU, Cicco SHS, Figueiredo RC, Sales GA, Figueiredo NC, Nunes CA, Schmitz-Esser S, Mann E, Wagner M, Souza MR. Microbial shifts in Minas artisanal cheeses from the Serra do Salitre region of Minas Gerais, Brazil throughout ripening time. Food Microbiol 2019; 82:349-362. [PMID: 31027793 DOI: 10.1016/j.fm.2019.02.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/12/2019] [Accepted: 02/28/2019] [Indexed: 01/01/2023]
Abstract
The Minas artisanal cheese is a traditional product in its way of producing. Produced in the Minas Gerais state, Brazil, this cheese is made using raw cow's milk with the addition of an endogenous starter culture called "pingo", responsible for inoculating specific microorganisms that could enhance flavor and sensorial aspects. There are seven regions able to produce and commercialize this product - Araxá, Campo das Vertentes, Canastra Cerrado, Serra do Salitre, Serro and Triângulo Mineiro. This study aimed to assess the bacterial community of raw milk, endogenous starter culture and to uncover possible shifts in the bacterial community of the rind and core of cheeses at sixty days of ripening located in the Serra do Salitre region by Illumina MiSeq 16S rRNA gene amplicon sequencing. Raw milk and starter culture are responsible for inoculating specific bacteria into the cheese, with Planococcaceae and Streptococcaceae being prevalent throughout ripening time. The Planococcaceae family seems to develop strong interactions with the Leuconostocaceae family on the surface of these cheeses, and is associated with environmental aspects of the region, probably leading to a microbial signature of these products. Additionally, abiotic factors such as geographical location, moisture and acidity are major drivers in the microbial shift.
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Affiliation(s)
- Felipe Machado Sant'Anna
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil.
| | - Stefanie Urimarie Wetzels
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Veterinaerplatz 1, 1210, Vienna, Austria; Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Sávio Henrique Sandes Cicco
- Department of General Biology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Ranier Chaves Figueiredo
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Gilson Assis Sales
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Naiara Chaves Figueiredo
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Cantini Alvaro Nunes
- Department of General Biology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, 3222 NSRIC, 1029 North University Boulevard, 50011, Ames, IA, USA
| | - Evelyne Mann
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Martin Wagner
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Vienna, Veterinaerplatz 1, 1210, Vienna, Austria; Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Marcelo Resende Souza
- Department of Technology and Inspection of Products of Animal Origin, Veterinary School, Universidade Federal de Minas Gerais, Pampulha, 31270-901, Belo Horizonte, Minas Gerais, Brazil
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