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Lutin J, Dufrene F, Guyot P, Palme R, Achilleos C, Bouton Y, Buchin S. Microbial composition and viability of natural whey starters used in PDO Comté cheese-making. Food Microbiol 2024; 121:104521. [PMID: 38637083 DOI: 10.1016/j.fm.2024.104521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/20/2024]
Abstract
Natural whey starters (NWS) are cultures with undefined multiple-strains species commonly used to speed up the fermentation process of cheeses. The aim of this study was to explore the diversity and the viability of Comté cheese NWS microbiota. Culture-dependent methods, i.e. plate counting and genotypic characterization, and culture-independent methods, i.e. qPCR, viability-qPCR, fluorescence microscopy and DNA metabarcoding, were combined to analyze thirty-six NWS collected in six Comté cheese factories at two seasons. Our results highlighted that NWS were dominated by Streptococcus thermophilus (ST) and thermophilic lactobacilli. These species showed a diversity of strains based on Rep-PCR. The dominance of Lactobacillus helveticus (LH) over Lactobacillus delbrueckii (LD) varied depending on the factory and the season. This highlighted two types of NWS: the type-ST/LD (LD > LH) and the type-ST/LH (LD < LH). The microbial composition varied depending on cheese factory. One factory was distinguished by its level of culturable microbial groups (ST, enterococci and yeast) and its fungi diversity. The approaches used to estimate the viability showed that most NWS cells were viable. Further investigations are needed to understand the microbial diversity of these NWS.
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Affiliation(s)
- Jade Lutin
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Franck Dufrene
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Philippe Guyot
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France
| | - Romain Palme
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Christine Achilleos
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
| | - Yvette Bouton
- Comité Interprofessionnel de Gestion du Comté - Unité R&D, Bât. INRAE, F-39800, Poligny, France.
| | - Solange Buchin
- INRAE, Institut Agro, Université de Bourgogne, UMR PAM, F-39800, Poligny, France
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2
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Gapp C, Dijamentiuk A, Mangavel C, Callon C, Theil S, Revol-Junelles AM, Chassard C, Borges F. Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization. mSystems 2024:e0044524. [PMID: 39041801 DOI: 10.1128/msystems.00445-24] [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: 03/28/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping, which consists of using part of the previous production to inoculate a new one, can be used as a model engineering approach to investigate community dynamics during serial propagations. In this study, 26 raw milk samples were serially propagated 6 times each, giving rise to 26 community lineages. Bacterial community structures were analyzed by metabarcoding, and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high variability of structure and diverse acidification properties between community lineages. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure. IMPORTANCE Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.
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Affiliation(s)
- Chloé Gapp
- Université de Lorraine, LIBio, Nancy, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | | | | | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | - Sébastien Theil
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
| | | | - Christophe Chassard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 0545 Fromage, Aurillac, France
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3
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Rossi A, Marroni F, Renoldi N, Di Filippo G, Gover E, Marino M, Innocente N. An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking. J Dairy Sci 2024; 107:4288-4297. [PMID: 38462069 DOI: 10.3168/jds.2024-24463] [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: 11/23/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
The use of natural milk culture (NMC) represents a key factor in Protected Designation of Origin (PDO) Montasio cheese, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMC is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMC collected from 10 PDO Montasio cheese dairies was investigated by employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMC, and a subdominant population made of other streptococci and Ligilactobacillus salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMC. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staphylococcus aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMC and clarify their role in the creation of the characteristics of PDO Montasio cheese.
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Affiliation(s)
- Anna Rossi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Fabio Marroni
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Niccolò Renoldi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Giulia Di Filippo
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Elisabetta Gover
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
| | - Marilena Marino
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy.
| | - Nadia Innocente
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, 33100, Udine, Italy
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4
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Zhang P, Liu Y, Li H, Hui M, Pan C. Strategies and Challenges of Microbiota Regulation in Baijiu Brewing. Foods 2024; 13:1954. [PMID: 38928896 PMCID: PMC11202514 DOI: 10.3390/foods13121954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/09/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The traditional Chinese Baijiu brewing process utilizes natural inoculation and open fermentation. The microbial composition and abundance in the microecology of Baijiu brewing often exhibit unstable characteristics, which directly results in fluctuations in Baijiu quality. The microbiota plays a crucial role in determining the quality of Baijiu. Analyzing the driving effect of technology and raw materials on microorganisms. Elucidating the source of core microorganisms and interactions between microorganisms, and finally utilizing single or multiple microorganisms to regulate and intensify the Baijiu fermentation process is an important way to achieve high efficiency and stability in the production of Baijiu. This paper provides a systematic review of the composition and sources of microbiota at different brewing stages. It also analyzes the relationship between raw materials, brewing processes, and brewing microbiota, as well as the steps involved in the implementation of brewing microbiota regulation strategies. In addition, this paper considers the feasibility of using Baijiu flavor as a guide for Baijiu brewing regulation by synthesizing the microbiota, and the challenges involved. This paper is a guide for flavor regulation and quality assurance of Baijiu and also suggests new research directions for regulatory strategies for other fermented foods.
