1
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Khalifa ME, MacDiarmid RM. Molecular Characterization of Two Totiviruses from the Commensal Yeast Geotrichum candidum. Viruses 2023; 15:2150. [PMID: 38005831 PMCID: PMC10674808 DOI: 10.3390/v15112150] [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: 09/13/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Mycoviruses can infect many of the major taxa of fungi including yeasts. Mycoviruses in the yeast fungus Geotrichum candidum are not well studied with only three G. candidum-associated viral species characterized to date, all of which belong to the Totiviridae genus Totivirus. In this study, we report the molecular characteristics of another two totiviruses co-infecting isolate Gc6 of G. candidum. The two totiviruses were tentatively named Geotrichum candidum totivirus 2 isolate Gc6 (GcTV2-Gc6) and Geotrichum candidum totivirus 4 isolate Gc6 (GcTV4-Gc6). Both viruses have the typical genome organization of totiviruses comprising two ORFs encoding capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) at the N and C termini, respectively. The genomes of GcTV2-Gc6 and GcTV4-Gc6 are 4592 and 4530 bp long, respectively. Both viruses contain the-frameshifting elements and their proteins could be expressed as a single fusion protein. GcTV2-Gc6 is closely related to a totivirus isolated from the same host whereas GcTV4-Gc6 is related to insect-associated totiviruses. The phylogenetic analysis indicated that GcTV2-Gc6 and GcTV4-Gc6 belong to two different sister clades, I-A and I-B, respectively. It is interesting that all viruses identified from G. candidum belong to the genus Totivirus; however, this might be due to the lack of research reporting the characterization of mycoviruses from this fungal host. It is possible that the RNA interference (RNAi) mechanism cannot actively suppress totivirus accumulation in G. candidum Gc6.
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Affiliation(s)
- Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta 34517, Egypt;
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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2
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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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3
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Szudera-Kończal K, Myszka K, Kubiak P, Drabińska N, Majcher MA. The Combined Effect of Lactic Acid Bacteria and Galactomyces geotrichum Fermentation on the Aroma Composition of Sour Whey. Molecules 2023; 28:molecules28114308. [PMID: 37298782 DOI: 10.3390/molecules28114308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
The increase in demand for food flavorings due to the shortening and simplification of food production technology also entails an increase in the demand for new technologies for their production. The biotechnological production of aromas is a solution characterized by a high efficiency, an independence from environmental factors and a relatively low cost. In this study, the influence of the implementation of lactic acid bacteria pre-fermentation into the production of aroma compounds by Galactomyces geotrichum on a sour whey medium on the intensity of the obtained aroma composition was analyzed. The monitoring of the culture in terms of biomass buildup, the concentration of selected compounds, and the pH resulted in the confirmation of interactions between the analyzed microorganisms. The post-fermentation product underwent a comprehensive sensomic analysis for the identification and quantification of the aroma-active compounds. The use of gas chromatography-olfactometry (GC-O) analysis and the calculation of odor activity values (OAVs) allowed 12 key odorants to be identified in the post-fermentation product. The highest OAV was found for phenylacetaldehyde with a honey odor (1815). The following compounds with the highest OAVs were 2,3-butanedione with a buttery aroma (233), phenylacetic acid with a honey aroma (197), 2,3-butanediol with a buttery aroma (103), 2-phenylethanol with a rosy aroma (39), ethyl octanoate with a fruity aroma (15), and ethyl hexanoate with a fruity aroma (14).
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Affiliation(s)
- Kamila Szudera-Kończal
- Faculty of Food Science and Nutrition, Poznań University of Life Sciences, 60-624 Poznań, Poland
| | - Kamila Myszka
- Faculty of Food Science and Nutrition, Poznań University of Life Sciences, 60-624 Poznań, Poland
| | - Piotr Kubiak
- Faculty of Food Science and Nutrition, Poznań University of Life Sciences, 60-624 Poznań, Poland
| | - Natalia Drabińska
- Faculty of Food Science and Nutrition, Poznań University of Life Sciences, 60-624 Poznań, Poland
| | - Małgorzata Anna Majcher
- Faculty of Food Science and Nutrition, Poznań University of Life Sciences, 60-624 Poznań, Poland
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4
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Abi Khalil R, Yvon S, Couderc C, Belahcen L, Jard G, Sicard D, Bigey F, El Rammouz R, Abi Nakhoul P, Eutamène H, Tormo H, Ayoub MJ. Microbial communities and main features of labneh Ambaris, a traditional Lebanese fermented goat milk product. J Dairy Sci 2023; 106:868-883. [PMID: 36543637 DOI: 10.3168/jds.2022-22275] [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: 05/05/2022] [Accepted: 09/04/2022] [Indexed: 12/24/2022]
Abstract
Labneh Ambaris is a traditional Lebanese dairy product typically made using goat milk in special earthenware jars. Its production is characterized by the regular additions of milk and coarse salt, all while draining the whey throughout a process that lasts for a minimum of 2 mo. In this study, 20 samples of labneh Ambaris, all produced by spontaneous fermentation, were studied. They were collected at the end of fermentation from different regions in Lebanon. Physicochemical and sensory properties were studied and microbial diversity was analyzed using culture-dependent and independent techniques. The V3-V4 region of the 16S rRNA gene and the ITS2 region were sequenced by DNA metabarcoding analyses for the identification of bacteria and yeast communities, respectively. Out of 160 bacterial and 36 fungal taxa, 117 different bacterial species and 24 fungal species were identified among all labneh Ambaris samples studied. The remaining ones were multi-affiliated and could not be identified at the species level. Lactobacillus was the dominant bacterial genus, followed by Lentilactobacillus, Lactiplantibacillus, Lacticaseibacillus, and Lactococcus genera, whereas Geotrichum and Pichia were the dominant fungal genera. The 20 samples tested had varying levels of salt, protein, and fat contents, but they were all highly acidic (mostly having a pH < 4). According to the sensory scores generated by classical descriptive analysis, all samples were described as having basic similar characteristics such as goat smell and flavor, but they could be differentiated based on various intensities within the same descriptors like salty and acidic. This work could be considered as a base toward obtaining a quality label for labneh Ambaris.
