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Alexa EA, Cobo-Díaz JF, Renes E, O Callaghan TF, Kilcawley K, Mannion D, Skibinska I, Ruiz L, Margolles A, Fernández-Gómez P, Alvarez-Molina A, Puente-Gómez P, Crispie F, López M, Prieto M, Cotter PD, Alvarez-Ordóñez A. The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits. MICROBIOME 2024; 12:78. [PMID: 38678226 PMCID: PMC11055350 DOI: 10.1186/s40168-024-01790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese. RESULTS Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product. CONCLUSION Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.
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Affiliation(s)
- Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Erica Renes
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Tom F O Callaghan
- School of Food and Nutritional Sciences, University College Cork, Cork, T12 Y337, Ireland
| | | | - David Mannion
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
| | | | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011, Oviedo, Asturias, Spain
| | | | | | - Paula Puente-Gómez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co., Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain.
- Institute of Food Science and Technology, Universidad de León, León, Spain.
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Cardin M, Cardazzo B, Coton M, Carraro L, Lucchini R, Novelli E, Coton E, Mounier J. Ecological diversity and associated volatilome of typical mountain Caciotta cheese from Italy. Int J Food Microbiol 2024; 411:110523. [PMID: 38134579 DOI: 10.1016/j.ijfoodmicro.2023.110523] [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: 07/19/2023] [Revised: 11/24/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
Traditional products are particularly appreciated by consumers and among these products, cheese is a major contributor to the Italian mountainous area economics. In this study, shotgun metagenomics and volatilomics were used to understand the biotic and abiotic factors contributing to mountain Caciotta cheese typicity and diversity. Results showed that the origin of cheese played a significant role; however, curd cooking temperature, pH, salt concentration and water activity also had an impact. Viral communities exhibited higher biodiversity and discriminated cheese origins in terms of production farms. Among the most dominant bacteria, Streptococcus thermophilus showed higher intraspecific diversity and closer relationship to production farm when compared to Lactobacillus delbrueckii. However, despite a few cases in which the starter culture was phylogenetically separated from the most dominant strains sequenced in the cheese, starter cultures and dominant cheese strains clustered together suggesting substantial starter colonization in mountain Caciotta cheese. The Caciotta cheese volatilome contained prominent levels of alcohols and ketones, accompanied by lower proportions of terpenes. Volatile profile not only demonstrated a noticeable association with production farm but also significant differences in the relative abundances of enzymes connected to flavor development. Moreover, correlations of different non-homologous isofunctional enzymes highlighted specific contributions to the typical flavor of mountain Caciotta cheese. Overall, this study provides a deeper understanding of the factors shaping typical mountain Caciotta cheese, and the potential of metagenomics for characterizing and potentially authenticating food products.
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Affiliation(s)
- Marco Cardin
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy; Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy.
| | - Monika Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Rosaria Lucchini
- Italian Health Authority and Research Organization for Animal Health and Food Safety (Istituto zooprofilattico sperimentale delle Venezie), Viale Università 10, 35020 Legnaro, PD, Italy
| | - Enrico Novelli
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale Università 16, 35020 Legnaro, PD, Italy
| | - Emmanuel Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
| | - Jérôme Mounier
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
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Thierry A, Madec MN, Chuat V, Bage AS, Picard O, Grondin C, Rué O, Mariadassou M, Marché L, Valence F. Microbial communities of a variety of 75 homemade fermented vegetables. Front Microbiol 2023; 14:1323424. [PMID: 38163080 PMCID: PMC10757351 DOI: 10.3389/fmicb.2023.1323424] [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: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
Fermentation is an ancient practice of food preservation. Fermented vegetables are popular in Eastern European and Asian countries. They have received a growing interest in Western countries, where they are mainly manufactured at domestic and artisanal scales and poorly characterized. Our aim was to investigate the microbial communities and the safety of French homemade fermented vegetables, in the frame of a citizen science project. Fermented vegetables and the data associated with their manufacture were collected from citizens and characterized for pH, NaCl concentration, and microbiology by culturomics and 16S DNA metabarcoding analysis. Lactic acid bacteria (LAB) and yeast isolates were identified by 16S rRNA gene sequencing and D1/D2 domains of the large subunit of the rRNA gene, respectively. The 75 collected samples contained 23 types of vegetables, mainly cabbage, followed by carrots and beets, and many mixtures of vegetables. They were 2 weeks to 4 years old, and their median pH was 3.56, except for two samples with a pH over 4.5. LAB represented the dominant viable bacteria. LAB concentrations ranged from non-detectable values to 8.7 log colony-forming units (CFU)/g and only depended on the age of the samples, with the highest most frequently observed in the youngest samples (<100 days). The 93 LAB isolates identified belonged to 23 species, the two mains being Lactiplantibacillus pentosus/plantarum and Levilactobacillus brevis. The other microbial groups enumerated (total aerobic bacteria, halotolerant bacteria, Gram-negative bacteria, and acetic acid bacteria) generally showed lower concentrations compared to LAB concentrations. No pathogenic bacteria were detected. Viable yeasts were observed in nearly half the samples, at concentrations reaching up to 8.0 log CFU/g. The 33 yeast clones identified belonged to 16 species. Bacterial metabarcoding showed two main orders, namely, Lactobacillales (i.e., LAB, 79% of abundance, 177 of the 398 total ASVs) and Enterobacterales (19% of abundance, 191 ASVs). Fifteen LAB genera were identified, with Lactiplantibacillus and Levilactobacillus as the most abundant, with 41 and 12% of total reads, respectively. Enterobacterales members were mainly represented by Enterobacteriaceae and Yersiniaceae. This study is the first wide description of the microbiota of a large variety of homemade fermented vegetables and documents their safety.