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Affiliation(s)
- Pengpeng Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; (P.Z.); (H.L.); (M.H.)
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Yanbo Liu
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Haideng Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; (P.Z.); (H.L.); (M.H.)
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Ming Hui
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China; (P.Z.); (H.L.); (M.H.)
| | - Chunmei Pan
- College of Food and Biological Engineering (Liquor College), Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
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5
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Lahmamsi H, Ananou S, Lahlali R, Tahiri A. Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects. Folia Microbiol (Praha) 2024; 69:465-489. [PMID: 38393576 DOI: 10.1007/s12223-024-01146-3] [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: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.
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Affiliation(s)
- Haitam Lahmamsi
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco
| | - Samir Ananou
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
| | - Rachid Lahlali
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
| | - Abdessalem Tahiri
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
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6
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Fusco V, Chieffi D, De Angelis M. Invited review: Fresh pasta filata cheeses: Composition, role, and evolution of the microbiota in their quality and safety. J Dairy Sci 2022; 105:9347-9366. [DOI: 10.3168/jds.2022-22254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
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Sola L, Quadu E, Bortolazzo E, Bertoldi L, Randazzo CL, Pizzamiglio V, Solieri L. Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait. Sci Rep 2022; 12:17322. [PMID: 36243881 PMCID: PMC9569347 DOI: 10.1038/s41598-022-22207-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.
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Affiliation(s)
- Laura Sola
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Emanuele Quadu
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Elena Bortolazzo
- grid.423913.eCentro Ricerche Produzioni Animali, 42121 Reggio Emilia, Italy
| | | | - Cinzia L. Randazzo
- grid.8158.40000 0004 1757 1969Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy ,ProBioEtna Srl, 95123 Catania, Italy
| | - Valentina Pizzamiglio
- grid.433295.aConsorzio del Formaggio Parmigiano Reggiano, 42124 Reggio Emilia, Italy
| | - Lisa Solieri
- grid.7548.e0000000121697570Department of Life Sciences, University of Modena and Reggio Emilia, 42122 Reggio Emilia, Italy ,NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
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8
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Ban GH, Kim BK, Kim SR, Rhee MS, Kim SA. Bacterial microbiota profiling of oyster mushrooms (Pleurotus ostreatus) based on cultivation methods and distribution channels using high-throughput sequencing. Int J Food Microbiol 2022; 382:109917. [PMID: 36116389 DOI: 10.1016/j.ijfoodmicro.2022.109917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/30/2022] [Accepted: 09/04/2022] [Indexed: 11/25/2022]
Abstract
The annual consumption and production of oyster mushrooms (Pleurotus ostreatus) have continued to rise due to its nutritive and health-promoting benefits. Cultivated mushrooms are mostly grown in small to medium-scaled scale production plants that present hygienic challenges which could, in turn, increase associated foodborne pathogenic outbreaks. The present study aimed to investigate the shift in microbial ecologies of oyster mushrooms from pre-distribution (cultivation in bottles or on shelves) to post-distribution at supermarkets and open-air markets. Aerobic plate counts and coliforms were quantified using traditional microbiological techniques, and the microbiome associated with oyster mushrooms (n = 70) was analyzed using 16S rRNA amplicon sequencing for an enhanced level of bacterial microbiota profiling. Overall, coliforms recovered from pre-distribution bottle-cultivated mushrooms were 1.9 log CFU/g higher (p < 0.05) than that of shelf-cultivated mushrooms. The mean aerobic plate counts of oyster mushrooms distributed to open-air markets was 1.2 log CFU/g higher (p < 0.05) than packaged mushrooms from supermarkets while there were no significant differences in coliform counts. The pattern of bacterial composition differed by post-distribution channels, with oyster mushrooms collected from the open-air markets demonstrating the richest microbiome diversity. An increase in the relative abundance of Enterobacteriaceae (55-68 %) and Pseudomonadaceae (27-35 %) was observed in pre- and post-distribution mushrooms, respectively. However, no distinct bacterial microbiota differences were observed for the different cultivation methods or different geographical locations for each market type. The current findings add to our understanding of the effects of cultivation methods and commercial distribution channels regarding the microbiome of oyster mushrooms and may inform potential intervention strategies for future production and distribution processes. Furthermore, the tandem analyses of culture-dependent and culture-independent methods can provide more comprehensive information than that obtained when using each approach independently.