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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; Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France
| | - Sophie Yvon
- Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France; Toxalim UMR 1331, INRA, INP-ENVT, INP-PURPAN, Université de Toulouse, Toulouse, 31027 Toulouse, France
| | - Christel Couderc
- Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France
| | - Loubnah Belahcen
- Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France
| | - Gwenaelle Jard
- Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France
| | - Delphine Sicard
- SPO, Univ. Montpellier, INRAE, Institut Agro Montpellier, 34060 Montpellier, France
| | - Frédéric Bigey
- SPO, Univ. Montpellier, INRAE, Institut Agro 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
- Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France; Toxalim UMR 1331, INRA, INP-ENVT, INP-PURPAN, Université de Toulouse, Toulouse, 31027 Toulouse, France
| | - Hélène Tormo
- Departement Sciences de l'Agroalimentaire et de la Nutrition INP-EI Purpan, Université de Toulouse; 75, voie du TOEC, BP 57611, F-31076 Toulouse, Cedex 3, France.
| | - Marie-José Ayoub
- Department of Food Sciences and Technologies, Faculty of Agricultural and Veterinary Sciences, Lebanese University, Beirut 14-6573, Lebanon.
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5
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Morin MA, Morrison AJ, Harms MJ, Dutton RJ. Higher-order interactions shape microbial interactions as microbial community complexity increases. Sci Rep 2022; 12:22640. [PMID: 36587027 PMCID: PMC9805437 DOI: 10.1038/s41598-022-25303-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/28/2022] [Indexed: 01/01/2023] Open
Abstract
Non-pairwise interactions, or higher-order interactions (HOIs), in microbial communities have been described as significant drivers of emergent features in microbiomes. Yet, the re-organization of microbial interactions between pairwise cultures and larger communities remains largely unexplored from a molecular perspective but is central to our understanding and further manipulation of microbial communities. Here, we used a bottom-up approach to investigate microbial interaction mechanisms from pairwise cultures up to 4-species communities from a simple microbiome (Hafnia alvei, Geotrichum candidum, Pencillium camemberti and Escherichia coli). Specifically, we characterized the interaction landscape for each species combination involving E. coli by identifying E. coli's interaction-associated mutants using an RB-TnSeq-based interaction assay. We observed a deep reorganization of the interaction-associated mutants, with very few 2-species interactions conserved all the way up to a 4-species community and the emergence of multiple HOIs. We further used a quantitative genetics strategy to decipher how 2-species interactions were quantitatively conserved in higher community compositions. Epistasis-based analysis revealed that, of the interactions that are conserved at all levels of complexity, 82% follow an additive pattern. Altogether, we demonstrate the complex architecture of microbial interactions even within a simple microbiome, and provide a mechanistic and molecular explanation of HOIs.
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Affiliation(s)
- Manon A. Morin
- grid.266100.30000 0001 2107 4242School of Biological Science, University of California San Diego, San Diego, 92093 USA
| | - Anneliese J. Morrison
- grid.170202.60000 0004 1936 8008Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR USA ,grid.170202.60000 0004 1936 8008Institute of Molecular Biology, University of Oregon, Eugene, OR USA
| | - Michael J. Harms
- grid.170202.60000 0004 1936 8008Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR USA ,grid.170202.60000 0004 1936 8008Institute of Molecular Biology, University of Oregon, Eugene, OR USA
| | - Rachel J. Dutton
- grid.266100.30000 0001 2107 4242School of Biological Science, University of California San Diego, San Diego, 92093 USA
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Purification, De Novo Characterization and Antibacterial Properties of a Novel, Narrow-Spectrum Bacteriostatic Tripeptide from Geotrichum candidum OMON-1. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-020-05024-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Koňuchová M, Valík Ľ. Modelling the Radial Growth of Geotrichum candidum: Effects of Temperature and Water Activity. Microorganisms 2021; 9:532. [PMID: 33807629 PMCID: PMC7999232 DOI: 10.3390/microorganisms9030532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
Modelling the growth of microorganisms in relation to environmental factors provides quantitative knowledge that can be used to predict their behaviour in foods. For this reason, the effects of temperature and water activity (aw) adjusted with NaCl on the surface growth of two isolates and one culture strain of Geotrichum candidum were studied. A dataset of growth parameters obtained from almost 600 growth curves was employed for secondary modelling with cardinal models (CMs). The theoretical minimal temperature resulting from the modelling of the mycelium proliferation rate ranged from -5.2 to -0.4 °C. Optimal and maximal temperatures were calculated and found to have narrow ranges of 25.4 to 28.0 °C and 34.2 to 37.6 °C, respectively. Cardinal aw values associated with radial growth (awmin from 0.948-0.960 and awopt from 0.992-0.993) confirmed the salt sensitivity of the species. Model goodness-of-fit was evaluated by the coefficient of determination R2, which ranged from 0.954 to 0.985, and RMSE, which ranged from 0.28 to 0.42. Substantially higher variability accompanied the lag time for growth modelling than the radial growth rate modelling despite the square root transformation of the reciprocal lag phase data (R2 = 0.685 to 0.808). Nevertheless, the findings demonstrate that the outputs of growth modelling can be applied to the quantitative evaluation of the roles of G. candidum in fresh cheese spoilage as well as the ripening of Camembert-type cheeses or various artisanal cheeses. Along with validation, the interactions with lactic acid bacteria can be included to improve the predictions of G. candidum in the future.