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Affiliation(s)
| | | | | | | | | | - Cécile Grondin
- INRAE, Université de Montpellier, Institut Agro, URM SPO, Montpellier, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France
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Hu X, Liu S, Li E. Microbial community succession and its correlation with the dynamics of flavor compound profiles in naturally fermented stinky sufu. Food Chem 2023; 427:136742. [PMID: 37393638 DOI: 10.1016/j.foodchem.2023.136742] [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: 02/08/2023] [Revised: 06/04/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
Wuhan stinky sufu is a traditional fermented soybean product with a short ripening period and unique flavor. The aim of this study was to explore the characteristic flavor compounds and core functional microbiota of naturally fermented Wuhan stinky sufu. The results indicated that 11 volatile compounds including guaiacol, 2-pentylfuran, dimethyl trisulfide, dimethyl disulfide, acetoin, 1-octen-3-ol, (2E)-2-nonenal, indole, propyl 2-methylbutyrate, ethyl 4-methylvalerate, nonanal were characteristic aroma compounds, and 6 free amino acids (Ser, Lys, Arg, Glu, Met and Pro) were identified as taste-contributing compounds. 4 fungal genera (Kodamaea, unclassified_Dipodascaceae, Geotrichum, Trichosporon), and 9 bacterial genera (Lysinibacillus, Enterococcus, Acidipropionibacterium, Bifidobacterium, Corynebacterium, Lactococcus, Pseudomonas, Enterobacter, and Acinetobacter) were identified as the core functional microbiota with positive effects on the production of flavor compounds. These findings would enhance the understanding of core flavor-producing microorganisms in naturally fermented soybean products and potentially provide guidance for enhancing the quality of sufu.
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Affiliation(s)
- Xuefen Hu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Shaoquan Liu
- Department of Food Science and Technology, National University of Singapore, Science Drive 2, Singapore 117543, Singapore
| | - Erhu Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Key Laboratory of Fruit & Vegetable Processing & Quality Control, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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Bonilla-Luque OM, Possas A, Cabo ML, Rodríguez-López P, Valero A. Tracking microbial quality, safety and environmental contamination sources in artisanal goat cheesemaking factories. Food Microbiol 2023; 114:104301. [PMID: 37290877 DOI: 10.1016/j.fm.2023.104301] [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: 12/15/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023]
Abstract
A harmonised microbiological survey was performed in two artisanal factories of raw goat milk cheeses (A and B) located in the Andalusian region (Spain). A total of 165 different control points or samples (raw materials, final products, food-contact surfaces [FCS], and air) were examined as microbial and pathogen sources of contamination of artisanal goat raw milk cheeses. For raw milk samples analysed from both producers, the concentrations of aerobic-mesophilic bacteria (AMB), total coliforms, coagulase-positive Staphylococcus spp. (CPS), lactic-acid bacteria (LAB) and moulds and yeasts ranged between 3.48 and 8.59, 2.45-5.48, 3.42-4.81, 4.99-8.59 and 3.35-6.85 log cfu/mL respectively. For the same microbial groups, the analysis of raw milk cheeses revealed concentrations ranging from 7.82 to 8.88, 2.00-6.82, 2.00-5.28, 8.11-9.57 and 2.00-5.76 log cfu/g, respectively. Although the raw material analysed from producer A presented higher microbial loads and between-batch variability, it was B the producer with the most loaded final products. Regarding the microbial air quality, the fermentation area, storage room, milk reception and packaging room were the most AMB loaded places, while the ripening chamber was the area with higher fungal loads in bioareosol from both producers. Conveyor belts, cutting machine, storage boxes and brine tank were highlighted as the most contaminated FCS evaluated. Staphylococcus aureus was the only pathogen detected within the set of 51 isolates from samples as revealed by MALDI-TOF and molecular PCR, with a prevalence of 12.5% for samples from the producer B. The public health risk attributed to the consumption of artisanal goat cheese should not be neglected, and may consider the whole cheesemaking processing chain, from microbiological quality of raw milk to the ready-to-eat final product, especially concerning the presence of S. aureus.