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Affiliation(s)
- Ga-Hee Ban
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, South Korea
| | - Bo-Kyeong Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, South Korea
| | - Se-Ri Kim
- Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, South Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Sun Ae Kim
- Department of Food Science and Biotechnology, Ewha Womans University, Seoul, South Korea.
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9
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Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. MICROBIOME 2022; 10:137. [PMID: 36028909 PMCID: PMC9419375 DOI: 10.1186/s40168-022-01328-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/17/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. RESULTS We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. CONCLUSIONS Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | - Thibault Schowing
- Agroscope, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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10
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Barzideh Z, Siddiqi M, Mohamed HM, LaPointe G. Dynamics of Starter and Non-Starter Lactic Acid Bacteria Populations in Long-Ripened Cheddar Cheese Using Propidium Monoazide (PMA) Treatment. Microorganisms 2022; 10:microorganisms10081669. [PMID: 36014087 PMCID: PMC9413250 DOI: 10.3390/microorganisms10081669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The microbial community of industrially produced Canadian Cheddar cheese was examined from curd to ripened cheese at 30-32 months using a combination of viable plate counts of SLAB (GM17) and NSLAB (MRSv), qPCR and 16S rRNA gene amplicon sequencing. Cell treatment with propidium monoazide excluded DNA of permeable cells from amplification. The proportion of permeable cells of both Lactococcus spp. and Lacticaseibacillus spp. was highest at 3-6 months. While most remaining Lacticaseibacillus spp. cells were intact during later ripening stages, a consistent population of permeable Lactococcus spp. cells was maintained over the 32-month period. While Lactococcus sequence variants were significant biomarkers for viable cheese curd communities at 0-1 m, Lacticaseibacillus was identified as a distinctive biomarker for cheeses from 7 to 20 months. From 24 to 32 months, Lacticaseibacillus was replaced in significance by four genera (Pediococcus and Latilactobacillus at 24 m and at 30-32 m, Secundilactobacillus and Paucilactobacillus). These results underscore the importance of monitoring potential defects in cheeses aged over 24 months, which could be diagnosed early through microbial DNA profiling to minimize potential waste of product. Future perspectives include correlating volatile flavor compounds with microbial community composition as well as the investigation of intra-species diversity.
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Affiliation(s)
- Zoha Barzideh
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Myra Siddiqi
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Hassan Mahmoud Mohamed
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada
- Faculty of Computer and Artificial Intelligence, Benha University, Banha 13518, Egypt
| | - Gisèle LaPointe
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
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11
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Isolation and Identification of Lactic Acid Bacteria from Natural Whey Cultures of Buffalo and Cow Milk. Foods 2022; 11:foods11020233. [PMID: 35053966 PMCID: PMC8774387 DOI: 10.3390/foods11020233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/24/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
In southern Italy, some artisanal farms produce mozzarella and caciocavallo cheeses by using natural whey starter (NWS), whose microbial diversity is responsible for the characteristic flavor and texture of the final product. We studied the microbial community of NWS cultures of cow’s milk (NWSc) for the production of caciocavallo and buffalo’s milk (NWSb) for the production of mozzarella, both from artisanal farms. Bacterial identification at species and strain level was based on an integrative strategy, combining culture-dependent (sequencing of the 16S rDNA, species/subspecies-specific Polymerase Chain Reaction (PCR) and clustering by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) and culture-independent (next-generation sequencing analysis, NGS) approaches. Results obtained with both approaches showed the occurrence of five species of lactic acid bacteria in NWSb (Lactococcus lactis subsp. lactis, Lactobacillus fermentum, Streptococcus thermophilus, Lactobacillus delbrueckii, and Lactobacillus helveticus) and five species in NWSc (Lc. lactis subsp. lactis, Enterococcus faecium, and S. thermophilus, Lb. helveticus, and Lb. delbrueckii), with the last two found only by the NGS analysis. Moreover, RAPD profiles, performed on Lc. lactis subsp. lactis different isolates from both NWSs, showed nine strains in NWSb and seven strains in NWSc, showing a microbial diversity also at strain level. Characterization of the microbiota of natural whey starters aims to collect new starter bacteria to use for tracing microbial community during the production of artisanal cheeses, in order to preserve their quality and authenticity, and to select new Lactic Acid Bacteria (LAB) strains for the production of functional foods.