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Affiliation(s)
- Martina Koňuchová
- Department of Nutrition and Food Quality Assessment, Institute of Food Science and Nutrition, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinskeho 9, SK-812 37 Bratislava, Slovakia;
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8
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Li Y, Zhang X, Yang J, Ma X, Jia X, Du P, Li A. Influence of the addition of
Geotrichum candidum
on the microbial, chemical, textural, and sensory features of soft soy cheese. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ying Li
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
| | - Xin Zhang
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
| | - Jia‐Jie Yang
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
| | - Xiang‐Yang Ma
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
| | - Xin‐Dong Jia
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
| | - Peng Du
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
| | - Ai‐li Li
- Key Laboratory of Dairy Science, Ministry of Education Food College, Northeast Agriculture University Harbin China
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9
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Łopusiewicz Ł, Drozłowska E, Tarnowiecka-Kuca A, Bartkowiak A, Mazurkiewicz-Zapałowicz K, Salachna P. Biotransformation of Flaxseed Oil Cake into Bioactive Camembert-Analogue Using Lactic Acid Bacteria, Penicillium camemberti and Geotrichum candidum. Microorganisms 2020; 8:E1266. [PMID: 32825460 PMCID: PMC7565573 DOI: 10.3390/microorganisms8091266] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022] Open
Abstract
This study aimed at investigating the antioxidant activity, oxidative stability, physicochemical and microbial changes of innovative vegan Camembert-analogue based on flaxseed oil cake (FOC) which was produced using lactic acid bacteria (LAB), mold Penicillium camemberti (PC) and yeast Geotrichum candidum (GC). Two variants were prepared, namely with LAB + PC and LAB + PC + GC. After fermentation for 24 h at room temperature, the samples were stored for 14 days at 12 °C and maturated for 14 days at 6 °C. Changes in microbial population, polyphenolics, flavonoids, radical scavenging capacity were evaluated. Additionally, textural changes, pH, acidity, levels of proteins, free amino acids, reducing sugars, oil content and its oxidative stability were determined. Results showed that LAB as well as fungi were capable of growing well in the FOC without any supplementation and the products were characterized by a high antioxidant potential (high polyphenolics and flavonoids contents as well as 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), superoxide (O2-) and hydroxyl (·OH) radicals scavenging activity). This study has demonstrated that bioactivity as well as the physicochemical properties depend on the starter culture used. Due to functional and biochemical characteristics conferred to the obtained Camembert-analogues, the use of P. camemberti and G. candidum showed a potential for industrial application. There is a potential for these products to be used where non-dairy alternatives are desired.
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Affiliation(s)
- Łukasz Łopusiewicz
- Center of Bioimmobilisation and Innovative Packaging Materials, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology in Szczecin, Janickiego, 35, 71-270 Szczecin, Poland; (E.D.); (A.T.-K.); (A.B.)
| | - Emilia Drozłowska
- Center of Bioimmobilisation and Innovative Packaging Materials, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology in Szczecin, Janickiego, 35, 71-270 Szczecin, Poland; (E.D.); (A.T.-K.); (A.B.)
| | - Alicja Tarnowiecka-Kuca
- Center of Bioimmobilisation and Innovative Packaging Materials, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology in Szczecin, Janickiego, 35, 71-270 Szczecin, Poland; (E.D.); (A.T.-K.); (A.B.)
| | - Artur Bartkowiak
- Center of Bioimmobilisation and Innovative Packaging Materials, Faculty of Food Sciences and Fisheries, West Pomeranian University of Technology in Szczecin, Janickiego, 35, 71-270 Szczecin, Poland; (E.D.); (A.T.-K.); (A.B.)
