En la presente Tesis Doctoral se estudió la capacidad de conservación y la calidad sensorial de diversos platos preparados a base de carne o pescado cocinados mediante la tecnología sous vide y conservados en refrigeración. El objetivo fue estudiar el deterioro y determinar la vida comercial con el fin de introducir mejoras tecnológicas. Se determinaron diversos parámetros microbiológicos (enterobacterias totales, aerobios y anaerobios psicrófilos, bacterias ácido lácticas y mohos y levaduras), físico-químicos (pH, aw, acidez, textura instrumental y color CIELab) y sensoriales (análisis descriptivo cuantitativo del aspecto, olor, olor, sabor y textura). Los resultados obtenidos indican que los tiempos y temperaturas recomendados para cocinar la carne y/o el pescado sous vide aseguraron una correcta pasteurización. No se detectaron cambios apreciables de humedad, acidez, color o textura. Sólo el análisis sensorial permitió evaluar el deterioro de la carne y/o pescado sous vide durante su almacenamiento. La tecnología sous vide proporcionó platos refrigerados a base de carne y/o pescado con una alta aceptación y una vida comercial adecuada para su distribución en sistemas de catering. / The present PhD thesis analyses the preserving capacity and the sensory quality of different meat-or-fish-based dishes which are cooked by using the sous vide method and recreating the conditions of catering industry.The aim was to study the spoilage and to determine the shelf-life of these products to introduce technological improvements. For this purpose, several parameters were established: microbiological (aerobic and anaerobic psychrotrophs, lactic acid bacteria, Enterobacteriaceae, mould and yeasts), physical-chemical (pH, aw, acidity, instrumental texture and colour CIELab) and sensory (QDA of the appearance, colour, odour, flavour and texture). The results indicated that the periods of time and temperatures which are recommended to cook sous vide meat or fish guaranteed a correct pasteurization which prevented the proliferation, at 2 ºC, of Enterobacteriaceae and altering microorganisms. Only the sensory analysis permitted the evaluation of the spoilage of the sous vide cooked meat or fish during their storage. All this would leave a considerable safety margin in the cooking process so that the sensory quality could be adjusted. Besides, no noticeable variations of humidity, acidity, colour or texture were detected by the physical-chemical techniques, which were employed.

This thesis purposes and develops inductively coupled LC (inductive-capacitive) pH sensors based on pH-sensitive electrode pair. The LC resonator circuit is based on a varactor and measures the low frequency potential difference. For wireless pH monitoring, the resonator circuit is integrated with a pH-sensitive electrode pair. This sensor demonstrates a linear response over 2 to 12 pH dynamic range, 0.1 pH accuracy and long-term stability. Accurate measurement of pH using electrode-based sensors is affected by temperature variation. A technique of simultaneously measuring two parameters, pH and temperature, with a single RLC resonator based sensor is presented. An algorithm is developed, which applies both pH and temperature measurement to incorporate temperature compensation in pH measurement. For in-fluid applications, an encapsulation method is applied to the LC resonator based sensor to reduce the influence of medium permittivity and conductivity on the sensor measurement. Non-invasive way to obtain reliable pH information from bacterial culture bioprocesses is demonstrated with the fluid embeddable sensor. The pH sensor is remodeled to an acidic and basic volatile sensor by embedding the electrodes in a hydrogel host electrolyte. Tests demonstrate that the volatile sensor has a detection limit of 1.5 ppm and 2 ppm for ammonia and acetic acid vapor, respectively. Application of the volatile sensor to fish spoilage monitoring shows that the sensor is capable of detecting the product rejection level with good sensitivity in real-time. It is important to develop low cost wireless passive pH sensor technologies for embedded applications such as bioprocess and food spoilage monitoring. The electrode-based passive LC sensor approach employed in this thesis overcomes drawbacks of some of the early developed passive pH sensors and can lead to an inexpensive implementation using printed electronics technology.