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12
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Garofalo G, Busetta G, Maniaci G, Sardina MT, Portolano B, Badalamenti N, Maggio A, Bruno M, Gaglio R, Settanni L. Development of "Quadrello di Ovino", a Novel Fresh Ewe's Cheese. Foods 2021; 11:25. [PMID: 35010151 PMCID: PMC8750039 DOI: 10.3390/foods11010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
This work was performed to produce a new soft ewe's milk cheese, namely "Quadrello di ovino" (QdO) cheese, to enlarge ewe's dairy product portfolio of South Italy, barely limited to Pecorino cheese typology. Cheese making was performed applying the technology for "Crescenza" cheese typology with some modifications. In particular, pasteurized ewes' milk was inoculated with two commercial starter formulations (SF1 and SF2) of Streptococcus thermophilus to obtain two different productions (QdO-P1 and QdO-P2, respectively). Plate counts demonstrated the ability of both starter formulations to drive the fermentation process, since S. thermophilus counts reached 109 CFU/g in both productions. Generally, the two starter formulations did not affect the chemical composition of QdO cheeses that contained, on average, 64.08% dry matter of which approximately 54.99% were fats and 36.39% proteins. Among chemical parameters, significant differences were registered for secondary lipid oxidation state (significantly lower for QdO-P2), fatty acids and volatile organic compounds (VOCs). However, the differences registered among cheese VOCs from were not perceived by the panelists who recognized both cheese productions highly similar, although QdO-P2 cheeses were mostly appreciated by the judges. This study allowed to produce a novel fresh ovine cheese with specific chemical and sensorial characteristics well appreciated by consumers.
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Affiliation(s)
- Giuliana Garofalo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
| | - Gabriele Busetta
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
| | - Giuseppe Maniaci
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
| | - Maria Teresa Sardina
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
| | - Natale Badalamenti
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (N.B.); (A.M.); (M.B.)
| | - Antonella Maggio
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (N.B.); (A.M.); (M.B.)
| | - Maurizio Bruno
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy; (N.B.); (A.M.); (M.B.)
| | - Raimondo Gaglio
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
| | - Luca Settanni
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Ed. 5, 90128 Palermo, Italy; (G.G.); (G.B.); (G.M.); (M.T.S.); (B.P.); (R.G.)
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Ferrocino I, Rantsiou K, Cocolin L. Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity. Curr Opin Biotechnol 2021; 73:164-170. [PMID: 34474311 DOI: 10.1016/j.copbio.2021.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022]
Abstract
A detailed understanding of the microbiome of cheese and dairy products is key to the optimization of flavour, appearance, overall quality and safety. Microorganisms (including bacteria, yeasts, moulds and viruses, especially bacteriophages) from the environment can enter the dairy supply chain at multiple stages with several implications. The ability to track these microorganisms and to understand their function and interaction can be greatly enhanced by the use of high-throughput sequencing. Depending on the specific production technology, dairy products can harbor several strains and antibiotic-resistance genes that can potentially interact with the gut microbiome, once the product is ingested. Milk-associated or cheese-associated microbial communities with their interaction, function and diversity are a key factor for the dairy industry. Multi-omics approaches have been seldom utilized in literature and they need to be further considered. Studying the role, origin, diversity and function of the microbial species involved in the complex system of dairy production can help improve processes in several fields of application. Integrating an extensive sampling procedure with an extensive culture based methodology is necessary. To this end, local producers, and in general stakeholders, should be guided to discover and maintain their microbial diversity. A better management of microbial resources through precision fermentation processes will in turn reduce overall food losses and increase the possibility to use the microbiome in order to increase the local producers' income.
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Affiliation(s)
- Ilario Ferrocino
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Kalliopi Rantsiou
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy
| | - Luca Cocolin
- DISAFA-Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy.