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Affiliation(s)
- Olga María Bonilla-Luque
- Department of Food Science and Technology, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), CeiA3, Universidad de Córdoba, Campus Rabanales, 14014, Córdoba, Spain.
| | - Arícia Possas
- Department of Food Science and Technology, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), CeiA3, Universidad de Córdoba, Campus Rabanales, 14014, Córdoba, Spain.
| | - Marta L Cabo
- Laboratory of Microbiology and Technology of Marine Products (MICROTEC), Instituto de Investigacións Mariñas, CSIC, Eduardo Cabello, 6, 36208, Vigo, Spain.
| | - Pedro Rodríguez-López
- Laboratory of Microbiology and Technology of Marine Products (MICROTEC), Instituto de Investigacións Mariñas, CSIC, Eduardo Cabello, 6, 36208, Vigo, Spain; Department of Animal and Food Science, Faculty of Veterinary Medicine, Universitat Autònoma de Barcelona, Travessera Dels Turons S/n, 08193, Bellaterra, Cerdanyola Del Vallès, Spain.
| | - Antonio Valero
- Department of Food Science and Technology, UIC Zoonosis y Enfermedades Emergentes (ENZOEM), CeiA3, Universidad de Córdoba, Campus Rabanales, 14014, Córdoba, Spain.
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Abi Khalil R, Couderc C, Yvon S, Sicard D, Bigey F, Jard G, El Rammouz R, Abi Nakhoul P, Eutamène H, Ayoub MJ, Tormo H. Microbial Dynamics during labneh Ambaris Production in Earthenware Jars. Foods 2023; 12:3131. [PMID: 37628130 PMCID: PMC10453334 DOI: 10.3390/foods12163131] [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: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations already present, are the main factors that shape microbial dynamics in that matrix. This work focused on the study of microbial dynamics during labneh Ambaris production, a traditional Lebanese concentrated fermented goat milk made in jars during 3 months. This was assessed in two earthenware jars at a production facility. DNA metabarcoding of the ITS2 region as well as the V3-V4 region of the 16S rRNA gene was used to characterize the fungal and bacterial communities, respectively. Viable bacterial isolates were also identified by Sanger sequencing of the V1-V4 region of the 16S rRNA gene. Our results showed that the dominant microorganisms identified within labneh Ambaris (Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Lactococcus lactis, Geotrichum candidum, Pichia kudriavzevii and Starmerella sp.) settle early in the product and remain until the end of maturation with varying abundances throughout fermentation. Microbial counts increased during early fermentation stage, and remained stable during mid-fermentation, then declined during maturation. While microbial compositions were globally comparable between the two jars during mid-fermentation and maturation stages, differences between the two jars were mainly detected during early fermentation stage (D0 until D10). No significant sensorial differences were observed between the final products made in the two jars. Neither coliforms nor Enterobacteriaceae were detected in their viable state, starting D7 in both jars, suggesting the antimicrobial properties of the product.
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Affiliation(s)
- Reine Abi Khalil
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon; (R.A.K.); (P.A.N.)
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
| | - Christel Couderc
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
| | - Sophie Yvon
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
- Toxalim, UMR 1331, INRA, INP-ENVT, INP EI-Purpan, Université de Toulouse, F-31027 Toulouse, France
| | - Delphine Sicard
- SPO, INRAE, Institut Agro Montpellier, Université de Montpellier, F-34060 Montpellier, France; (D.S.); (F.B.)
| | - Frédéric Bigey
- SPO, INRAE, Institut Agro Montpellier, Université de Montpellier, F-34060 Montpellier, France; (D.S.); (F.B.)
| | - Gwenaelle Jard
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
| | - Rabih El Rammouz
- Department of Animal production, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon;
| | - Pierre Abi Nakhoul
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon; (R.A.K.); (P.A.N.)
| | - Hélène Eutamène
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
- Toxalim, UMR 1331, INRA, INP-ENVT, INP EI-Purpan, Université de Toulouse, F-31027 Toulouse, France
| | - Marie-José Ayoub
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon; (R.A.K.); (P.A.N.)
| | - Hélène Tormo
- Département des Sciences de l’Agroalimentaire et de la Nutrition, INP EI-Purpan, Université de Toulouse, 75 voie du TOEIC, BP 57611, F-31076 Toulouse, CEDEX 3, France; (C.C.); (S.Y.); (G.J.); (H.E.)