Thesis (MSc Food Sc)--University of Stellenbosch, 2001. / ENGLISH ABSTRACT:Aspalafhus linearis is an indigenous fynbos plant cultivated in the Clanwilliam area of the Western Cape, South Africa. The rooibos tea that is prepared from this plant, has become popular worldwide mainly due to the alleged health properties. Studies on the anti-microbial properties of green, black and oolong teas have shown that these teas have strong anti-microbial activity against a wide range of microbes. No studies have been done on the anti-microbial activity of rooibos tea and the aim of this study was to determine what impact rooibos tea extracts would have on the growth of different food spoilage and potential pathogenic microbes. Water and ethyl acetate extracts of fermented and unfermented rooibos tea were used to determine the inhibitory effect on the growth of an Escherichia coli strain. The E. coli culture was grown in tea-MRS with either added fermented or unfermented rooibos tea extracts. Both the water and ethyl acetate extracts showed a strong inhibitory effect against the E. coli strain in that there was a decrease in the final bacterial cell density (Nmax)(from 0.59 00 to 0.25 00) and the maximum specific growth rate (~max)(from 1.12 h-1 to 0.20 h-1) and an increase in the doubling time (~) (from 0.59 h to 1.80 h) and lag time (tlag)(from 4.81 h to 6.60 h) as the concentration of the soluble solids of the tea extracts was increased from 0.5 to 5.0 g.r1 . Furthermore, it was found that the fermented rooibos tea had a much stronger inhibitory effect (69% decrease in growth at 5.0 g.r1 soluble solids) compared to the unfermented rooibos tea extracts (35.1% decrease in growth at 5.0 g.r1 soluble solids). The resulting data indicated that rooibos tea had a very strong inhibitory effect on the growth of the E. coli strain. It was also found that the water extracts of rooibos tea showed a stronger inhibitory effect on the growth of the E. coli than the ethyl acetate extracts, indicating that the antimicrobial activity of rooibos tea is not exclusively due to the polyphenolic content - individual compounds. It was also determined that the rooibos tea water extracts showed a bacteriostatic action against the E. coli strain in that as soon as the tea is no longer part of the growth medium, the E. coli resumed a normal growth pattern. The data obtained showed that the inhibitory effect of rooibos tea water extracts (69% decrease in growth) against the growth of E. coli was more pronounced than that found when black tea water extracts (25.7% decrease in growth) at the same concentrations were used.Rooibos tea water extracts (0.5 - 5.0 g.r1) of fermented and unfermented tea were also used to determine the inhibitory effect on other food spoilage microbes and potential pathogens. Strains of Staphylococcus aureus, Bacillus cereus, Listeria monocytogenes, Streptococcus mutans, Saccharomyces cerevisiae and Zygosaccharomyces rouxii were grown in the presence of fermented and unfermented rooibos tea water extracts. The effect that fermented rooibos tea had on the growth of all the microbes tested was in the following order: Staph. aureus (90.8% decrease in growth) > L. monocytogenes (89.2% decrease in growth) > Strep. mutans (84.1% decrease in growth) > B. cereus (80.3% decrease in growth) > Sacch. cerevisiae (77.7% decrease in growth) > E. coli (69.0% decrease in growth). The rooibos tea clearly had an inhibitory effect on the growth of all the microbes, with the exception of the Z. rouxii strain where the presence of the tea water extracts was found to enhance the growth. The inhibitory effect of rooibos tea on the growth of these microbes was shown by changes in the growth parameters with Nmax and IJmaxshowing decreases, while the ld and tlagincreased as the concentration of the tea soluble solids was increased. As with E. coli, the fermented rooibos tea water extracts showed the stronger inhibitory effect on the growth of the various microbes. The data obtained in this study suggests that rooibos tea is not effective as an anti-microbial agent against all yeast species, but will strongly retard the growth of specific Gram-positive and Gram-negative bacteria. As long as rooibos tea is present, strong anti-microbial activity will be observed at a cup of tea concentration of 2.5 g.r1 soluble