Fermentation was empirically developed by several ancient societies with the aim of preserving foods and enhancing their nutritional and sensory attributes. To date, fermented foods deeply characterize the eating habits and folklore of numerous countries around the world. The present Ph.D. thesis is aimed to explore the microbiota and its impact on microbiological and physico-chemical traits of European traditional fermented foods of animal origin. Spontaneously fermented fish-based products of Northern European countries (Swedish sour herring Surströmming, Icelandic fermented shark Hákarl, fermented fish sausage of Southern Italy) and meat-based products of Mediterranean countries (Ciauscolo salami and fermented liver sausage, both handcrafted in the Marche Region of Italy, Cacholeira blood sausage and Painho de Porco Preto sausage, both manufactured in Portugal) were considered. To reach this goal, a combined approach of different analytical techniques was applied. First, culture-dependent methods, including the use of growth selective media and genotypic identification of selected isolates, were used. Among culture-independent methods, qPCR with specific primers of microbiological interest, and NGS of bacteria and eumycete conserved regions were adopted. In addition, physico-chemical measurements on key parameters affecting microbial growth were carried out. The major contribution of lactic acid bacteria during the fermentative process of both fish-based and meat-based products was clearly confirmed. Although there was variation between lactic acid bacteria populations of meat-based (i.e., Leuconostoc carnosum, Dellaglioa algida) and fish-based products (i.e., Tetragenococcus halophilus, Lactiplantibacillus plantarum), the regular detection of Latilactobacillus sakei in both the food matrices was highlighted. The data collected allowed to notice also minor microbial populations constantly occurring in typical fermented foods of animal origin, namely coagulase-negative staphylococci (the species Staphylococcus succinus, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus xylosus, Staphylococcus sciuri, Staphylococcus saprophyticus, and Staphylococcus caprae were identified) and yeasts (Debaryomyces hansenii was prevalent). The occurrence of genes involved in histamine production as well as its quantification in Surströmming, Hákarl and fermented fish sausage were assessed. In addition, a first sight on the occurrence of genes involved in tetracycline resistance in Surströmming samples was given. The detection of histamine and genes related both to histamine production and tetracycline resistance suggested the need for continuous monitoring and further investigations, including the application of microorganisms selected for the absence of such extrinsic determinants. In order to obtain specific adjunct or starter cultures for safety and quality assurance of both fish-based and meat-based products, lactic acid bacteria species, namely L. sakei e Latilactobacillus curvatus, were isolated from fermented fish sausage and Ciauscolo salami samples. The characterization of these isolates allowed to collect few candidates with potential pro-technological features. The present Ph.D. thesis allowed to build the first foundations of biodiversity sources not yet explored. The collected information provides solid ground for future studies aimed to comprehend fermentation dynamics and optimize production processes of typical delicacies analyzed.
La pratica della fermentazione è stata sviluppata empiricamente da varie civiltà antiche con lo scopo di preservare gli alimenti ed esaltare le loro caratteristiche nutrizionali e sensoriali. Ad oggi, gli alimenti fermentati caratterizzano profondamente le abitudini alimentari e il folclore di numerosi paesi del mondo. La presente tesi di dottorato ha lo scopo di esplorare il microbiota e il suo impatto sui tratti microbiologici e fisico-chimici di alimenti fermentati di origine animale tipici europei. Sono stati presi in considerazione prodotti caratterizzati da una fermentazione spontanea, tra cui alimenti a base di pesce (l'aringa acida svedese Surströmming, lo squalo fermentato islandese Hákarl, i salami di pesce fermentati del Sud Italia) e a base di carne (il Ciauscolo e i salami di fegato fermentati, entrambi derivanti dalla regione Marche d'Italia, i salami Cacholeira e Painho de Porto Preto, entrambi derivanti dal Portogallo). A tale scopo, è stato adottato un approccio combinato di differenti tecniche analitiche. Inizialmente, sono stati utilizzati metodi coltura-dipendenti, tra cui l'uso di terreni selettivi di crescita e l'identificazione genotipica di isolati. Tra i metodi coltura-indipendenti, sono stati utilizzati la qPCR con specifici primer di interesse microbiologico, e il NGS di regioni conservate di batteri ed eumiceti. Inoltre, sono state condotte misurazioni fisico-chimiche di parametri chiave che influenzano la crescita microbica. I risultati hanno confermato il maggior contributo dei batteri lattici durante il processo fermentativo sia di prodotti a base di pesce che di carne. Nonostante ci fossero variazioni tra le popolazioni di batteri lattici degli alimenti a base di carne (ad esempio, Leuconostoc carnosum, Dellaglioa algida) e di pesce (ad esempio, Tetragenococcus halophilus, Lactiplantibacillus plantarum), è stata evidenziata la costante presenza di Latilactobacillus sakei in entrambe le matrici. I dati raccolti hanno mostrato anche popolazioni microbiche