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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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Involvement of Versatile Bacteria Belonging to the Genus Arthrobacter in Milk and Dairy Products. Foods 2023; 12:foods12061270. [PMID: 36981196 PMCID: PMC10048301 DOI: 10.3390/foods12061270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Milk is naturally a rich source of many essential nutrients; therefore, it is quite a suitable medium for bacterial growth and serves as a reservoir for bacterial contamination. The genus Arthrobacter is a food-related bacterial group commonly present as a contaminant in milk and dairy products as primary and secondary microflora. Arthrobacter bacteria frequently demonstrate the nutritional versatility to degrade different compounds even in extreme environments. As a result of their metabolic diversity, Arthrobacter species have long been of interest to scientists for application in various industry and biotechnology sectors. In the dairy industry, strains from the Arthrobacter genus are part of the microflora of raw milk known as an indicator of hygiene quality. Although they cause spoilage, they are also regarded as important strains responsible for producing fermented milk products, especially cheeses. Several Arthrobacter spp. have reported their significance in the development of cheese color and flavor. Furthermore, based on the data obtained from previous studies about its thermostability, and thermoacidophilic and thermoresistant properties, the genus Arthrobacter promisingly provides advantages for use as a potential producer of β-galactosidases to fulfill commercial requirements as its enzymes allow dairy products to be treated under mild conditions. In light of these beneficial aspects derived from Arthrobacter spp. including pigmentation, flavor formation, and enzyme production, this bacterial genus is potentially important for the dairy industry.
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De Respinis S, Caminada A, Pianta E, Buetti-Dinh A, Riva Scettrini P, Petrini L, Tonolla M, Petrini O. Fungal communities on alpine cheese rinds in Southern Switzerland. BOTANICAL STUDIES 2023; 64:6. [PMID: 36905471 PMCID: PMC10008522 DOI: 10.1186/s40529-023-00371-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The biodiversity of the mycobiota of soft cheese rinds such as Brie or Camembert has been extensively studied, but scant information is available on the fungi colonizing the rinds of cheese produced in the Southern Switzerland Alps. This study aimed at exploring the fungal communities present on rinds of cheese matured in five cellars in Southern Switzerland and to evaluate their composition with regards to temperature, relative humidity, type of cheese, as well as microenvironmental and geographic factors. We used macro- and microscopical morphology, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, and sequencing to characterize the fungal communities of the cheeses, and compared them with metabarcoding targeting the ITS region. RESULTS Isolation by serial dilution yielded 201 isolates (39 yeasts and 162 filamentous fungi) belonging to 9 fungal species. Mucor and Penicillium were dominant, with Mucor racemosus, M. lanceolatus, P. biforme, and P. chrysogenum/rubens being the most frequent species. All but two yeast isolates were identified as Debaryomyces hansenii. Metabarcoding detected 80 fungal species. Culture work and metabarcoding produced comparable results in terms of similarity of the fungal cheese rind communities in the five cellars. CONCLUSIONS Our study has shown that the mycobiota on the rinds of the cheeses studied is a comparatively species-poor community influenced by temperature, relative humidity, type of cheese, and manufacturing steps, as well as microenvironmental and possibly geographic factors.
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Affiliation(s)
- Sophie De Respinis
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - AnnaPaola Caminada
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Elisa Pianta
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Antoine Buetti-Dinh
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Patrizia Riva Scettrini
- Agriculture Advisory Service, Republic and Canton of Ticino, Viale Stefano Franscini 17, 6501, Bellinzona, Switzerland
| | | | - Mauro Tonolla
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland
| | - Orlando Petrini
- Institute of Microbiology , University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Via Mirasole 22A, 6500, Bellinzona, Switzerland.
- POLE Pharma Consulting, Via Al Perato 15C, 6932, Breganzona, Switzerland.