solids. These results may be of value to support the health claims associated with rooibos tea and may in the future lead to the use of rooibos tea as a "natural" food preservative. / AFRIKAANSE OPSOMMING:Aspalathus linearis is 'n inheemse fynbosplant wat gekultiveer word in die Clanwilliam area van die Wes Kaap, Suid-Afrika. Rooibostee, wat gemaak word van hierdie plante, het baie gewild geword wereldwyd a.g.v. die gesondheidsaspekte van hierdie tee. Studies toon dat groen, swart en oolong tee sterk anti-mikrobiese aktiwiteit het teen 'n wye reeks mikrobes. Aangesien daar voorheen geen studies gedoen is op die anti-mikrobiese aktiwiteit van rooibostee nie, was die doel van hierdie studie om die effek van rooibostee te bepaal op die groei van verskillende voedselbederwers en potensiele patogeniese mikrobes. Water- en etielasetaat-ekstrakte van gefermenteerde en ongefermenteerde rooibos tee is gebruik om die inhiberende effek op die groei van Escherichia coli te bepaal. Escherichia coli is gegroei in tee-MRS met bygevoegde gefermenteerde of ongefermenteerde rooibostee-ekstrakte. Seide die water- en etielasetaatekstrakte van rooibostee het 'n sterk inhiberende effek gewys teen E. coli en dit word gestaaf deur 'n afname in die finale bakteriese seldigtheid (Nmax)(vanaf 0.59 00 tot 0.25 00) en die maksimum spesifieke groeitempo (lJmax) (vanaf 1.12 h-1 tot 0.20 h-1) en 'n toename in die verdubbelingstyd (~) (vanaf 0.59 h tot 1.80 h) en die sloerfase (tlag)(vanaf 4.81 h tot 6.60 h) 5005 wat die konsentrasie van oplosbare vastestowwe van die tee toeneem van 0.5 tot 5.0 g.r1 . Verder is daar gevind dat die gefermenteerde rooibostee 'n baie sterker inhiberende effek het (69% afname in groei by 5.0 g.r1 oplosbare vastestowwe) in vergelyking met die ongefermenteerde rooibostee-ekstrakte (35.1% afname in groei by 5.0 g.r1 oplosbare vastestowwe). Die resultate van die data dui aan dat rooibos tee 'n baie sterk inhiberende effek het op die groei van die E. coli spesie. Die waterekstrakte van rooibostee het 'n sterker inhibisie getoon teen die groei van E. coli as die etielasetaat-ekstrakte, wat aandui dat die anti-mikrobiese aktiwiteit van rooibostee nie eksklusief toegeskryf kan word aan die polifenoliese samestelling nie. Daar is ook gevind dat rooibostee water-ekstrakte 'n bakteriostatiese effek het teen E. coli, want sodra die tee ekstrakte nie meer teenwoordig is in die groeimedium nie, hervat E. coli normale groei. Die data wys ook dat die inhiberende effek van rooibostee water-ekstrakte (69.0% afname in goei) teen E. coli baie sterker is as die van swart tee water-ekstrakte (25.7% afname in groei) by dieselfde konsentrasies.Rooibostee water-ekstrakte (0.5 - 5.0 g.r1) van gefermenteerde en ongefermenteerde rooibostee is ook gebruik om die inhiberende effek te bepaal teen ander voedselbederwers en potensiele patogene. Spesies van Staphylococcus aureus, Bacillus cereus, Listeria monocytogenes, Streptococcus mutans, Saccharomyces cerevisiae en Zygosaccharomyces rouxii is gegroei in die teenwoordigheid van gefermenteerde en ongefermenteerde rooibostee waterekstrakte. Die effek wat gefermenteerde rooibostee het op die groei van die getoetste mikrobes is 5005 volg: Staph. aureus (90.8% afname in groei) > L. monocytogenes (89.2% afname in groei) > Strep. mutans (84.1% afname in groei) > B. cereus (80.3% afname in groei) > Sacch. cerevisiae (77.7% afname in groei) > E. coli (69.0% afname in groei). Rooibostee het 'n duidelike inhiberende effek gehad teen al die organismes, behalwe teen Z. rouxii spes ie, waar die teenwoordigheid van rooibostee die groei van die organisme bevorder het. Die inhiberende effek van rooibostee teen die groei van hierdie mikrobes word ondersteun deur die groei parameters waar die Nmaxen IJmaxafgeneem het terwyl die ~ en tlagtoegeneem het 5005 wat die konsentrasie van die oplosbare vastestowwe toeneem. Die gefermenteerde rooibostee water-ekstrakte het ook 'n sterker inhiberende effek op die groei van die verskillende mikrobes net 5005 met E. coli. Die data wat verkry is van hierdie studie dui aan dat rooibostee nie effektief sal wees as 'n anti-mikrobiese middel teen aile gis spesies nie, maar dit sal die groei van spesifieke Gram-positiewe en Gram-negatiewe bakterie sterk vertraag. So lank as wat rooibostee teenwoordig is, sal sterk anti-mikrobiese aktiwiteit waargeneem word by 'n koppie-tee konsentrasie van 2.5 g.r1 oplosbare vastestowwe. Hierdie resultate kan help om die gesondheidseienskappe geassosieer met rooibostee te ondersteun en help om die gebruik van rooibostee as 'n "natuurlike" preserveermiddel te bevorder. dedicated to my parents