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Piqueras J, Chassard C, Callon C, Rifa E, Theil S, Lebecque A, Delbès C. Lactic Starter Dose Shapes S. aureus and STEC O26:H11 Growth, and Bacterial Community Patterns in Raw Milk Uncooked Pressed Cheeses. Microorganisms 2021; 9:microorganisms9051081. [PMID: 34069983 PMCID: PMC8157849 DOI: 10.3390/microorganisms9051081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023] Open
Abstract
Adding massive amounts of lactic starters to raw milk to manage the sanitary risk in the cheese-making process could be detrimental to microbial diversity. Adjusting the amount of the lactic starter used could be a key to manage these adverse impacts. In uncooked pressed cheeses, we investigated the impacts of varying the doses of a lactic starter (the recommended one, 1×, a 0.1× lower and a 2× higher) on acidification, growth of Staphylococcus aureus SA15 and Shiga-toxin-producing Escherichia coli (STEC) O26:H11 F43368, as well as on the bacterial community patterns. We observed a delayed acidification and an increase in the levels of pathogens with the 0.1× dose. This dose was associated with increased richness and evenness of cheese bacterial community and higher relative abundance of potential opportunistic bacteria or desirable species involved in cheese production. No effect of the increased lactic starter dose was observed. Given that sanitary criteria were paramount to our study, the increase in the pathogen levels observed at the 0.1× dose justified proscribing such a reduction in the tested cheese-making process. Despite this, the effects of adjusting the lactic starter dose on the balance of microbial populations of potential interest for cheese production deserve an in-depth evaluation.
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Affiliation(s)
- Justine Piqueras
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Christophe Chassard
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Cécile Callon
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Etienne Rifa
- UMR INSA/INRA 792, Toulouse Biotechnology Institute, INSA/CNRS 5504, 135 Avenue de Rangueil, F-31077 Toulouse, France;
| | - Sébastien Theil
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Annick Lebecque
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
| | - Céline Delbès
- UMR 0545 Fromage, Université Clermont Auvergne, INRAE, VetAgro Sup, 20 Côte de Reyne, F-15000 Aurillac, France; (J.P.); (C.C.); (C.C.); (S.T.); (A.L.)
- Correspondence: ; Tel.: +33-471-456-419
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Asimakoula S, Giaka K, Fanitsios C, Kakouri A, Vandera E, Samelis J, Koukkou AI. Monitoring Growth Compatibility and Bacteriocin Gene Transcription of Adjunct and Starter Lactic Acid Bacterial Strains in Milk. J Food Prot 2021; 84:509-520. [PMID: 33108438 DOI: 10.4315/jfp-20-317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/22/2020] [Indexed: 01/13/2023]
Abstract
ABSTRACT When developing protective starter cultures for application in cheese technologies, monitoring growth interactions between starter and adjunct lactic acid bacterial (LAB) species and in situ expression of bacteriocin genes in the mixtures is crucial. This study first aimed to monitor the growth of mixed LAB strain populations during milk model fermentations by microbial counts and real-time quantitative PCR. The primary starter strains, Streptococcus thermophilus ST1 and costarter Lactococcus lactis subsp. cremoris M78, served as the basic starter composite coinoculated in all milk treatments. Adjunct bacteriocinogenic Enterococcus faecium strains KE82 and GL31 and the ripening Lactiplantibacillus plantarum H25 strain were added separately to the starter composite, resulting in four LAB combination treatments. The second aim was to quantify gene transcripts of nisin and enterocins B and A synthesized by strains M78, KE82, and GL31, respectively, by reverse transcription-real-time quantitative PCR and to detect the in situ antilisterial effects of the cocultures. Adjunct LAB strains showed growth compatibility with the starter, since all of them exhibited 2- to 3-log-unit increases in their population levels compared to their initial inoculation levels, with ST1 prevailing in all treatments. KE82 grew more competitively than GL31, whereas cocultures with KE82 displayed the strongest in situ antilisterial activity. Nisin gene expression levels were higher at the exponential phase of microbial growth in all treatments. Finally, the expression levels of nisin and enterocin A and B genes were interrelated, indicating an antagonistic activity. HIGHLIGHTS
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Affiliation(s)
- Stamatia Asimakoula
- Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Katerina Giaka
- Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Christos Fanitsios
- Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - Athanasia Kakouri
- Dairy Research Department, General Directorate of Agricultural Research, Hellenic Agricultural Organization DIMITRA, Katsikas, 45221 Ioannina, Greece
| | - Elpiniki Vandera
- Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
| | - John Samelis
- Dairy Research Department, General Directorate of Agricultural Research, Hellenic Agricultural Organization DIMITRA, Katsikas, 45221 Ioannina, Greece
| | - Anna-Irini Koukkou
- Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece
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16
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Zotta T, Ricciardi A, Condelli N, Parente E. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci Nutr 2021; 62:3898-3912. [PMID: 33455430 DOI: 10.1080/10408398.2020.1870927] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.