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10
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Savary O, Coton E, Maillard MB, Gaucheron F, Le Meur C, Frisvad J, Thierry A, Jany JL, Coton M. Functional diversity of Bisifusarium domesticum and the newly described Nectriaceae cheese-associated species. Food Res Int 2023; 168:112691. [PMID: 37120186 DOI: 10.1016/j.foodres.2023.112691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023]
Abstract
Bisifusarium domesticum is among the main molds used during cheese-making for its "anticollanti" property that prevents the sticky smear defect of some cheeses. Previously, numerous cheese rinds were sampled to create a working collection and not only did we isolate B. domesticum but we observed a completely unexpected diversity of "Fusarium-like" fungi belonging to the Nectriaceae family. Four novel cheese-associated species belonging to two genera were described: Bisifusarium allantoides, Bisifusarium penicilloides, Longinectria lagenoides, and Longinectria verticilliformis. In this study, we thus aimed at determining their potential functional impact during cheese-making by evaluating their lipolytic and proteolytic activities as well as their capacity to produce volatile (HS-Trap GC-MS) and non-volatile secondary metabolites (HPLC & LC-Q-TOF). While all isolates were proteolytic and lipolytic, higher activities were observed at 12 °C for several B. domesticum, B. penicilloides and L. lagenoides isolates, which is in agreement with typical cheese ripening conditions. Using volatilomics, we identified multiple cheese-related compounds, especially ketones and alcohols. B. domesticum and B. penicilloides isolates showed higher aromatic potential although compounds of interest were also produced by B. allantoides and L. lagenoides. These species were also lipid producers. Finally, an untargeted extrolite analysis suggested a safety status of these strains as no known mycotoxins were produced and revealed the production of potential novel secondary metabolites. Biopreservation tests performed with B. domesticum suggested that it may be an interesting candidate for biopreservation applications in the cheese industry in the future.
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11
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Proteomics as a New-Generation Tool for Studying Moulds Related to Food Safety and Quality. Int J Mol Sci 2023; 24:ijms24054709. [PMID: 36902140 PMCID: PMC10003330 DOI: 10.3390/ijms24054709] [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: 01/31/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Mould development in foodstuffs is linked to both spoilage and the production of mycotoxins, provoking food quality and food safety concerns, respectively. The high-throughput technology proteomics applied to foodborne moulds is of great interest to address such issues. This review presents proteomics approaches useful for boosting strategies to minimise the mould spoilage and the hazard related to mycotoxins in food. Metaproteomics seems to be the most effective method for mould identification despite the current problems related to the bioinformatics tool. More interestingly, different high resolution mass spectrometry tools are suitable for evaluating the proteome of foodborne moulds able to unveil the mould's response under certain environmental conditions and the presence of biocontrol agents or antifungals, being sometimes combined with a method with limited ability to separate proteins, the two-dimensional gel electrophoresis. However, the matrix complexity, the high ranges of protein concentrations needed and the performing of multiple steps are some of the proteomics limitations for the application to foodborne moulds. To overcome some of these limitations, model systems have been developed and proteomics applied to other scientific fields, such as library-free data independent acquisition analyses, the implementation of ion mobility, and the evaluation of post-translational modifications, are expected to be gradually implemented in this field for avoiding undesirable moulds in foodstuffs.
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12
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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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13
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Nelli A, Venardou B, Skoufos I, Voidarou C(C, Lagkouvardos I, Tzora A. An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota. Microorganisms 2023; 11:microorganisms11010123. [PMID: 36677415 PMCID: PMC9863150 DOI: 10.3390/microorganisms11010123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes’ authenticity and cheese quality.
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Abi Khalil R, Couderc C, Yvon S, Jard G, Sicard D, Bigey F, El Rammouz R, Abi Nakhoul P, Eutamène H, Tormo H, Ayoub MJ. Artisanal Household Milk Pasteurization Is Not a Determining Factor in Structuring the Microbial Communities of Labneh Ambaris: A Pilot Study. Foods 2022; 11:foods11233874. [PMID: 36496682 PMCID: PMC9740543 DOI: 10.3390/foods11233874] [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: 09/08/2022] [Revised: 11/10/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Labneh Ambaris is a traditional Lebanese dairy product traditionally made using raw goat's milk in earthenware jars, but recently the use of artisanally pasteurized milk was introduced for safety reasons. In this study, 12 samples of labneh Ambaris were studied, six made using raw goat's milk and six others using artisanally pasteurized goat's milk. These samples were collected during fermentation and their microbial compositions were analyzed. The 16S V3-V4 and the ITS2 regions of the rDNA were sequenced by DNA metabarcoding analyses for the identification and comparison of bacterial and fungal communities, respectively. The samples had high microbial diversity but differences in samples microbiota were unrelated to whether or not milk was pasteurized. The samples were consequently clustered on the basis of their dominant bacterial or fungal species, regardless of the milk used. Concerning bacterial communities, samples were clustered into 3 groups, one with a higher abundance of Lactobacillus helveticus, another with Lactobacillus kefiranofaciens as the dominant bacterial species, and the third with Lentilactobacillus sp. as the most abundant species. Species belonging to the Enterobacteriaceae family were detected in higher abundance in all raw milk samples than in artisanally pasteurized milk samples. As for fungal communities, the samples were clustered into two groups, one dominated by Geotrichum candidum and the other by Pichia kudriavzevii.