Parmi les desserts à base d’ovoproduits, l’île flottante est reconnue comme particulièrement sensible d’un point de vue microbiologique car sa commercialisation souffre de la survenue intempestive d’altérations que les industriels souhaitent maîtriser. Les travaux réalisés au cours de cette thèse avaient pour objectif de mieux appréhender ces phénomènes afin de mieux les contrôler. Nous avons montré que l’altération de l’île flottante concernait principalement la crème anglaise et qu’elle s’accompagnait d’un développement bactérien conséquent, d’une fréquente diminution du pH et de modifications sensorielles liées à l’aspect et à l’odeur. Les principales bactéries détectées ont été identifiées comme appartenant au groupe Bacillus cereus et aux genres Staphylococcus et Enterococcus. Le blanc d’œuf pasteurisé, utilisé pour la fabrication des œufs en neige, s’est avéré être une source de contamination possible.Cependant, l’implication de bactéries installées sous forme de biofilms dans l’environnement de production ou véhiculées par d’autres ingrédients a aussi été fortement envisagée. La ré-inoculation, en culture pure, d’une collection bactérienne représentative dans de la crème anglaise stérile a montré que différents types de modifications sensorielles et physico-chimiques s’exprimaient d’un genre bactérien à l’autre et qu’ils étaient notamment corrélés à la capacité des bactéries à consommer les sucres et les protéines de la crème anglaise et à produire des métabolites dont des composés volatils odorants. Ces résultats à l’appui, différents tests ont pu être proposés, p / Among the chilled egg products-based desserts, the French dessert “île flottante” is recognized as particularly sensitive from a microbiological point of view, because marketing is suffering from untimely spoilage occurrence that manufacturers wish to control. The work done in this thesis aimed to better understand these phenomena in order to better control them. We have shown that the dessert spoilage mainly concerned the custard cream and it was characterized by high bacterial count, frequent pH decreasing and sensory changes of appearance and smell. The main bacteria detected were identified as belonging to the Bacillus cereus group and Staphylococcus and Enterococcus genera. The possible involvement of bacteria from the pasteurized egg white, used for the egg white foaming, in the dessert spoilage issue was established.However, the involvement of bacteria from biofilms installed in the production environment or provided by other ingredients was also strongly suspected. The spoilage potential assessment of pure culture of a representative bacterial collection in sterile custard cream has shown that different types of sensory and physicochemical changes were expressed according to bacterial genus and that these changes were particularly correlated with the ability of bacteria to consume sugars and proteins of custard and to produce various volatile compounds with specific odorous. With these results, various tests have been proposed for a better control of the white egg batches orientation according to their microbiological quality and so to guarantee their safety with

Dans le contexte fromager, les champignons filamenteux du genre Mucor ont un rôle ambivalent. En fonction du fromage considéré, ils peuvent être assimilés à des microorganismes d’altération responsables de défauts de fabrication ou au contraire contribuer au développement des qualités organoleptiques des produits. Dans le cadre de ce travail, nous avons souhaité confirmer et objectiver la dichotomie classiquement faite en industrie fromagère entre espèces technologiques et espèces contaminantes, et investiguer les mécanismes d’adaptation potentiels mis en oeuvre chez les espèces technologiques. La morphologie et la croissance radiale de 7 souches représentatives d’espèces technologiques, contaminantes et non-fromagères (endophyte) de Mucor ont été étudiées sur différents milieux (synthétique, mimant le fromage et fromager) en fonction de facteurs