| | - Kinga Mazurkiewicz-Zapałowicz
- Department of Hydrobiology, Ichthyology and Biotechnology of Reproduction, West Pomeranian University of Technology in Szczecin, Kazimierza Królewicza, 4, 71-899 Szczecin, Poland;
| | - Piotr Salachna
- Department of Horticulture, West Pomeranian University of Technology in Szczecin, Papieża Pawła, VI 3, 71-459 Szczecin, Poland;
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10
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Perkins V, Vignola S, Lessard MH, Plante PL, Corbeil J, Dugat-Bony E, Frenette M, Labrie S. Phenotypic and Genetic Characterization of the Cheese Ripening Yeast Geotrichum candidum. Front Microbiol 2020; 11:737. [PMID: 32457706 PMCID: PMC7220993 DOI: 10.3389/fmicb.2020.00737] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/30/2020] [Indexed: 01/04/2023] Open
Abstract
The yeast Geotrichum candidum (teleomorph Galactomyces candidus) is inoculated onto mold- and smear-ripened cheeses and plays several roles during cheese ripening. Its ability to metabolize proteins, lipids, and organic acids enables its growth on the cheese surface and promotes the development of organoleptic properties. Recent multilocus sequence typing (MLST) and phylogenetic analyses of G. candidum isolates revealed substantial genetic diversity, which may explain its strain-dependant technological capabilities. Here, we aimed to shed light on the phenotypic and genetic diversity among eight G. candidum and three Galactomyces spp. strains of environmental and dairy origin. Phenotypic tests such as carbon assimilation profiles, the ability to grow at 35°C and morphological traits on agar plates allowed us to discriminate G. candidum from Galactomyces spp. The genomes of these isolates were sequenced and assembled; whole genome comparison clustered the G. candidum strains into three subgroups and provided a reliable reference for MLST scheme optimization. Using the whole genome sequence as a reference, we optimized an MLST scheme using six loci that were proposed in two previous MLST schemes. This new MLST scheme allowed us to identify 15 sequence types (STs) out of 41 strains and revealed three major complexes named GeoA, GeoB, and GeoC. The population structure of these 41 strains was evaluated with STRUCTURE and a NeighborNet analysis of the combined six loci, which revealed recombination events between and within the complexes. These results hint that the allele variation conferring the different STs arose from recombination events. Recombination occurred for the six housekeeping genes studied, but most likely occurred throughout the genome. These recombination events may have induced an adaptive divergence between the wild strains and the cheesemaking strains, as observed for other cheese ripening fungi. Further comparative genomic studies are needed to confirm this phenomenon in G. candidum. In conclusion, the draft assembly of 11 G. candidum/Galactomyces spp. genomes allowed us to optimize a genotyping MLST scheme and, combined with the assessment of their ability to grow under different conditions, provides a reliable tool to cluster and eventually improves the selection of G. candidum strains.
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Affiliation(s)
- Vincent Perkins
- Department of Food Sciences and Nutrition, STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Quebec City, QC, Canada
| | - Stéphanie Vignola
- Department of Food Sciences and Nutrition, STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Quebec City, QC, Canada
| | - Marie-Hélène Lessard
- Department of Food Sciences and Nutrition, STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Quebec City, QC, Canada
| | - Pier-Luc Plante
- Big Data Research Center, Université Laval, Quebec City, QC, Canada
| | - Jacques Corbeil
- Big Data Research Center, Université Laval, Quebec City, QC, Canada
| | - Eric Dugat-Bony
- Department of Food Sciences and Nutrition, STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Quebec City, QC, Canada
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, Thiverval-Grignon, France
| | - Michel Frenette
- Oral Ecology Research Group, Faculty of Dental Medicine, Université Laval, Quebec City, QC, Canada
- Faculty of Science and Engineering, Department of Biochemistry, Microbiology, and Bioinformatics, Université Laval, Quebec City, QC, Canada
| | - Steve Labrie
- Department of Food Sciences and Nutrition, STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Quebec City, QC, Canada
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11
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Wan H, Liu T, Su C, Ji X, Wang L, Zhao Y, Wang Z. Evaluation of bacterial and fungal communities during the fermentation of Baixi sufu, a traditional spicy fermented bean curd. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1448-1457. [PMID: 31756265 DOI: 10.1002/jsfa.10151] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/28/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Baixi sufu (BS) is a traditional Chinese spicy fermented bean curd manufactured with a natural starter. In this study, the bacterial and fungal communities during BS fermentation were determined by culture and by the culture-independent method of high-throughput sequencing (HTS). Correlation analyses were performed to select the microorganisms potentially contributing to this fermentation. RESULTS During the fermentation of BS, 162 bacterial and 97 fungal strains were isolated and identified, and a total of 268 314 bacterial and 287 844 fungal high-quality sequences were analyzed. In general, lactic acid bacteria (LAB), especially Enterococcus and Lactococcus, were dominant in the early stage of fermentation, and spore-forming bacteria, especially Bacillus spp., became the predominant bacteria by the end of fermentation. Geotrichum, Mortierella, and unclassified Ascomycota, were the major fungal populations, which could not be detected in the final product. Correlation analyses indicated that Enterococcus, Bacillus, Geotrichum, and unclassified Ascomycota correlated significantly and positively with amino nitrogen. However, due to the sporulation characteristics of Bacillus, they may have little effect on BS ripening. The presence of Bifidobacterium spp. in sufu is reported for the first time, but the excessive counts of the Bacillus cereus group (>105 CFU g-1 ) indicate a potential hazard to consumers. CONCLUSION The profiles obtained from this study will contribute to the development of autochthonous starter cultures to control BS fermentation, and may lead to the development of novel strategies to shorten the fermentation time of sufu products. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Hongfang Wan
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Ting Liu
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Caiwei Su
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Xu Ji
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Liping Wang
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai, China
| | - Yong Zhao
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
| | - Zhengquan Wang
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China
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12
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Mane A, McSweeney PLH. Proteolysis in Irish farmhouse Camembert cheese during ripening. J Food Biochem 2019; 44:e13101. [PMID: 31782198 DOI: 10.1111/jfbc.13101] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/26/2019] [Accepted: 11/01/2019] [Indexed: 01/05/2023]
Abstract
Proteolysis in an Irish farmhouse Camembert cheese was studied during 10 weeks of ripening. Urea-polyacrylamide gel electrophoresis of pH 4.6-insoluble fractions of cheese showed the degradation of caseins, initially due to the action of chymosin and plasmin and later due to Penicillium camemberti proteinases. Proteolytic specificities of Penicillium camemberti proteinases on the caseins in milk hydrolysates were determined and 64, 6, 28, and 2 cleavage sites were identified in αs1 -, αs2 -, β-, and κ-casein, respectively. Proteolysis in cheese was studied and peptides produced were determined and compared to the cleavage specificities of Penicillium camemberti proteinases. Regions most susceptible to proteolysis were 1-40, 79-114, and 168-199 in αs1 -casein; 42-79 and 97-116 in αs2 -casein; 40-57, 101-125, 143-189, and 165-209 in β-casein; and 31-81 and 124-137 in κ-casein. The present study describes in detail the proteolytic action of proteinases from Penicillium camemberti in Camembert cheese during ripening. PRACTICAL APPLICATIONS: Camembert cheese is a major international cheese variety, made in many countries around the world. The ripening of the cheese involves many biochemical changes and this study provides new information on peptides produced during ripening. Penicillium camemberti is an important mold used in the production of this type of cheese and detailed information is provided on the action of its enzymes on the caseins. Data reported in this study furthers the understanding of the ripening of Camembert cheese.