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Affiliation(s)
- Reine Abi Khalil
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Christel Couderc
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Sophie Yvon
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
- Toxalim, UMR 1331, INRA, INP-ENVT, INP-PURPAN, Université de Toulouse, 31027 Toulouse, France
| | - Gwenaelle Jard
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
| | - Delphine Sicard
- INRAE, Institute Agro Montpellier, SPO, University Montpellier, 34060 Montpellier, France
| | - Frédéric Bigey
- INRAE, Institute Agro Montpellier, SPO, University Montpellier, 34060 Montpellier, France
| | - Rabih El Rammouz
- Department of Animal Production, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
| | - Pierre Abi Nakhoul
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
| | - Hélène Eutamène
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
- Toxalim, UMR 1331, INRA, INP-ENVT, INP-PURPAN, Université de Toulouse, 31027 Toulouse, France
| | - Hélène Tormo
- Département Sciences de l’agroalimentaire et de la Nutrition, Université de Toulouse, INP EI-Purpan, 75 voie du TOEIC, BP 57611, CEDEX 3, F-31076 Toulouse, France
- Correspondence: (H.T.); (M.-J.A.)
| | - Marie-José Ayoub
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon
- Correspondence: (H.T.); (M.-J.A.)
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15
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Paillet T, Lossouarn J, Figueroa C, Midoux C, Rué O, Petit MA, Dugat-Bony E. Virulent Phages Isolated from a Smear-Ripened Cheese Are Also Detected in Reservoirs of the Cheese Factory. Viruses 2022; 14:v14081620. [PMID: 35893685 PMCID: PMC9331655 DOI: 10.3390/v14081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Smear-ripened cheeses host complex microbial communities that play a crucial role in the ripening process. Although bacteriophages have been frequently isolated from dairy products, their diversity and ecological role in such this type of cheese remain underexplored. In order to fill this gap, the main objective of this study was to isolate and characterize bacteriophages from the rind of a smear-ripened cheese. Thus, viral particles extracted from the cheese rind were tested through a spot assay against a collection of bacteria isolated from the same cheese and identified by sequencing the full-length small subunit ribosomal RNA gene. In total, five virulent bacteriophages infecting Brevibacterium aurantiacum, Glutamicibacter arilaitensis, Leuconostoc falkenbergense and Psychrobacter aquimaris species were obtained. All exhibit a narrow host range, being only able to infect a few cheese-rind isolates within the same species. The complete genome of each phage was sequenced using both Nanopore and Illumina technologies, assembled and annotated. A sequence comparison with known phages revealed that four of them may represent at least new genera. The distribution of the five virulent phages into the dairy-plant environment was also investigated by PCR, and three potential reservoirs were identified. This work provides new knowledge on the cheese rind viral community and an overview of the distribution of phages within a cheese factory.
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Affiliation(s)
- Thomas Paillet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France; (J.L.); (M.-A.P.)
| | - Clarisse Figueroa
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
| | - Cédric Midoux
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350 Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, PROSE, 92761 Antony, France
| | - Olivier Rué
- Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France; (C.M.); (O.R.)
- Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, 78350 Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352 Jouy-en-Josas, France; (J.L.); (M.-A.P.)
| | - Eric Dugat-Bony
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 91120 Palaiseau, France; (T.P.); (C.F.)
- Correspondence:
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16
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Understanding of microbial diversity in three representative Qu in China and characterization of the volatile compounds in the corresponding Chinese rice wine. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Boussekine R, Bekhouche F, Debaets S, Thierry A, Maillard MB, Falentin H, Pawtowski A, Barkat M, Coton M, Mounier J. Deciphering the Microbiota and Volatile Profiles of Algerian Smen, a Traditional Fermented Butter. Microorganisms 2022; 10:microorganisms10040736. [PMID: 35456786 PMCID: PMC9028027 DOI: 10.3390/microorganisms10040736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 12/04/2022] Open
Abstract
In Algeria, Smen is a fermented butter produced in households using empirical methods. Smen fermentation is driven by autochthonous microorganisms; it improves butter shelf-life and yields highly fragrant products used as ingredients in traditional dishes as well as in traditional medicine. The present study is aimed at investigating microbial diversity and dynamics during Algerian Smen fermentation using both culture-dependent and culture-independent approaches, as well as by monitoring volatile organic compound production. To reach this goal, fifteen Smen samples (final products) produced in households from different regions in Algeria were collected and analyzed. In addition, microbial and volatile compound dynamics at the different stages of Smen manufacturing were investigated for one Smen preparation. The results showed that Smen is a microbiologically safe product, as all hygiene and safety criteria were respected. The dominant microorganisms identified by both techniques were LAB and yeasts. Lactococcus spp. and Streptococcus thermophilus were the main bacterial species involved in spontaneous raw milk fermentation preceding butter-making, while lactobacilli and enterococci were the only bacteria found to be viable during Smen maturation. Regarding fungal diversity, yeast species were only recovered from two mature Smen samples by culturing, while different species (e.g., Geotrichum candidum, Moniliella sp.) were identified in all samples by the culture-independent approach. Using microbial analysis of a single batch, many of these were found viable during manufacturing. Concerning the volatile profiles, they were highly diverse and characterized by a high prevalence of short chain fatty acids, methylketones, and esters. Correlation analysis between microbial diversity and volatile profiles showed that several yeast (Moniliella sp., K. marxianus) and LAB (e.g., Lactococcus spp., S. thermophilus) species were strongly correlated with one or more volatile organic compound families, including several ethyl esters and methyl ketones that can be linked to pleasant, sweetly floral, fruity, buttery, and creamy odors. This study clearly identified key microorganisms involved in Smen fermentation and maturation that could be used in the future for better fermentation control and improvement of quality attributes.
