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Magliulo R, Valentino V, Balivo A, Esposito A, Genovese A, Ercolini D, De Filippis F. Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas. Food Res Int 2024; 192:114798. [PMID: 39147499 DOI: 10.1016/j.foodres.2024.114798] [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: 06/09/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024]
Abstract
Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.
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Affiliation(s)
- Raffaele Magliulo
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy; NBFC - National Biodiversity Future Center, Palermo, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Andrea Balivo
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Alessia Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Alessandro Genovese
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Piazza Carlo di Borbone 1, 80055 Portici, Naples, Italy; NBFC - National Biodiversity Future Center, Palermo, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
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Alexandraki V, Kazou M, Blom J, Pot B, Papadimitriou K, Tsakalidou E. Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species. Front Microbiol 2019; 10:2916. [PMID: 31956321 PMCID: PMC6951406 DOI: 10.3389/fmicb.2019.02916] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs). Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.
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Affiliation(s)
- Voula Alexandraki
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Bruno Pot
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Effie Tsakalidou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
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Autochthonous and Probiotic Lactic Acid Bacteria Employed for Production of "Advanced Traditional Cheeses". Foods 2019; 8:foods8090412. [PMID: 31540237 PMCID: PMC6769867 DOI: 10.3390/foods8090412] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Microbial characterization of two Italian traditional cheeses, Giuncata and Caciotta Leccese, was carried out, with the aim to isolate autochthonous bacterial strains to be used as starters to improve and standardize the quality of these cheeses. More than 400 bacterial isolates were found, using PCR-based identification, to belong to 12 species of the Streptococcus, Lactococcus, Lactobacillus, and Leuconostoc genera. The dominant strains were screened for antagonistic activity against pathogenic and spoilage bacteria and exopolysaccharide production, acidification, and proteolytic activity. Since Streptococcus macedonicus was found to be the most prevalent lactic acid bacteria species present in milk and in both types of cheese, the best performing strain of this species was successfully used, alone or in combination with a selected autochthonous Lactococcus lactis strain, in pilot-scale productions of Giuncata and Caciotta Leccese cheeses, respectively. The combined inoculums of selected autochthonous strains positively influenced the sensory characteristics of both Giuncata and Caciotta cheeses. Finally, the selected autochthonous cultures were enriched with a potentially probiotic Lactobacillus rhamnosus strain and successfully used in pilot-scale productions of these traditional cheeses. To the best of our knowledge, this is the first study reporting the use of an autochthonous S. macedonicus strain as a starter for the production of cheeses with added probiotics. In addition, the identification of the probiotic strain in the feces of healthy volunteers fed with the advanced traditional cheese proved its effectiveness as a carrier for the delivery of probiotics to the human body.
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Delorme C, Legravet N, Jamet E, Hoarau C, Alexandre B, El-Sharoud WM, Darwish MS, Renault P. Study of Streptococcus thermophilus population on a world-wide and historical collection by a new MLST scheme. Int J Food Microbiol 2016; 242:70-81. [PMID: 27894009 DOI: 10.1016/j.ijfoodmicro.2016.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/27/2023]
Abstract
We analyzed 178 Streptococcus thermophilus strains isolated from diverse products, from around the world, over a 60-year period with a new multilocus sequence typing (MLST) scheme. This collection included isolates from two traditional cheese-making sites with different starter-use practices, in sampling campaigns carried out over a three years period. The nucleotide diversity of the S. thermophilus population was limited, but 116 sequence types (ST) were identified. Phylogenetic analysis of the concatenated sequences of the six housekeeping genes revealed the existence of groups confirmed by eBURST analysis. Deeper analyses performed on 25 strains by CRISPR and whole-genome analysis showed that phylogenies obtained by MLST and whole-genome analysis were in agreement but differed from that inferred by CRISPR analysis. Strains isolated from traditional products could cluster in specific groups indicating their origin, but also be mixed in groups containing industrial starter strains. In the traditional cheese-making sites, we found that S. thermophilus persisted on dairy equipment, but that occasionally added starter strains may become dominant. It underlined the impact of starter use that may reshape S. thermophilus populations including in traditional products. This new MLST scheme thus provides a framework for analyses of S. thermophilus populations and the management of its biodiversity.