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Affiliation(s)
- Anuya Mane
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Paul L H McSweeney
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
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13
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Dugat-Bony E, Bonnarme P, Fraud S, Catellote J, Sarthou AS, Loux V, Rué O, Bel N, Chuzeville S, Helinck S. Effect of sodium chloride reduction or partial substitution with potassium chloride on the microbiological, biochemical and sensory characteristics of semi-hard and soft cheeses. Food Res Int 2019; 125:108643. [DOI: 10.1016/j.foodres.2019.108643] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 10/26/2022]
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14
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The expression, secretion and activity of the aspartic protease MpAPr1 in Metschnikowia pulcherrima IWBT Y1123. J Ind Microbiol Biotechnol 2019; 46:1733-1743. [PMID: 31420798 DOI: 10.1007/s10295-019-02227-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Abstract
Protease-secreting yeasts have broad biotechnological potential for application to various industrial processes, including winemaking. However, this activity is influenced by the yeast response to environmental factors such as nitrogen and protein sources, as are found in grape juice. In this study, the wine-relevant yeast Metschnikowia pulcherrima IWBT Y1123, with known protease-secreting ability, was subjected to different nitrogen-containing compounds to monitor their impact on protease secretion and activity. Protease activity increased above basal levels for haemoglobin-containing treatments, indicating an inductive influence of proteins. On the other hand, treatments containing both haemoglobin and assimilable nitrogen sources led to a delayed increase in protease activity and protein degradation, suggesting a nitrogen catabolite repression mechanism at work. Protease activity and expression were furthermore evaluated in grape juice, which revealed increased expression and activity levels over time as promising results for further investigations into the impact of this yeast on wine properties.
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15
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Snyman C, Theron LW, Divol B. Understanding the regulation of extracellular protease gene expression in fungi: a key step towards their biotechnological applications. Appl Microbiol Biotechnol 2019; 103:5517-5532. [PMID: 31129742 DOI: 10.1007/s00253-019-09902-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022]
Abstract
The secretion of proteases by certain species of yeast and filamentous fungi is of importance not only for their biological function and survival, but also for their biotechnological application to various processes in the food, beverage, and bioprocessing industries. A key step towards understanding the role that these organisms play in their environment, and how their protease-secreting ability may be optimally utilised through industrial applications, involves an evaluation of those factors which influence protease production. The objective of this review is to provide an overview of the findings from investigations directed at elucidating the regulatory mechanisms underlying extracellular protease secretion in yeast and filamentous fungi, and the environmental stimuli that elicit these responses. The influence of nitrogen-, carbon-, and sulphur-containing compounds, as well as proteins, temperature, and pH, on extracellular protease regulation, which is frequently exerted at the transcriptional level, is discussed in particular depth. Protease-secreting organisms of biotechnological interest are also presented in this context, in an effort to explore the areas of industrial significance that could possibly benefit from such knowledge. In this way, the establishment of a platform of existing knowledge regarding fungal protease regulation is attempted, with the particular goal of aiding in the practical application of these organisms to processes that require secretion of this enzyme.
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Affiliation(s)
- C Snyman
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa
| | - L W Theron
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa
| | - B Divol
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Private Bag X1, Matieland, 7602, South Africa.
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16
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JASTER H, JUDACEWSKI P, RIBEIRO JCB, ZIELINSKI AAF, DEMIATE IM, LOS PR, ALBERTI A, NOGUEIRA A. Quality assessment of the manufacture of new ripened soft cheese by Geotrichum candidum: physico-chemical and technological properties. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.25717] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | - Ivo Mottin DEMIATE
- Universidade Estadual de Ponta Grossa, Brasil; Universidade Estadual de Ponta Grossa, Brasil
| | | | - Aline ALBERTI
- Universidade Estadual de Ponta Grossa, Brasil; Universidade Estadual de Ponta Grossa, Brasil
| | - Alessandro NOGUEIRA
- Universidade Estadual de Ponta Grossa, Brasil; Universidade Estadual de Ponta Grossa, Brasil
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17
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Morin M, Pierce EC, Dutton RJ. Changes in the genetic requirements for microbial interactions with increasing community complexity. eLife 2018; 7:e37072. [PMID: 30211673 PMCID: PMC6175579 DOI: 10.7554/elife.37072] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/09/2018] [Indexed: 12/17/2022] Open
Abstract
Microbial community structure and function rely on complex interactions whose underlying molecular mechanisms are poorly understood. To investigate these interactions in a simple microbiome, we introduced E. coli into an experimental community based on a cheese rind and identified the differences in E. coli's genetic requirements for growth in interactive and non-interactive contexts using Random Barcode Transposon Sequencing (RB-TnSeq) and RNASeq. Genetic requirements varied among pairwise growth conditions and between pairwise and community conditions. Our analysis points to mechanisms by which growth conditions change as a result of increasing community complexity and suggests that growth within a community relies on a combination of pairwise and higher-order interactions. Our work provides a framework for using the model organism E. coli as a readout to investigate microbial interactions regardless of the genetic tractability of members of the studied ecosystem.