clés du processus de production des fromages (température, aw, pH). Les valeurs cardinales de croissance ont été déterminées sur milieu synthétique, un modèle prédictif a été proposé et validé sur matrices fromagères pour le facteur température et la meilleure faculté de croissance des souches technologiques sur milieux fromagers par rapport au milieu synthétique a été démontrée. Une approche de protéomique comparée a permis de décrire les voies métaboliques mises en jeu par 4 de ces souches dans les deux types d’environnement, fromager et non-fromager, et 35 protéines spécifiquement surexprimées par la souche technologique M. lanceolatus UBOCC-A-109153 sur milieu mimant le fromage ont été identifiées. Les avantages compétitifs associés à ces potentiels marqueurs d’adaptation vont faire l’objet d’investigations complémentaires. / In the cheese industry context, Mucor species exhibit an ambivalent behavior, as some species are essential technological organisms contributing to the required organoleptic characteristics of some cheeses while some others can be spoiling agents. The present study aimed at better understanding this ambivalence and investigating the putative adaptation mechanisms to cheese existing in Mucor technological species. Morphology and radial growth of 7 representative Mucor species: technological, contaminant and non-cheese related (plant endophyte) species were monitored on different media (synthetic, cheese-mimicking media and cheese) in function of key parameters for cheese manufacture (temperature, aw, pH). Cardinal values were determined on synthetic medium and as a result a predictive model was proposed and validated on cheese matrices for the temperature parameter. Interestingly, cheese technological species exhibited higher optimal growth rates on cheese related matrices than on synthetic media, while the opposite was observed for non-technological species. A comparative proteomic approach allowed unraveling the main metabolic pathways playing a role in growth of 4 of the 7 studied strains on both synthetic medium and cheese-mimicking medium. This proteomic study also highlighted the occurrence of 35 proteins specifically expressed by the technological strains M. lanceolatus UBOCC-A-109153 on the cheese-mimicking medium. Putative competitive and adaptative advantages of these hypothetical adaptation markers will be tested through additional investigations.

M. Tech. (Biotechnology, Department of Biosciences, Faculty of Applied and Computer Sciences), Vaal University of Technology. / The Organization for Economic Co-operation and Development (OECD) and the Food and Agriculture Organization (FAO) of the United Nations predict that milk production and the dairy sector will remain one of the fastest-growing agricultural subsectors over the coming decade. The global milk production is projected to expand over the 2011-2020 period at an annual rate of 2%. In South Africa alone, approximately 14 – 15 million litres of milk are wasted annually due to microbial spoilage. Therefore, the identification of the spoilage microorganisms in the milk products is necessary. This will contribute towards the design of appropriate measures to prevent wastage due to spoilage and in turn contribute towards sustainability of the sector. Accordingly, one hundred samples of spoiled full cream UHT milk were collected from two plants of each of the two largest milk processors. These samples were examined visually, and the pH was measured. A presumptive identification up to genus level was conducted by examining morphological features and conducting Gram-stain, catalase and oxidase tests. Species-specific identification was done by using the Analytical Profile Index and Biolog system. Molecular profiling was done by sequencing the rDNA genes. The main spoilage organisms identified in the samples were Pseudomonas, Micrococcus, Bacillus, Enterococcus and Lactobacillus. All organisms belonging to the five genera were psychrotrophs, which are commonly found in biofilms in UHT milk processing equipment. Therefore, according to the study, the spoilage bacteria apparently entered into the milk due to inadequate cleaning-in-place (CIP) processes. More importantly, further studies should be conducted in order to identify the spoilage microbes and how CIP processes can be improved.