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Affiliation(s)
- Teresa Zotta
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Annamaria Ricciardi
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Nicola Condelli
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari e Ambientali, Università degli Studi della Basilicata, Potenza, Italy
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Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase ( pheS) Gene Amplicon Sequencing Approach. Appl Environ Microbiol 2020; 87:AEM.02191-20. [PMID: 33097506 DOI: 10.1128/aem.02191-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/06/2020] [Indexed: 01/04/2023] Open
Abstract
The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.
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Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis. Food Microbiol 2020; 93:103613. [PMID: 32912585 DOI: 10.1016/j.fm.2020.103613] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.
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Kamilari E, Tomazou M, Antoniades A, Tsaltas D. High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? INTERNATIONAL JOURNAL OF FOOD SCIENCE 2019; 2019:5837301. [PMID: 31886165 PMCID: PMC6925717 DOI: 10.1155/2019/5837301] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022]
Abstract
Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.
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Affiliation(s)
- Elena Kamilari
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
| | | | | | - Dimitrios Tsaltas
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
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21
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Santos ADOD, Ávila CLDS, Soares C, Carvalho BF, Schwan RF, Lima N. Lactic acid bacteria diversity in corn silage produced in Minas Gerais (Brazil). ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01528-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Abstract
Purpose
The diversity of lactic acid bacteria (LAB) in silages produced in warm climate countries is not well known. This study aimed to identify and characterise the metabolic and genotypic aspects of autochthonous LAB isolated from corn silage produced in the state of Minas Gerais, Brazil.
Methods
Eighty-eight LAB were isolated. To evaluate their performance at the strain level, all isolates were distinguished among strains using random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and repetitive extragenic palindromic PCR (REP-PCR) techniques. The organic acid and ethanol production were determined by high-performance liquid chromatography (HPLC).
Result
The fingerprints obtained by RAPD-PCR with a M13 primer were more discriminatory than those obtained with the REP-PCR technique using a (GACA)4 primer. Moreover, 28 representative isolates were identified as Lactobacillus acidophilus, L. buchneri, L. casei, L. diolivorans, L. hilgardii, L. paracasei, L. parafarraginis, L. plantarum, L. rhamnosus, L. zeae and Pediococcus acidilactici. Different fingerprinting profiles between isolates within the same species were observed. However, some strains isolated from different silages showed the same band profile, thus suggesting the presence of clusters with high similar fingerprints in silages from various regions.
Conclusion
A variation in LAB diversity was observed in the silages of the evaluated regions, with L. rhamnosus and L. buchneri showing the highest distribution. Differences in organic acid production were observed among the strains belonging to the same species. This research contributes to a better understanding of the LAB community present in corn silage produced in warm climates. These strains will be studied as potential silage starters.
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Milk and Dairy Products. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Du H, Wang X, Zhang Y, Xu Y. Exploring the impacts of raw materials and environments on the microbiota in Chinese Daqu starter. Int J Food Microbiol 2019; 297:32-40. [DOI: 10.1016/j.ijfoodmicro.2019.02.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/01/2023]
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Yeluri Jonnala BR, McSweeney PLH, Sheehan JJ, Cotter PD. Sequencing of the Cheese Microbiome and Its Relevance to Industry. Front Microbiol 2018; 9:1020. [PMID: 29875744 PMCID: PMC5974213 DOI: 10.3389/fmicb.2018.01020] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/30/2018] [Indexed: 12/28/2022] Open
Abstract
The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.