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Affiliation(s)
- Manon Morin
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Emily C Pierce
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Rachel J Dutton
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
- Center for Microbiome InnovationJacobs School of Engineering, University of California San DiegoLa JollaUnited States
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18
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Ceugniez A, Taminiau B, Coucheney F, Jacques P, Delcenserie V, Daube G, Drider D. Fungal diversity of “Tomme d'Orchies” cheese during the ripening process as revealed by a metagenomic study. Int J Food Microbiol 2017; 258:89-93. [DOI: 10.1016/j.ijfoodmicro.2017.07.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/16/2022]
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19
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Ozturkoglu-Budak S, Wiebenga A, Bron PA, de Vries RP. Protease and lipase activities of fungal and bacterial strains derived from an artisanal raw ewe's milk cheese. Int J Food Microbiol 2016; 237:17-27. [PMID: 27541978 DOI: 10.1016/j.ijfoodmicro.2016.08.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/07/2016] [Accepted: 08/08/2016] [Indexed: 11/30/2022]
Abstract
We previously identified the microbiota present during cheese ripening and observed high protease and lipase activity in Divle Cave cheese. To determine the contribution of individual isolates to enzyme activities, we investigated a range of species representing this microbiota for their proteolytic and lipolytic ability. In total, 17 fungal, 5 yeast and 18 bacterial strains, previously isolated from Divle Cave cheese, were assessed. Qualitative protease and lipase activities were performed on skim-milk agar and spirit-blue lipase agar, respectively, and resulted in a selection of strains for quantitative assays. For the quantitative assays, the strains were grown on minimal medium containing irradiated Divle Cave cheese, obtained from the first day of ripening. Out of 16 selected filamentous fungi, Penicillium brevicompactum, Penicillium cavernicola and Penicillium olsonii showed the highest protease activity, while Mucor racemosus was the best lipase producer. Yarrowia lipolytica was the best performing yeast with respect to protease and lipase activity. From the 18 bacterial strains, 14 and 11 strains, respectively showed protease and lipase activity in agar plates. Micrococcus luteus, Bacillus stratosphericus, Brevibacterium antiquum, Psychrobacter glacincola and Pseudomonas proteolytica displayed the highest protease and lipase activity. The proteases of yeast and filamentous fungi were identified as mainly aspartic protease by specific inhibition with Pepstatin A, whereas inhibition by PMSF (phenylmethylsulfonyl fluoride) indicated that most bacterial enzymes belong to serine type protease. Our results demonstrate that aspartic proteases, which usually have high milk clotting activity, are predominantly derived from fungal strains, and therefore fungal enzymes appear to be more suitable for use in the cheese industry. Microbial enzymes studied in this research might be alternatives for rennin (chymosin) from animal source because of their low cost and stable availability. Future studies will aim to purify these enzymes to test their suitability for use in similar artisanal cheeses or in large scale commercial cheeses.
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Affiliation(s)
- Sebnem Ozturkoglu-Budak
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, 3584 CT Utrecht, The Netherlands; Department of Dairy Technology, Faculty of Agriculture, University of Ankara, 06110, Ankara, Turkey.
| | - Ad Wiebenga
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, 3584 CT Utrecht, The Netherlands.
| | - Peter A Bron
- NIZO food research, Kernhemseweg 2, 6718ZB Ede, The Netherlands.
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, 3584 CT Utrecht, The Netherlands.
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20
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Abstract
The history of cheese manufacture is a "natural history" in which animals, microorganisms, and the environment interact to yield human food. Part of the fascination with cheese, both scientifically and culturally, stems from its ability to assume amazingly diverse flavors as a result of seemingly small details in preparation. In this review, we trace the roots of cheesemaking and its development by a variety of human cultures over centuries. Traditional cheesemakers observed empirically that certain environments and processes produced the best cheeses, unwittingly selecting for microorganisms with the best biochemical properties for developing desirable aromas and textures. The focus of this review is on the role of fungi in cheese ripening, with a particular emphasis on the yeast-like fungus Geotrichum candidum. Conditions that encourage the growth of problematic fungi such as Mucor and Scopulariopsis as well as Arachnida (cheese mites), and how such contaminants might be avoided, are discussed. Bethlehem cheese, a pressed, uncooked, semihard, Saint-Nectaire-type cheese manufactured in the United Sates without commercial strains of bacteria or fungi, was used as a model for the study of stable microbial succession during ripening in a natural environment. The appearance of fungi during a 60-day ripening period was documented using light and scanning electron microscopy, and it was shown to be remarkably reproducible and parallel to the course of ripening of authentic Saint-Nectaire cheese in the Auvergne region of France. Geotrichum candidum, Mucor, and Trichothecium roseum predominate the microbiotas of both cheese types. Geotrichum in particular was shown to have high diversity in different traditional cheese ripening environments, suggesting that traditional manufacturing techniques selected for particular fungi. This and other studies suggest that strain diversity arises in relation to the lore and history of the regions from which these types of cheeses arose.
