Background: A variety of microbial communities exist throughout the human and animal body. Genetics, environmental factors and long-term dietary habit contribute to shaping the composition of the gut microbiota. For this reason the study of the gut microbiota of a mammal exhibiting an extraordinary life span is of great importance. The naked mole-rat (Heterocephalus glaber) is a eusocial mammal known for its longevity and cancer resistance. Methods: Here we analyzed its gut microbiota by cultivating the bacteria under aerobic and anaerobic conditions and identifying their species by mass spectrometry. Results: Altogether, 29 species of microbes were identified, predominantly belonging to Firmicutes, and Bacteroidetes. The most frequent species were Bacillus megaterium (45.2 %), followed by Bacteroides thetaiotaomicron (19.4 %), Bacteroides ovatus, Staphylococcus sciuri and Paenibacillus spp., each with a frequency of 16.1 %. Conclusion: Overall, the gut of the naked mole-rat is colonized by diverse, but low numbers of cultivable microbes compared with humans and mice. The primary food plants of the rodents are rich in polyphenols and related compounds, possessing anti-microbial, anti-inflammatory, anti-oxidative as well as anti-cancer activity which may contribute to their exceptionally healthy life.

Η εντερική χλωρίδα θα μπορούσε να περιγραφεί ως ένα μικροβιακό όργανο, μείζονος σημασίας για την ομοιόσταση του οργανισμού, εξαιτίας της συμμετοχής του σε πολλαπλές και διαφορετικές λειτουργιές όπως η πέψη, η απορρόφηση των θρεπτικών συστατικών, η αποβολή των άχρηστων ουσιών και η φυσική ανοσία. Η σύστασή της έχει παρατηρηθεί ότι διαφέρει από άνθρωπο σε άνθρωπο. Ενώ οι κυριότεροι παράγοντες που διαμορφώνουν το τελικό μικροβιακό περιεχόμενο περιλαμβάνουν την ηλικία, το περιβάλλον, τις διαιτητικές συνήθειες, το γενετικό υπόβαθρο, την καταγωγή, την χρήση αντιβιοτικών, πρεβιοτικών ή προβιοτικών, την έκθεση σε ποικιλλία μικροβίων και τις χειρουργικές επεμβάσεις. Η ανθρώπινη εντερική χλωρίδα αποτελείται κατά κύριο λόγο από μόλις τέσσερα φύλα βακτηρίων, τα Bacteroidetes (23%), τα Firmicutes (64%), τα Actinobacteria (3%), και τα Proteobacteria (8%). Τα τελευταία χρόνια αρκετό είναι το ερευνητικό ενδιαφέρον στην μελέτη της σχέσης μεταξύ της σύνθεσης της εντερικής χλωρίδας και της παχυσαρκίας. Η έρευνα των πιθανών μηχανισμών αλληλεπίδρασης του μικροβιακού περιεχομένου και του ξενιστή εκτελείσεται τόσο με την χρήση πειραματοζώων όσο και σε ανθρώπινο επίπεδο. Έχει αποδειχθεί ότι σε παχύσαρκα άτομα υπάρχει χαμηλότερο ποσοστό Bacteroidetes και μεγαλύτερο Firmicutes, σε σύγκριση με άτομα κανονικού βάρους. Αν και έχουν επίσης διατυπωθεί αντίθετα αποτελέσματα. Οι διαιτητικές συνήθεις είναι ένας από τους κύριους παράγοντες που επηρεάζουν την σύσταση της εντερικής χλωρίδας. Παράλληλα, είναι γνωστό ότι το μοντέλο της οικογένειας και το γονεϊκό πρότυπο είναι καθοριστικής σημασίας στην διαμόρφωση διαιτητικών και διατροφικών επιλογών. Στην παρούσα μελέτη στόχος ήταν να ερευνήσουμε την επιρροή του οικογενειακού περιβάλλοντος, της μεσογειακής διατροφής και της παχυσαρκίας στην σύσταση της εντερικής χλωρίδας. Στην έρευνα συμμετείχαν 35 άτομα, από 12 οικογένειες, ηλικίας από 18 ετών έως και 77 ετών. Όλοι είναι μέλη οικογενειών που κατοικούν στην περιοχή της Πάτρας, και αφού πληροφορήθηκαν εκτενώς για τον σκοπό και την μεθεδολογιά της, συνένεσαν εθελοντικά. Μετρήθηκαν τα ανθρωπομετρικά χαρακτηριστικά κάθε εθελοντή, και υπολογίστηκε ο δείκτης μάζας σώματος (ΔΜΣ), καταγράφηκαν, μέσω ερωτηματολογίων, δημογραφικά, κοινωνικο-οικονομικά στοιχεία και οι διαιτητικές-διατροφικές τους συνήθειες. Ακόμα έγινε συλλογή κοπράνων, από όπου απομονώθηκε DNA και αναλύθηκε με την χρήση Real Time PCR. Μετά την στατιστική επεξεργασία, δεν επιβεβαιώθηκε η αρχική εκτίμηση για παρόμοια βακτηριακή κατανομή μεταξύ των μελών της κάθε οικογένειας και τελικά δεν σχετίστηκε στατιστικά σημαντικά η υιοθέτηση της Μεσογειακής διατροφής (MedDiet score) με την σύσταση της εντερικής χλωρίδας. / The intestinal flora is a microbial organ of major importance for the homeostasis of human organism, because of its participation in multiple and diverse functions such as digestion, absorption of nutrients, elimination of waste products and immunity. Gut flora is affected by various factors, such as the age, environment, dietary habits, host’s genotype, origin, using of antibiotics, prebiotics or probiotics, exposure to a variety of microbes and surgeries. Human intestinal flora consists primarily of four bacterial genders: the Bacteroidetes (23%), the Firmicutes (64%), the Actinobacteria (3%), and the Proteobacteria (8%). In the last years, many scientists study the correlation between the gut microbiota and obesity. Although, there are conflicting results, there is evidence that obese people have lower percentage of Bacteroides and higher percentage of Firmicutes, when compared with normal weight. It is known that dietary habits affect the composition of gut flora. Furthermore, it has also been proved that type of family and/or parenting model are crucial factors in shaping dietary and nutritional choices. The objective of this study was to investigate the correlation between the Mediterranean diet, obesity and family’s environment with gut microbiota. The survey involved 35 people, from 12 different families, aged from 18 years to 77 years. We measured anthropometric characteristics of each volunteer, calculated body mass index (BMI) and then demographic, socio-economic data and dietary-nutritional habits were recorded through questionnaires. We collected stool sample from every partitipant, DNA was isolated and analyzed using Real-Time PCR. Statistical analysis did not confirm the initial estimate for similar bacterial distribution among the members of each family, and eventually the adherence to Mediterranean Diet (MedDiet score) was not significally related with changes of the intestinal flora.