La viande de porc est l’un des produits alimentaires les plus consommés au monde. La demande pour des produits de viande salubres et de qualité par les consommateurs ne cesse d’augmenter à mesure que la consommation elle-même augmente. Pour pouvoir répondre à cette demande, la contamination microbienne doit être surveillée et maîtrisée. Il s’agit d’une préoccupation majeure pour les industries œuvrant en agroalimentaire, car la présence de bactéries pathogènes responsables de toxi-infections alimentaires chez les consommateurs est une menace pour la santé publique. De plus, la présence de bactéries d’altération rend la viande impropre à la consommation humaine et diminue la durée de vie des produits, entraînant un gaspillage alimentaire et des pertes économiques. La contamination initiale des carcasses de porc est un processus inévitable et se produit par l’apport continu de bactéries, particulièrement celles composant le microbiote (intestinal, oral) des porcs et de l’environnement de l’abattoir. Le contrôle de la qualité microbiologique et la description des communautés microbiennes retrouvées à la surface des carcasses et des viandes sont réalisés, en cultivant des micro-organismes indicateurs classiques tels que les bactéries aérobies mésophiles totales ou les entérobactéries. Aujourd’hui, de nouvelles approches existent pour caractériser l’ensemble des bactéries constituant un microbiote grâce à des méthodes de séquençage à haut débit dans le but d’en étudier toute sa diversité. Cependant, l’ensemble du microbiote des carcasses et des viandes, ainsi que sa diversité sont très peu connus en production porcine. Par conséquent, il y a un manque général d’information disponible sur la façon dont ce microbiote varie dans des conditions réelles de transformation et d’entreposage de la viande de porc. Ainsi, les principaux objectifs cette thèse étaient de décrire la variabilité du microbiote porcin retrouvé sur la surface des carcasses en fonction de la provenance de la ferme d’origine des animaux et des étapes du procédé d’abattage et celle du microbiote retrouvé sur la surface des viandes emballées sous vide en fonction des conditions d’entreposage, en plus de décrire la variation de ces microbiotes dans le temps. Pour cette thèse, trois échantillonnages ont été effectués dans un abattoir porcin au Québec, Canada. Des échantillons de surface de carcasses ont été prélevés à plusieurs étapes de la chaîne d’abattage et de transformation et ce, pendant plusieurs semaines. Des échantillons de longes de porc emballées sous vides et entreposées à plusieurs températures distinctes pendant 56 jours, pour imiter l’exportation de ces produits frais à l’étranger, ont également été prélevés. Des analyses microbiologiques classiques, à savoir le dénombrement d’indicateurs microbiens et la détection des bactéries pathogènes telles que Salmonella, ainsi que la caractérisation du microbiote via le séquençage de la région V4 de l’ARNr 16S sur la plateforme Illumina Miseq ont été réalisées. Globalement, les résultats ont montré que le microbiote de surface des carcasses de porc était similaire lorsque comparé après l’habillage des carcasse (jusqu’à la douche précèdent le refroidissement), et ce entre les zones basses (correspondant au cou) et hautes (correspondant au jambon), ainsi que selon l’origine des carcasses, provenant de différents élevages, abattues pendant une même journée. Le microbiote semblait être constitué de bactéries provenant du microbiote intestinal ou oral des porcs. À l’inverse, une différence entre les charges microbiennes était observée, avec des comptes bactériens plus élevés pour les indicateurs dans la partie correspondant au cou. Lorsque les microbiotes ont été comparés sur une période de quatre semaines, une plus grande diversité bactérienne a été observée sur les zones correspondant au jambon. La composition et la structure du microbiote à la surface des carcasses apparaissaient différentes selon les journées d’abattage et les différents quarts de production (matin vs après-midi). Après le refroidissement des carcasses, une diminution de la charge bactérienne ainsi que de la diversité ont été observées, telles qu’attendues, malgré le fait que la plupart des genres bactériens présents sur les carcasses avant le refroidissement ont également été détectés après ce même refroidissement. La caractérisation du microbiote de longes de porc emballées sous vide entreposées à des températures de −1,5°C et subissant des fluctuations de la température durant les 56 jours d’entreposage a démontré que la diversité, la composition et la structure du microbiote n’étaient pas impactées. Les communautés bactériennes identifiées sur les carcasses de porc avant et après le refroidissement, tels qu’Escherichia, Shigella et Lactobacillales_unclassified, semblaient contribuer au microbiote des longes tout au long de l’entreposage. Les résultats ont révélé que les microbiotes de longes de porc, similaires en début de l’entreposage, se différenciaient après 56 jours d’entreposage. Dans cette thèse, les faibles prévalences de Salmonella et de Listeria monocytogenes n’ont pas permis de décrire et d’identifier les changements du microbiote potentiellement associés à la présence de ces bactéries. La caractérisation du microbiote a néanmoins permis d’identifier des genres bactériens hébergeant des espèces reconnus pour être pathogènes pour l’humain, comme Campylobacter spp. et Yersinia spp. Les méthodes