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21
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Abstract
Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been "in culture" for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the "parts list" (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.
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22
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Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, Irlinger F, Landaud S, Leclercq-Perlat MN, Bento P, Fraud S, Gibrat JF, Aubert J, Fer F, Guédon E, Pons N, Kennedy S, Beckerich JM, Swennen D, Bonnarme P. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS One 2015; 10:e0124360. [PMID: 25867897 PMCID: PMC4395090 DOI: 10.1371/journal.pone.0124360] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.
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Affiliation(s)
- Eric Dugat-Bony
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Cécile Straub
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Aurélie Teissandier
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Djamila Onésime
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Valentin Loux
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Christophe Monnet
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Françoise Irlinger
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Marie-Noëlle Leclercq-Perlat
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bento
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | | | - Jean-François Gibrat
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Julie Aubert
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Frédéric Fer
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Eric Guédon
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Nicolas Pons
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Sean Kennedy
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Jean-Marie Beckerich
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Dominique Swennen
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bonnarme
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- * E-mail:
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23
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Leclercq-Perlat MN, Sicard M, Perrot N, Trelea IC, Picque D, Corrieu G. Temperature and relative humidity influence the ripening descriptors of Camembert-type cheeses throughout ripening. J Dairy Sci 2014; 98:1325-35. [PMID: 25497800 DOI: 10.3168/jds.2014-8916] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022]
Abstract
Ripening descriptors are the main factors that determine consumers' preferences of soft cheeses. Six descriptors were defined to represent the sensory changes in Camembert cheeses: Penicillium camemberti appearance, cheese odor and rind color, creamy underrind thickness and consistency, and core hardness. To evaluate the effects of the main process parameters on these descriptors, Camembert cheeses were ripened under different temperatures (8, 12, and 16°C) and relative humidity (RH; 88, 92, and 98%). The sensory descriptors were highly dependent on the temperature and RH used throughout ripening in a ripening chamber. All sensory descriptor changes could be explained by microorganism growth, pH, carbon substrate metabolism, and cheese moisture, as well as by microbial enzymatic activities. On d 40, at 8°C and 88% RH, all sensory descriptors scored the worst: the cheese was too dry, its odor and its color were similar to those of the unripe cheese, the underrind was driest, and the core was hardest. At 16°C and 98% RH, the odor was strongly ammonia and the color was dark brown, and the creamy underrind represented the entire thickness of the cheese but was completely runny, descriptors indicative of an over ripened cheese. Statistical analysis showed that the best ripening conditions to achieve an optimum balance between cheese sensory qualities and marketability were 13±1°C and 94±1% RH.
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Affiliation(s)
- M-N Leclercq-Perlat
- UMR GMPA, INRA 0782, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.; UMR GMPA, AgroParisTech, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.
| | - M Sicard
- UMR GMPA, INRA 0782, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.; UMR GMPA, AgroParisTech, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
| | - N Perrot
- UMR GMPA, INRA 0782, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.; UMR GMPA, AgroParisTech, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
| | - I C Trelea
- UMR GMPA, INRA 0782, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.; UMR GMPA, AgroParisTech, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
| | - D Picque
- UMR GMPA, INRA 0782, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.; UMR GMPA, AgroParisTech, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
| | - G Corrieu
- UMR GMPA, INRA 0782, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France.; UMR GMPA, AgroParisTech, 1 avenue Lucien Brétignières, 78850 Thiverval-Grignon, France
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Naz S, Gueguen-Minerbe M, Cretenet M, Vernoux JP. Aromatic amino acids as precursors of antimicrobial metabolites inGeotrichum candidum. FEMS Microbiol Lett 2013; 344:39-47. [DOI: 10.1111/1574-6968.12152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/03/2013] [Accepted: 04/03/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Saima Naz
- Research Unit Aliments Bioprocédés Toxicologie Environnements (URABTE) E.A. 4651; IFR146 ICORE; Université de Caen Basse-Normandie; Caen Cedex; France
| | - Marielle Gueguen-Minerbe
- Université Paris-Est; Institut Français de Sciences et Technologies des Transports, de l'Aménagements et des Réseaux; Marne-la-Vallée Cedex 2; France
| | - Marina Cretenet
- Research Unit Aliments Bioprocédés Toxicologie Environnements (URABTE) E.A. 4651; IFR146 ICORE; Université de Caen Basse-Normandie; Caen Cedex; France
| | - Jean-Paul Vernoux
- Research Unit Aliments Bioprocédés Toxicologie Environnements (URABTE) E.A. 4651; IFR146 ICORE; Université de Caen Basse-Normandie; Caen Cedex; France
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Genetic diversity of dairy Geotrichum candidum strains revealed by multilocus sequence typing. Appl Microbiol Biotechnol 2013; 97:5907-20. [PMID: 23467823 DOI: 10.1007/s00253-013-4776-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/07/2012] [Accepted: 12/12/2012] [Indexed: 01/20/2023]
Abstract
The introduction of multilocus sequence typing (MLST) for strain characterization provided the first sequence-based approach for genotyping many fungi, leading to reproducible, reliable, and exchangeable data. A MLST scheme based on the analysis of six housekeeping genes was developed for genotyping Geotrichum candidum. The scheme was first developed using 18 isolates for which the complete sequences of the alanyl-tRNA synthetase (ALA1), pyruvate kinase (CDC19), acetyl-coA acetyltransferase (ERG10), glutaminyl-tRNA synthase (GLN4), phosphoglucoisomerase (PGI1), and phosphoglucomutase (PGM2) housekeeping genes were determined. Multiple sequence alignments of these genes were used to define a set of loci showing, as closely as possible, the same phylogenetic resolution level as complete gene sequences. This scheme was subsequently validated with 22 additional isolates from dairy and non-dairy sources. Overall, 58 polymorphic sites were indexed among 3,009 nucleotides analyzed. Depending on the loci, four to eight alleles were detected, generating 17 different sequence types, of which ten were represented by a single strain. MLST analysis suggested a predominantly clonal population for the 40 G. candidum isolates. Phylogenetic analysis of the concatenated sequences revealed a distantly related group of four isolates. Interestingly, this group diverged with respect to internal transcribed spacers 1 (ITS1), 5.8S, and ITS2 analysis. The reproducibility of the MLST approach was compared to random amplification of microsatellites by PCR (RAM-PCR), a gel profiling method previously proposed for G. candidum strain typing. Our results found MLST differentiation to be more efficient than RAM-PCR, and MLST also offered a non-ambiguous, unique language, permitting data exchange and evolutionary inference.