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Affiliation(s)
- Christine Delorme
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nicolas Legravet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Emmanuel Jamet
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Caroline Hoarau
- Actilait, 419, route des champs laitiers, F-74 800 La Roche sur Foron, France
| | - Bolotin Alexandre
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Walid M El-Sharoud
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Mohamed S Darwish
- Food Safety and Microbial Physiology Laboratory, Dairy Department, Faculty of Agriculture, Mansoura University, Mansoura, Egypt
| | - Pierre Renault
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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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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The spxB gene as a target to identify Lactobacillus casei group species in cheese. Food Microbiol 2016; 59:57-65. [PMID: 27375244 DOI: 10.1016/j.fm.2016.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 03/17/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022]
Abstract
This study focused on the spxB gene, which encodes for pyruvate oxidase. The presence of spxB in the genome and its transcription could be a way to produce energy and allow bacterial growth during carbohydrate starvation. In addition, the activity of pyruvate oxidase, which produces hydrogen peroxide, could be a mechanism for interspecies competition. Because this gene seems to provide advantages for the encoding species for adaptation in complex ecosystems, we studied spxB in a large set of cheese isolates belonging to the Lactobacillus casei group. Through this study, we demonstrated that this gene is widely found in the genomes of members of the L. casei group and shows variability useful for taxonomic studies. In particular, the HRM analysis method allowed for a specific discrimination between Lactobacillus rhamnosus, Lactobacillus paracasei and L. casei. Regarding the coding region, the spxB functionality in cheese was shown for the first time by real-time PCR, and by exploiting the heterogeneity between the L. casei group species, we identified the bacterial communities encoding the spxB gene in this ecosystem. This study allowed for monitoring of the active bacterial community involved in different stages of ripening by following the POX pathway.
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Parente E, Guidone A, Matera A, De Filippis F, Mauriello G, Ricciardi A. Microbial community dynamics in thermophilic undefined milk starter cultures. Int J Food Microbiol 2016; 217:59-67. [DOI: 10.1016/j.ijfoodmicro.2015.10.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/28/2015] [Accepted: 10/13/2015] [Indexed: 02/08/2023]
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Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles. Lebensm Wiss Technol 2016. [DOI: 10.1016/j.lwt.2015.08.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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De Filippis F, La Storia A, Stellato G, Gatti M, Ercolini D. A selected core microbiome drives the early stages of three popular italian cheese manufactures. PLoS One 2014; 9:e89680. [PMID: 24586960 PMCID: PMC3933672 DOI: 10.1371/journal.pone.0089680] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/22/2014] [Indexed: 02/07/2023] Open
Abstract
Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In the three cheese manufactures the initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. In this study, NWCs and the corresponding curds from M, GP and PR manufactures were analyzed by culture-independent pyrosequencing of the amplified V1–V3 regions of the 16S rRNA gene, in order to provide insights into the microbiota involved in the curd acidification. Moreover, culture-independent high-throughput sequencing of lacS gene amplicons was carried out to evaluate the biodiversity occurring within the S. thermophilus species. Beta diversity analysis showed a species-based differentiation between GP-PR and M manufactures indicating differences between the preparations. Nevertheless, all the samples shared a naturally-selected core microbiome, that is involved in the curd acidification. Type-level variability within S. thermophilus species was also found and twenty-eight lacS gene sequence types were identified. Although lacS gene did not prove variable enough within S. thermophilus species to be used for quantitative biotype monitoring, the possibility of using non rRNA targets for quantitative biotype identification in food was highlighted.