de contrôles pour assurer le contrôle de la qualité microbiologique mises en place à l’abattoir ne permettent pas de caractériser toute la contamination microbienne. Par conséquent, la description complète des communautés microbiennes retrouvées à la surface des carcasses et viandes de porc est importante pour déterminer le rôle des conditions de transformation primaire et d’entreposage dans la composition et la diversité du microbiote. Ce projet permet d’ouvrir sur de nouvelles perspectives pour un meilleur contrôle de la qualité microbiologique et une meilleure prévention de la contamination microbienne des carcasses et viandes de porc. / Pork is one of the most consumed food products in the world. Requests for quality safe and high pork meat products is increasing too, as the consumption itself continues to increase. To be able to meet these requests, microbial contamination must be controlled. This is a major concern for the pig industry as the presence of pathogenic bacteria is responsible for human foodborne infections, making it a public health issue, as well as the presence of spoilage bacteria render meat unsuitable for human consumption, leading to food waste and economic losses. During pig meat processing, the initial carcass contamination appears inevitable and bacteria from the digestive tract and from the slaughterhouse environment contribute to the contamination of the carcass surface, both jeopardizing food safety and meat shelf life. The control of microbiological contamination and the description of the microbial communities on the surfaces of pork carcasses and meats are performed using culture-dependent methods, such as counting total aerobic bacteria or Enterobacteriaceae. Currently, new approaches allow to describe and analyze the entire composition of a microbial community using high-throughput sequencing. However, few studies have described the composition and diversity of all bacterial populations on carcass surfaces and fresh pork products during processing. To address this lack of available information on how the microbiota varies under actual processing and storage conditions, this thesis aims to describe the variability of surface microbiota of pig carcasses according to the animal origin, stage of the slaughter process, the variability of surface microbiota of vacuum-packed pork meats according to storage conditions and to study the variations of these microbiota over time. In this thesis, three samplings were carried out in a pig slaughterhouse in the province of Quebec, Canada. Samples from the surface of pig carcasses were collected at several stages during primary processing, as well as samples from the surface of fresh vacuum-packed pork loins stored for 56 days and subjected to different temperature deviations, to mimic overseas exportation. Culture-dependent methods such as enumeration of traditional indicator microorganisms, detection of pathogenic bacteria such as Salmonella, as well as high-throughput sequencing of the V4 region of the 16S rRNA gene on the Illumina platform were performed. Results showed that the microbiota of the carcass surfaces sampled was similar following primary processing (until the final wash that precedes cooling) between samples from the top (ham) and the bottom areas (neck), and between different pig batches slaughtered the same day. Bacteria which seem to come from the gut and oral cavity of pigs mainly contribute to the carcass microbiota composition. Microbial counts were different between areas, higher bacterial counts were observed for the bottom area. However, when the microbiota was compared over a four-week period, a higher bacterial diversity was observed on top areas, and the microbiota composition and diversity found on the pig carcass surface appear different according to different visits and work shifts (morning vs afternoon). After cooling, a decrease in bacterial counts and diversity were observed, even if most bacterial genera present on carcasses before cooling were also detected afterward. The microbiota composition, diversity, and structure of vacuum-packed pork loin stored at −1.5°C (Control) and at different temperature deviations over 56 days were not statistically different. Bacterial communities identified on pig carcasses before and after chilling, such as Escherichia, Shigella and Lactobacillales_unclassified, seemed to contribute to the vacuum-packed pork loin microbiota during storage. Results revealed that the vacuum-packed pork loin microbiota from the eight batches sampled were different after 56 days of storage, even though they appeared similar at the beginning of this storage period. In this thesis, the low prevalence of Salmonella and Listeria monocytogenes did not allow us to describe any potential changes in the microbiota associated with the presence of these bacteria. However, sequencing analysis revealed the frequent presence of known foodborne pathogens like Campylobacter spp. and Yersinia spp. The control methods to ensure microbiological quality control implemented at the slaughterhouse do not allow to characterize all microbial contamination. Therefore, the complete description of the microbial communities from carcass and meat surfaces is important in determining the role of primary processing and storage conditions in the composition and diversity of microbiota. This study is a step forward in the better control and prevention of microbial contamination of meat products.