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Abstract
Freeze-Drying Preservation of Yeast Adjunct Cultures for Cheese Production
Four yeast strains: Yarrowia lipolytica PII6a, Candida famata MI1a, C. kefyr PII1b, C. sphaerica FII7a, adjunct cultures for cheese production were preserved by freeze-drying. The effect of process parameters and cryoprotective agents on cell survival and stability of growth characteristics was evaluated. Among three lyophilisation protocols, the process with three-step drying at temperatures of -38°C, -20°C and -10°C assured the highest cell viability. The survival of yeast strains in the presence of multicomponent cryoprotective agents containing skimmed milk, trehalose and sodium glutamate in three combinations (MT, MG, MTG) was significantly higher than in the presence of those agents used alone. The best agent for Y. lipolytica, C. kefyr and C. sphaerica appeared to be MT, while for C. famata - MG. Cell viability of yeast strains directly after freeze-drying was in the range of 74-80% and was relatively stable during one-year storage except C. famata. Initial yeast growth patterns were very well preserved in most of the preparations during 6 months of storage.
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Yeasts from Colombian Kumis as source of peptides with Angiotensin I converting enzyme (ACE) inhibitory activity in milk. Int J Food Microbiol 2012; 159:39-46. [DOI: 10.1016/j.ijfoodmicro.2012.07.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/23/2012] [Accepted: 07/31/2012] [Indexed: 11/23/2022]
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Sacristán N, González L, Castro JM, Fresno JM, Tornadijo ME. Technological characterization of Geotrichum candidum strains isolated from a traditional Spanish goats’ milk cheese. Food Microbiol 2012; 30:260-6. [DOI: 10.1016/j.fm.2011.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/22/2011] [Accepted: 10/05/2011] [Indexed: 11/30/2022]
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Alper I, Frenette M, Labrie S. Ribosomal DNA polymorphisms in the yeast Geotrichum candidum. Fungal Biol 2011; 115:1259-69. [PMID: 22115445 DOI: 10.1016/j.funbio.2011.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 09/08/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
Abstract
The dimorphic yeast Geotrichum candidum (teleomorph: Galactomyces candidus) is commonly used to inoculate washed-rind and bloomy-rind cheeses. However, little is known about the phylogenetic lineage of this microorganism. We have sequenced the complete 18S, 5.8S, 26S ribosomal RNA genes and their internal transcribed spacers (ITS1) and ITS2 regions (5126 nucleotides) from 18 G. candidum strains from various environmental niches, with a focus on dairy strains. Multiple sequence alignments revealed the presence of 60 polymorphic sites, which is generally unusual for ribosomal DNA (rDNA) within a given species because of the concerted evolution mechanism. This mechanism drives genetic homogenization to prevent the divergent evolution of rDNA copies within individuals. While the polymorphisms observed were mainly substitutions, one insertion/deletion (indel) polymorphism was detected in ITS1. No polymorphic sites were detected downstream from this indel site, that is, in 5.8S and ITS2. More surprisingly, many sequence electrophoregrams generated during the sequencing of the rDNA had dual peaks, suggesting that many individuals exhibited intragenomic rDNA variability. The ITS1-5.8S-ITS2 regions of four strains were cloned. The sequence analysis of 68 clones revealed 32 different ITS1-5.8S-ITS2 variants within these four strains. Depending on the strain, from four to twelve variants were detected, indicating that multiple rDNA copies were present in the genomes of these G. candidum strains. These results contribute to the debate concerning the use of the ITS region for barcoding fungi and suggest that community profiling techniques based on rDNA should be used with caution.
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Affiliation(s)
- Iraz Alper
- Nutraceuticals and Functional Foods Institute, STELA Dairy Research Centre, Department of Food Sciences and Nutrition, Université Laval, Quebec City, QC, Canada G1V 0A6
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Jo AR, Noh HW, Kim KS, Chung KH, Jeon WM. The Development of Imitated Cheese Using Whole Milk Powder and Fermented Milk. Korean J Food Sci Anim Resour 2010. [DOI: 10.5851/kosfa.2010.30.1.102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Boutrou R, Aziza M, Amrane A. Enhanced proteolytic activities of Geotrichum candidum and Penicillium camembertii in mixed culture. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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