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Affiliation(s)
- Rania Boussekine
- Laboratoire de Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro-Alimentaires (INATAA), Université Frères Mentouri Constantine 1, Route de Ain-El-Bey, Constantine 25000, Algeria; (R.B.); (F.B.); (M.B.)
| | - Farida Bekhouche
- Laboratoire de Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro-Alimentaires (INATAA), Université Frères Mentouri Constantine 1, Route de Ain-El-Bey, Constantine 25000, Algeria; (R.B.); (F.B.); (M.B.)
| | - Stella Debaets
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, Univ Brest, F-29280 Plouzané, France; (S.D.); (A.P.); (M.C.)
| | - Anne Thierry
- STLO, Institut Agro, INRAE, F-35000 Rennes, France; (A.T.); (M.-B.M.); (H.F.)
| | | | - Hélène Falentin
- STLO, Institut Agro, INRAE, F-35000 Rennes, France; (A.T.); (M.-B.M.); (H.F.)
| | - Audrey Pawtowski
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, Univ Brest, F-29280 Plouzané, France; (S.D.); (A.P.); (M.C.)
| | - Malika Barkat
- Laboratoire de Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro-Alimentaires (INATAA), Université Frères Mentouri Constantine 1, Route de Ain-El-Bey, Constantine 25000, Algeria; (R.B.); (F.B.); (M.B.)
| | - Monika Coton
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, Univ Brest, F-29280 Plouzané, France; (S.D.); (A.P.); (M.C.)
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, Univ Brest, F-29280 Plouzané, France; (S.D.); (A.P.); (M.C.)
- Correspondence: ; Tel.: +33-(0)2-90-91-51-21
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18
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Frétin M, Gérard A, Ferlay A, Martin B, Buchin S, Theil S, Rifa E, Loux V, Rué O, Chassard C, Delbès C. Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition on Cantal-Type Cheese Microbiota. Microorganisms 2022; 10:microorganisms10020334. [PMID: 35208788 PMCID: PMC8879305 DOI: 10.3390/microorganisms10020334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 02/05/2023] Open
Abstract
A previous study identified differences in rind aspects between Cantal-type cheeses manufactured from the same skimmed milk, supplemented with cream derived either from pasture-raised cows (P) or from cows fed with maize silage (M). Using an integrated analysis of multiomic data, the present study aimed at investigating potential correlations between cream origin and metagenomic, lipidomic and volatolomic profiles of these Cantal cheeses. Fungal and bacterial communities of cheese cores and rinds were characterized using DNA metabarcoding at different ripening times. Lipidome and volatolome were obtained from the previous study at the end of ripening. Rind microbial communities, especially fungal communities, were influenced by cream origin. Among bacteria, Brachybacterium were more abundant in P-derived cheeses than in M-derived cheeses after 90 and 150 days of ripening. Sporendonema casei, a yeast added as a ripening starter during Cantal manufacture, which contributes to rind typical aspect, had a lower relative abundance in P-derived cheeses after 150 days of ripening. Relative abundance of this fungus was highly negatively correlated with concentrations of C18 polyunsaturated fatty acids and to concentrations of particular volatile organic compounds, including 1-pentanol and 3-methyl-2-pentanol. Overall, these results evidenced original interactions between milk fat composition and the development of fungal communities in cheeses.