As foodstuffs are being produced, transported and stored in greater quantities than ever before in human history and with an alarming amount of food products being lost to spoilage every year, new, environmentally friendly ways of preserving food products are being actively researched and developed in today’s world. Oxygen is a key pathway towards food decay and destruction, due to its dual roles as a source of respiration for the multitude of microorganisms that can cause food spoilage and through direct destruction through oxidation reactions within food products that cause oxidative deterioration. Fuel cells have the theoretical potential to be an energy efficient and environmentally friendly way of preserving food, such as fish, fruit and vegetables.  Because of their nature to consume oxygen through the electrochemical reactions that produces their electrical power, they have the potential to be used to reduce localised oxygen content for the storage and transportation of foods, minimising their spoilage, as well as potentially providing electrical energy for other components in potential control systems for the fuel cell. The purpose of this project is to design and build a PEM fuel cell and examine its potential for lowering of oxygen concentrations at the gas output at the cathode.  The outcome of these experiments are designed to validate the  theoretical capacity of fuel cells to reduce output oxygen concentrations to levels that are able to aid in the preservation of foodstuffs.  It is hoped that this study, in conjunction with the researched literature, can be used as a guide for future food shipping and storage methods. The experimental stage of this diploma work was unsatisfactory. The fuel cell was unable to produce a voltage and the reactant gases were unable to flow through the fuel cell due to a design flaw. Therefore the effectiveness of a fuel cell for depletion of oxygen to levels able to preserve food is based on the theoretical basis of the internal PEM fuel cell reactions, as well as studying past literature and patents. If the theoretical ability of the fuel cell is proven, it can be asserted that PEM fuel cells have the potential to be a real contender in the field of food preservation in shipping and storage, as well as offering greater levels of control for supplies for how and when they can ship their product. However this will require more independent research development work on the effects of low oxygen concentrations on a fuel cell operation as well as the preservation effects on a greater variety of foodstuffs. Furthermore, more research is required for more efficient and cheaper fuel cell catalysts or innovative designs are required to avoid concentration losses that arise from oxygen reduction at low oxygen levels.

Fruit and vegetables are often spoilt during storage, handling and transportation due to microorganisms. The common spoilage causes are fungi within the order Mucorales, the largest order of the class Zygomycetes. Such spoilage can result in reduced food supplies, poor quality and severe losses to producers and traders. The study was to investigate the type of Mucorales prevalent in various commodities and in a particular market than others. Fifty infected papaya, peaches and strawberries were collected at five occasions from large, medium and small markets. Isolation was done aseptically in a biosafety cabinet. Mucorales were identified morphologically, through culture based tests and molecular techniques. Mucorales isolated are Rhizopus stolonifer, Mucor circinelloides and Mucor racemosus. Mucorales were isolated at a higher rate in samples collected from the small market than other two markets. Spoilage in all three markets is assumed to be influenced by lack of modified temperatures in the storage room. / Life and Consumer Sciences / M. Sc. (Life Sciences)

Fruit and vegetables are often spoilt during storage, handling and transportation due to microorganisms. The common spoilage causes are fungi within the order Mucorales, the largest order of the class Zygomycetes. Such spoilage can result in reduced food supplies, poor quality and severe losses to producers and traders. The study was to investigate the type of Mucorales prevalent in various commodities and in a particular market than others. Fifty infected papaya, peaches and strawberries were collected at five occasions from large, medium and small markets. Isolation was done aseptically in a biosafety cabinet. Mucorales were identified morphologically, through culture based tests and molecular techniques. Mucorales isolated are Rhizopus stolonifer, Mucor circinelloides and Mucor racemosus. Mucorales were isolated at a higher rate in samples collected from the small market than other two markets. Spoilage in all three markets is assumed to be influenced by lack of modified temperatures in the storage room. / Life and Consumer Sciences / M. Sc. (Life Sciences)