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Affiliation(s)
- Francesca De Filippis
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Antonietta La Storia
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Giuseppina Stellato
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Gatti
- Department of Food Science, University of Parma, Parma, Italy
- Multidisciplinary Interdepartmental Dairy Center - MILC, University of Parma, Parma, Italy
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- * E-mail:
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Novel Streptococcus infantarius subsp. infantarius variants harboring lactose metabolism genes homologous to Streptococcus thermophilus. Food Microbiol 2012; 31:33-42. [DOI: 10.1016/j.fm.2012.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 02/03/2012] [Accepted: 02/06/2012] [Indexed: 02/07/2023]
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A real-time PCR method targeting a gene sequence encoding 16S rRNA processing protein, rimM, for detection and enumeration of Streptococcus thermophilus in dairy products. Food Res Int 2009. [DOI: 10.1016/j.foodres.2009.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lazzi C, Bove CG, Sgarbi E, Gatti M, Monica G, La Gioia F, Torriani S, Sandra T, Neviani E. Application of AFLP fingerprint analysis for studying the biodiversity of Streptococcus thermophilus. J Microbiol Methods 2009; 79:48-54. [PMID: 19647766 DOI: 10.1016/j.mimet.2009.07.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 07/22/2009] [Indexed: 11/16/2022]
Abstract
Streptococcus thermophilus is a lactic acid bacteria (LAB) widely used in milk fermentation processes as a starter culture. In this work the genetic diversity of S. thermophilus isolates from different sources was analyzed using Amplified Fragment Length Polymorphism fingerprinting (AFLP). Since this is the first report that indicates the application of AFLP in order to study genotypic polymorphism in S. thermophilus species, an optimization of experimental conditions was carried out to decide the optimal AFLP analysis protocol. Furthermore the fingerprinting resolutions of AFLP and RAPD (Random Amplified Polymorphic DNA) were evaluated and compared. The overall data suggest that genotypic characterization performed by AFLP provide a better view of microbial diversity of S. thermophilus, indicating that RAPD is less discriminating than AFLP. The successful use of AFLP analysis in the characterization of S. thermophilus strains reported in this study suggests the potential uses for this technique to define the whole-genome diversity of each specific strain, as an alternative to the fingerprinting methods used till now.
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Affiliation(s)
- Camilla Lazzi
- Dipartimento di Genetica, Biologia dei Microrganismi, Antropologia, Evoluzione, Università degli Studi di Parma, Viale Usberti 11/A, 43100 Parma, Italy.
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Tyvaert G, Morel C, Joly JP, Decaris B, Charron-Bourgoin F. The constant gene orf14.9, which belongs to the variable eps (exopolysaccharide) cluster, is involved in the cell growth of Streptococcus thermophilus. Can J Microbiol 2006; 52:908-12. [PMID: 17110984 DOI: 10.1139/w06-047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Streptococcus thermophilus, the eps clusters involved in exopolysaccharide (EPS) biosynthesis are very polymorphic, nevertheless they all contain a highly conserved sequence corresponding to that of orf14.9. This open reading frame (ORF) is transcribed in a reverse direction with respect to eps genes. Amino acid sequence analysis showed a possible transmembrane location of the putative Orf14.9 protein but did not permit a proposed function. Insertional mutants of orf14.9 were obtained in strains NST2280 and A054 of S. thermophilus. EPS yields of these mutants are similar to those of their respective wild strains, suggesting that orf14.9 does not modify the quantity of produced EPS. Growth parameter determination for wild strains and their respective mutants showed that orf14.9 is involved in the cell growth of S. thermophilus.Key words: Streptococcus thermophilus, eps cluster, orf14.9, sequence analysis, exopolysaccharide biosynthesis, cell growth.
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Affiliation(s)
- Guillaume Tyvaert
- Laboratoire de génétique et microbiologie, Université Henri Poincaré, Faculté des sciences et techniques, Vandoeuvre-lès-Nancy, France
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Hols P, Hancy F, Fontaine L, Grossiord B, Prozzi D, Leblond-Bourget N, Decaris B, Bolotin A, Delorme C, Dusko Ehrlich S, Guédon E, Monnet V, Renault P, Kleerebezem M. New insights in the molecular biology and physiology ofStreptococcus thermophilusrevealed by comparative genomics. FEMS Microbiol Rev 2005. [DOI: 10.1016/j.fmrre.2005.04.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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