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Affiliation(s)
- Marie Frétin
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
| | - Amaury Gérard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
- Laboratory of Quality and Safety of Agrofood Products, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, 5030 Gembloux, Belgium
| | - Anne Ferlay
- UMR 1213 Herbivores, Université Clermont Auvergne, INRAE, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (A.F.); (B.M.)
| | - Bruno Martin
- UMR 1213 Herbivores, Université Clermont Auvergne, INRAE, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (A.F.); (B.M.)
| | | | - Sébastien Theil
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
| | - Etienne Rifa
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, F-31077 Toulouse, France;
- Plateforme Genome et Transcriptome (GeT), Genopole Toulouse, F-31077 Toulouse, France
| | - Valentin Loux
- MIGALE Bioinformatics Facility, Université Paris-Saclay, INRAE, BioinfOmics, F-78350 Jouy-en-Josas, France; (O.R.); (V.L.)
- MaIAGE, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France
| | - Olivier Rué
- MIGALE Bioinformatics Facility, Université Paris-Saclay, INRAE, BioinfOmics, F-78350 Jouy-en-Josas, France; (O.R.); (V.L.)
- MaIAGE, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France
| | - Christophe Chassard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
| | - Céline Delbès
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (M.F.); (A.G.); (S.T.); (C.C.)
- Correspondence:
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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20
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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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21
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Sabater C, Cobo-Díaz JF, Álvarez-Ordóñez A, Ruas-Madiedo P, Ruiz L, Margolles A. Novel methods of microbiome analysis in the food industry. Int Microbiol 2021; 24:593-605. [PMID: 34686940 DOI: 10.1007/s10123-021-00215-8] [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: 06/10/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.
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Affiliation(s)
- Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, 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), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain. .,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain.
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.,Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
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22
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Zago M, Rossetti L, Bardelli T, Carminati D, Nazzicari N, Giraffa G. Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences. Foods 2021; 10:1826. [PMID: 34441603 PMCID: PMC8392751 DOI: 10.3390/foods10081826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
The microbiota of Protected Designation of Origin (PDO) cheeses plays an essential role in defining their quality and typicity and could be applied to protect these products from counterfeiting. To study the possible role of cheese microbiota in distinguishing Grana Padano (GP) cheese from generical hard cheeses (HC), the microbial structure of 119 GP cheese samples was studied by DNA metabarcoding and DNA metafingerprinting and compared with 49 samples of generical hard cheeses taken from retail. DNA metabarcoding highlighted the presence, as dominant taxa, of Lacticaseibacillus rhamnosus, Lactobacillus helveticus, Streptococcus thermophilus, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus spp., and Lactococcus spp. in both GP cheese and HC. Differential multivariate statistical analysis of metataxonomic and metafingerprinting data highlighted significant differences in the Shannon index, bacterial composition, and species abundance within both dominant and subdominant taxa between the two cheese groups. A supervised Neural Network (NN) classification tool, trained by metagenotypic data, was implemented, allowing to correctly classify GP cheese and HC samples. Further implementation and validation to increase the robustness and improve the predictive capacity of the NN classifier will be needed. Nonetheless, the proposed tool opens interesting perspectives in helping protection and valorization of GP and other PDO cheeses.
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Affiliation(s)
- Miriam Zago
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Lia Rossetti
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Tommaso Bardelli
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 26900 Lodi, Italy;
| | - Domenico Carminati
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
| | - Giorgio Giraffa
- Research Centre for Animal Production and Aquaculture (CREA-ZA), Council for Agricultural Research and Economics, 26900 Lodi, Italy; (M.Z.); (L.R.); (D.C.); (N.N.)
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23
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Del Matto I, Rossi F, Iannitto G, Petrone D, Mastrodomenico MT, Alessiani A, Sacchini L, Amadoro C, Tucci P, Marino L. Variability of the microbiota in traditional Caciocavallo, Scamorza and Caciotta cheeses manufactured with raw milk and natural cultures. INT J DAIRY TECHNOL 2021. [DOI: 10.1111/1471-0307.12787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Ilaria Del Matto
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
| | - Franca Rossi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
| | - Giorgio Iannitto
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
| | - Domenico Petrone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
| | - Maria Teresa Mastrodomenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
| | - Alessandra Alessiani
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoReparto di BatteriologiaCampo Boario Teramo64100Italy
| | - Lorena Sacchini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoReparto di BatteriologiaCampo Boario Teramo64100Italy
| | - Carmela Amadoro
- Dipartimento di Medicina e Scienze della Salute ‘V. Tiberio’ Università degli Studi del Molise Via De Sanctis 1 Campobasso86100Italy
| | - Patrizia Tucci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
| | - Lucio Marino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise (IZSAM) TeramoSezione di CampobassoVia Garibaldi 155 Campobasso86100Italy
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