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Affiliation(s)
- Bhagya R Yeluri Jonnala
- Food and Nutrition Deptartment, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Fermoy, Ireland
| | | | | | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Ireland.,APC Microbiome Ireland, Cork, Ireland
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Parente E, Zotta T, Faust K, De Filippis F, Ercolini D. Structure of association networks in food bacterial communities. Food Microbiol 2017. [PMID: 29526226 DOI: 10.1016/j.fm.2017.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of microbial association networks was investigated for seventeen studies on food bacterial communities using the CoNet app. The results were compared with those for host and environmental microbiomes. Microbial association networks of food bacterial communities shared several properties with those of host microbiomes, although they were less complex and lacked a scale-free, small world structure that is characteristic of environmental microbial communities. This may depend on both the initial contamination pattern, whose main source is the raw material microbiome, and on the copiotrophic nature of food environments, with lack of well defined, specific niches. The selective factors which are characteristic of fermentation and spoilage drastically simplified microbial association networks and showed the emergence of negative hubs. Co-presence and mutual exclusion networks had a radically different structure, with high clustering coefficient in the first and high heterogeneity in the latter. Node properties (degree, positive degree, betweenness centrality, abundance) can be combined in plots, which allow a rapid identification of hub species. The combined use of three network inference tools (CoNet, SparCC, and SPIEC-EASI) confirmed that microbial association network detection is method specific, but several coherent copresence or mutual exclusion relationships were detected by at least two different methods.
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Affiliation(s)
- Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, 85100 Potenza, Italy.
| | - Teresa Zotta
- Istituto di Scienze dell'Alimentazione, CNR, 83100 Avellino, Italy
| | - Karoline Faust
- Department of Microbiology and Immunology, REGA Institute, KU Leuven, 3000, Belgium
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
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26
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Kłopot A, Zakrzewska A, Lecion D, Majewska JM, Harhala MA, Lahutta K, Kaźmierczak Z, Łaczmański Ł, Kłak M, Dąbrowska K. Real-Time qPCR as a Method for Detection of Antibody-Neutralized Phage Particles. Front Microbiol 2017; 8:2170. [PMID: 29163448 PMCID: PMC5672142 DOI: 10.3389/fmicb.2017.02170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/23/2017] [Indexed: 01/08/2023] Open
Abstract
The most common method for phage quantitation is the plaque assay, which relies on phage ability to infect bacteria. However, non-infective phage particles may preserve other biological properties; specifically, they may enter interactions with the immune system of animals and humans. Here, we demonstrate real-time quantitative polymerase chain reaction (qPCR) detection of bacteriophages as an alternative to the plaque assay. The closely related staphylococcal bacteriophages A3R and 676Z and the coliphage T4 were used as model phages. They were tested in vivo in mice, ex vivo in human sera, and on plastic surfaces designed for ELISAs. T4 phage was injected intravenously into pre-immunized mice. The phage was completely neutralized by specific antibodies within 5 h (0 pfu/ml of serum, as determined by the plaque assay), but it was still detected by qPCR in the amount of approximately 107 pfu/ml of serum. This demonstrates a substantial timelapse between "microbiological disappearance" and true clearance of phage particles from the circulation. In human sera ex vivo, qPCR was also able to detect neutralized phage particles that were not detected by the standard plaque assay. The investigated bacteriophages differed considerably in their ability to immobilize on plastic surfaces: this difference was greater than one order of magnitude, as shown by qPCR of phage recovered from plastic plates. The ELISA did not detect differences in phage binding to plates. Major limitations of qPCR are possible inhibitors of the PCR reaction or free phage DNA, which need to be considered in procedures of phage sample preparation for qPCR testing. We propose that phage pharmacokinetic and pharmacodynamic studies should not rely merely on detection of antibacterial activity of a phage. Real-time qPCR can be an alternative for phage detection, especially in immunological studies of bacteriophages. It can also be useful for studies of phage-based drug nanocarriers or biosensors.