minori regolarmente identificate negli alimenti fermentati di origine animale, ossia gli stafilococchi coagulasi-negativi (sono state identificate le specie Staphylococcus succinus, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus xylosus, Staphylococcus sciuri, Staphylococcus saprophyticus, e Staphylococcus caprae) e i lieviti (Debaryomyces hansenii era prevalente). Sono state condotte analisi per verificare la presenza di geni coinvolti nella produzione di istamina, così come la sua quantificazione, nel Surströmming, nell'Hákarl e nei salami fermentati di pesce. In più, è stato dato un primo sguardo alla presenza di geni coinvolti nella resistenza alle tetracicline nei campioni di Surströmming. La determinazione di istamina e di geni relativi sia alla produzione di istamina che alla resistenza alle tetracicline hanno dimostrato la necessità per un monitoraggio costante e ulteriori investigazioni, inclusa l'applicazione di microrganismi selezionati in base all'assenza di tali determinanti estrinseci. Per ottenere specifiche colture aggiunte o starter in grado di assicurare sicurezza e qualità di prodotti fermentati sia a base di carne che di pesce, sono state isolate specie di batteri lattici, tra cui L. sakei e Latilactobacillus curvatus. La caratterizzazione di questi isolati ha permesso di collezionare alcuni candidati con caratteristiche pro-tecnologiche. La presente tesi di dottorato getta le fondamenta di fonti di biodiversità non ancora esplorate. Le informazioni ottenute forniscono un terreno solido per studi futuri mirati a comprendere le dinamiche di fermentazione e ottimizzare i processi di produzione delle prelibatezze tipiche analizzate.
New insights into the microbiota of European typical fermented foods of animal origin / Belleggia, Luca. - (2023 Jun 14).
New insights into the microbiota of European typical fermented foods of animal origin
BELLEGGIA, LUCA
2023-06-14
Abstract
Fermentation was empirically developed by several ancient societies with the aim of preserving foods and enhancing their nutritional and sensory attributes. To date, fermented foods deeply characterize the eating habits and folklore of numerous countries around the world. The present Ph.D. thesis is aimed to explore the microbiota and its impact on microbiological and physico-chemical traits of European traditional fermented foods of animal origin. Spontaneously fermented fish-based products of Northern European countries (Swedish sour herring Surströmming, Icelandic fermented shark Hákarl, fermented fish sausage of Southern Italy) and meat-based products of Mediterranean countries (Ciauscolo salami and fermented liver sausage, both handcrafted in the Marche Region of Italy, Cacholeira blood sausage and Painho de Porco Preto sausage, both manufactured in Portugal) were considered. To reach this goal, a combined approach of different analytical techniques was applied. First, culture-dependent methods, including the use of growth selective media and genotypic identification of selected isolates, were used. Among culture-independent methods, qPCR with specific primers of microbiological interest, and NGS of bacteria and eumycete conserved regions were adopted. In addition, physico-chemical measurements on key parameters affecting microbial growth were carried out. The major contribution of lactic acid bacteria during the fermentative process of both fish-based and meat-based products was clearly confirmed. Although there was variation between lactic acid bacteria populations of meat-based (i.e., Leuconostoc carnosum, Dellaglioa algida) and fish-based products (i.e., Tetragenococcus halophilus, Lactiplantibacillus plantarum), the regular detection of Latilactobacillus sakei in both the food matrices was highlighted. The data collected allowed to notice also minor microbial populations constantly occurring in typical fermented foods of animal origin, namely coagulase-negative staphylococci (the species Staphylococcus succinus, Staphylococcus epidermidis, Staphylococcus equorum, Staphylococcus xylosus, Staphylococcus sciuri, Staphylococcus saprophyticus, and Staphylococcus caprae were identified) and yeasts (Debaryomyces hansenii was prevalent). The occurrence of genes involved in histamine production as well as its quantification in Surströmming, Hákarl and fermented fish sausage were assessed. In addition, a first sight on the occurrence of genes involved in tetracycline resistance in Surströmming samples was given. The detection of histamine and genes related both to histamine production and tetracycline resistance suggested the need for continuous monitoring and further investigations, including the application of microorganisms selected for the absence of such extrinsic determinants. In order to obtain specific adjunct or starter cultures for safety and quality assurance of both fish-based and meat-based products, lactic acid bacteria species, namely L. sakei e Latilactobacillus curvatus, were isolated from fermented fish sausage and Ciauscolo salami samples. The characterization of these isolates allowed to collect few candidates with potential pro-technological features. The present Ph.D. thesis allowed to build the first foundations of biodiversity sources not yet explored. The collected information provides solid ground for future studies aimed to comprehend fermentation dynamics and optimize production processes of typical delicacies analyzed.File | Dimensione | Formato | |
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