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Lecaudé C, Orieux N, Chuzeville S, Bertry A, Coissac E, Boyer F, Bonin A, Colomb-Boeckler N, Mathieu B, Recour M, Vindret J, Pignol C, Romand S, Petite C, Taberlet P, Charles C, Bel N, Hauwuy A. Deciphering microbial communities of three Savoyard raw milk cheeses along ripening and regarding the cheese process. Int J Food Microbiol 2024; 418:110712. [PMID: 38723541 DOI: 10.1016/j.ijfoodmicro.2024.110712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/27/2024]
Abstract
Different Savoyard cheeses are granted with PDO (Protected Designation or Origin) and PGI (Protected Geographical Indication) which guarantees consumers compliance with strict specifications. The use of raw milk is known to be crucial for specific flavor development. To unravel the factors influencing microbial ecosystems across cheese making steps, according to the seasonality (winter and summer) and the mode of production (farmhouse and dairy factory ones), gene targeting on bacteria and fungus was used to have a full picture of 3 cheese making technologies, from the raw milk to the end of the ripening. Our results revealed that Savoyard raw milks are a plenteous source of biodiversity together with the brines used during the process, that may support the development of specific features for each cheese. It was shown that rinds and curds have very contrasted ecosystem diversity, composition, and evolution. Ripening stage was selective for some bacterial species, whereas fungus were mainly ubiquitous in dairy samples. All ripening stages are impacted by the type of cheese technologies, with a higher impact on bacterial communities, except for fungal rind communities, for which the technology is the more discriminant. The specific microorganism's abundance for each technology allow to see a real bar-code, with more or less differences regarding bacterial or fungal communities. Bacterial structuration is shaped mainly by matrices, differently regarding technologies while the influence of technology is higher for fungi. Production types showed 10 differential bacterial species, farmhouses showed more ripening taxa, while dairy factory products showing more lactic acid bacteria. Meanwhile, seasonality looks to be a minor element for the comprehension of both microbial ecosystems, but the uniqueness of each dairy plant is a key explicative feature, more for bacteria than for fungus communities.
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Affiliation(s)
- Cresciense Lecaudé
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France.
| | - Nicolas Orieux
- ENILV, Ecole Nationale des industries du lait et de la viande, 212Rue Anatole France, 74800 La Roche-sur-Foron, France
| | - Sarah Chuzeville
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Alicia Bertry
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Eric Coissac
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Frederic Boyer
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Aurélie Bonin
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Nelly Colomb-Boeckler
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Bruno Mathieu
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Manon Recour
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Joël Vindret
- sifa syndicat interprofessionnel du fromage abondance, 16 chemin d'Hirmentaz, 74200 Thonon-les-Bains, France
| | - Céline Pignol
- Savoicime, Syndicat Interprofessionnel de la Tomme de Savoie, 10 Allée Jules Vernes, 74150 Rumilly, France
| | - Stéphane Romand
- Syndicat Interprofessionnel du Reblochon, 28 Rue Louis Haase, 74230 Thônes, France
| | - Caroline Petite
- Syndicat Interprofessionnel de la Tome des Bauges, Rue Henri Bouvier, 73630 Le Chatelard, France
| | - Pierre Taberlet
- Université Grenoble Alpes, Université Savoie Mont-Blanc, CNRS, LECA, Laboratoire d'Ecologie Alpine, 38000 Grenoble, France
| | - Cécile Charles
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
| | - Nadège Bel
- ACTALIA, Centre technique d'expertise agroalimentaire, Division d'expertise analytique sur le lait et les produits laitiers, 419 Rte des Champs Laitiers, 74800 Eteaux, France
| | - Agnès Hauwuy
- CERAQ, Centre de ressources pour l'agriculture de qualité et de montagne, 40 Rue du Terraillet, 73190 Saint-Baldoph, France
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Kamarinou CS, Kiousi DE, Repanas P, Argyri AA, Chorianopoulos NG, Galanis A. Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10. Microorganisms 2024; 12:93. [PMID: 38257920 PMCID: PMC10820299 DOI: 10.3390/microorganisms12010093] [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: 12/09/2023] [Revised: 12/30/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products.
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Affiliation(s)
- Christina S. Kamarinou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, 14123 Lycovrissi, Greece;
| | - Despoina E. Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| | - Panagiotis Repanas
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
| | - Anthoula A. Argyri
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization-DIMITRA, 14123 Lycovrissi, Greece;
| | - Nikos G. Chorianopoulos
- Laboratory of Microbiology and Biotechnology of Foods, School of Food and Nutritional Sciences, Department of Food Science and Human Nutrition, Agricultural University of Athens, 11855 Athens, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (C.S.K.); (D.E.K.); (P.R.)
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [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: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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Abdulsalam RA, Ijabadeniyi OA, Cason ED, Sabiu S. Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques. Microorganisms 2023; 11:2337. [PMID: 37764180 PMCID: PMC10534366 DOI: 10.3390/microorganisms11092337] [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: 08/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars' diversity and abundance differences.
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Affiliation(s)
- Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
| | | | - Errol D. Cason
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
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Olmo R, Wetzels SU, Berg G, Cocolin L, Hartmann M, Hugas M, Kostic T, Rattei T, Ruthsatz M, Rybakova D, Sessitsch A, Shortt C, Timmis K, Selberherr E, Wagner M. Food systems microbiome-related educational needs. Microb Biotechnol 2023; 16:1412-1422. [PMID: 37338855 DOI: 10.1111/1751-7915.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 06/21/2023] Open
Abstract
Within the European-funded Coordination and Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), the Workshop 'Education in Food Systems Microbiome Related Sciences: Needs for Universities, Industry and Public Health Systems' brought together over 70 researchers, public health and industry partners from all over the world to work on elaborating microbiome-related educational needs in food systems. This publication provides a summary of discussions held during and after the workshop and the resulting recommendations.
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Affiliation(s)
- Rocío Olmo
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie Urimare Wetzels
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin, Italy
| | - Moritz Hartmann
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Marta Hugas
- European Food Safety Authority (EFSA), EU, Parma, Italy
| | - Tanja Kostic
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Daria Rybakova
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Kenneth Timmis
- Institute of Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Evelyne Selberherr
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Martin Wagner
- FFoQSI GmbH - Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, Tulln, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [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: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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