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Affiliation(s)
- Anna Kłopot
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Adriana Zakrzewska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Dorota Lecion
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Joanna M Majewska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Marek A Harhala
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Karolina Lahutta
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Zuzanna Kaźmierczak
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Łukasz Łaczmański
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Research and Development Center, Regional Specialist Hospital, Wrocław, Poland
| | - Marlena Kłak
- Research and Development Center, Regional Specialist Hospital, Wrocław, Poland
| | - Krystyna Dąbrowska
- Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland.,Research and Development Center, Regional Specialist Hospital, Wrocław, Poland
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Cardinali G, Corte L, Robert V. Next Generation Sequencing: problems and opportunities for next generation studies of microbial communities in food and food industry. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Levante A, De Filippis F, La Storia A, Gatti M, Neviani E, Ercolini D, Lazzi C. Metabolic gene-targeted monitoring of non-starter lactic acid bacteria during cheese ripening. Int J Food Microbiol 2017; 257:276-284. [PMID: 28735145 DOI: 10.1016/j.ijfoodmicro.2017.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 06/23/2017] [Accepted: 07/02/2017] [Indexed: 02/04/2023]
Abstract
Long ripened cheeses, such as Grana Padano (GP), a Protected Designation of Origin (PDO) Italian cheese, harbor a viable microbiota mainly composed of non-starter lactic acid bacteria (NSLAB), which contribute to the final characteristics of cheese. The NSLAB species Lactobacillus rhamnosus, Lb. casei and Lb. paracasei are frequently found in GP, and form a closely related taxonomic group (Lb. casei group), making it difficult to distinguish the three species through 16S rRNA sequencing. SpxB, a metabolic gene coding for pyruvate oxidase in Lb. casei group, was recently used to distinguish the species within this bacterial group, both in pure cultures and in cheese, where it could provide an alternative energy source through the conversion of pyruvate to acetate. The aim of this work was to study the evolution of the metabolically active microbiota during different stages of GP ripening, targeting 16S rRNA to describe the whole microbiota composition, and spxB gene to monitor the biodiversity within the Lb. casei group. Furthermore, activation of pyruvate oxidase pathway was measured directly in cheese by reverse transcription real time PCR (RT-qPCR). The results showed that Lb. casei group dominates throughout the ripening and high-throughput sequencing of spxB allowed to identify four clusters inside the Lb. casei group. The dynamics of the sequence types forming the clusters were followed during ripening. Pyruvate oxidase pathway was expressed in cheese, showing a decreasing trend over ripening time. This work highlights how the composition of the microbiota in the early manufacturing stages influences the microbial dynamics throughout ripening, and how targeting of a metabolic gene can provide an insight into the activity of strains relevant for dairy products.
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Affiliation(s)
- Alessia Levante
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy.
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici, Italy.
| | - Antonietta La Storia
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Monica Gatti
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy
| | - Erasmo Neviani
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Camilla Lazzi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 49/A, 43124 Parma, Italy
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29
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De Filippis F, Parente E, Ercolini D. Metagenomics insights into food fermentations. Microb Biotechnol 2016; 10:91-102. [PMID: 27709807 PMCID: PMC5270737 DOI: 10.1111/1751-7915.12421] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 11/26/2022] Open
Abstract
This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.
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Affiliation(s)
- Francesca De Filippis
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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30
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Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population diversity. Int J Food Microbiol 2016; 236:138-47. [PMID: 27497152 DOI: 10.1016/j.ijfoodmicro.2016.07.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/07/2016] [Accepted: 07/26/2016] [Indexed: 02/05/2023]
Abstract
The phosphoserine phosphatase gene (serB) of Streptococcus thermophilus is the most polymorphic gene among those used in Multilocus Sequence Typing schemes for this species and has been used for both genotyping of isolates and for evaluation of population diversity. However, the information on the potential of this gene as a marker for diversity in S. thermophilus species is still fragmentary. In this study, we evaluated serB nucleotide polymorphism and its potential impact on protein structure using data from traditional sequencing. In addition we evaluated the ability of serB targeted high-throughput sequencing in studying the diversity of S. thermophilus populations in cheese and starter cultures. Data based on traditional cultivation based techniques and sequencing provided evidence that the distribution of serB alleles varies significantly in some environments (commercial starter cultures, traditional starter cultures, cheese). Mutations had relatively little impact on predicted protein structure and were not found in domains that are predicted to be important for its functionality. Cultivation independent, serB targeted high-throughput sequencing provided evidence for significantly different alleles distribution in different cheese types and detected fluctuations in alleles abundance in a mixed strain starter reproduced by backslopping. Notwithstanding some shortcomings of this method that are discussed here, the cultivation independent approach appears to be more sensitive than cultivation based approaches based on isolation and traditional sequencing.
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31
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Parente E, Cocolin L, De Filippis F, Zotta T, Ferrocino I, O'Sullivan O, Neviani E, De Angelis M, Cotter PD, Ercolini D. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis. Int J Food Microbiol 2015; 219:28-37. [PMID: 26704067 DOI: 10.1016/j.ijfoodmicro.2015.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/27/2015] [Accepted: 12/04/2015] [Indexed: 12/12/2022]
Abstract
Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry.
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Affiliation(s)
- Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy.
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Science, University of Torino, Grugliasco, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Teresa Zotta
- Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Science, University of Torino, Grugliasco, Italy
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Institute, Cork, Ireland
| | - Erasmo Neviani
- Department of Food Science, Parma University, Parco Area delle Scienze 48, /A, Parma, Italy
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland; APC Microbiome Institute, Cork, Ireland
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
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