Gut microbial communities exist in the vast majority of animals, and often form complex symbioses with their hosts that affect their host's biology in numerous ways. To date, the majority of studies of these complex interactions have focused on the nutritional benefits provided by the microbiota; however, the natural microbiota can also influence development, immunity, and the metabolism of its host. Apis mellifera, the honey bee, harbors a distinctive bacterial community that is present in individuals from distant locations around the world; however, the basis of the bee-microbiota association is unknown. This dissertation explores properties of the bacterial microbiota within bees, including its persistence of this association, mechanisms of transmission, localization through host ontogeny, and basic metabolic capabilities that define and maintain the symbiotic relationship. Apis and Bombus species (honey and bumble bees) share a distinct bacterial microbiota that is not present in other bees and wasps. Close analysis of the A. mellifera microbiota revealed consistent communities in adult worker gut organs and a general lack of bacteria in larvae. Contact between workers and with hive materials were identified as major routes of transmission for bacterial communities, showing the importance of social behavior in this association. Genomic analysis of a gut bacterium co-sequenced with the Bombus impatiens genome revealed it as a divergent lineage of Gammaproteobacteria, and deletions of conserved metabolic pathways, reduction in genome size, and its low GC content all suggest that the bacterial species has had a long association with its host.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: A 2010 Food and Agriculture Organization (FAO) report indicated that 85% of the world´s fish stocks overexploited. This highlights the importance of commercial aquaculture as a sustainable alternative to capture fisheries. Growth rates for international aquaculture production are slowing, although an average annual increase of 12.6% occurred in Africa between 1970 and 2008. Sub-Saharan Africa accounted for 0.50% of the total world aquaculture production in 2008. The South African aquafeed industry recognized the need for aquaculture research in alternative feed ingredients to ensure a more sustainable future. With routine use of antibiotics in aquaculture, antibiotic resistance have emerged, and novel strategies are needed. Currently, alternative feed ingredients and practical substitution of antibiotics are two of the major challenges faced in aquaculture. The use of plant proteins is preferred over animal proteins such as fish meal. By developing sustainable aquafeeds, that have both nutritional and health benefits, the gastrointestinal tract (GIT) microbiota of the host should be considered. The fish GIT is an open system and acts as a route of infection for pathogenic bacteria. A comparative study was done to determine the structure of the GIT microbiota in Mozambique tilapia (Oreochromis mossambicus) and rainbow trout (Oncorhynchus mykiss). Tilapia and trout are important freshwater aquaculture species in South Africa. Tilapia is a warmwater herbivorous fish with a long coiled GIT, whereas trout is a coldwater carnivore and its GIT is short and compartmentalized. Tilapia was reared in recirculation systems with lower water pH and trout in flow-through systems with higher water pH. Tilapia diets consisted of plant-based protein, whereas trout diets contained animal-based proteins. To understand the role of the autochthonous bacteria in the GITs of these fish, we determined community structure along the length of the respective GITs. A highly reproducible DNA fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used that targeted the intergenic spacer region (ITS) in bacteria. Community analysis based on operational taxonomic units (OTUs) was used to statistically compare the microbiota in different segments. The different GIT compartments in trout also showed distinct bacterial community structures. However, the degree of variation between identical segments between different fish was shown, and consequently, individual microbiotas was not seen. ARISA was further used to determine if formulations containing dietary phytogenics will modify the GIT microbiota. The GIT of fish plays a role in food digestion, while the resident GIT bacteria are important contributors to disease control and nutrient utilization. During two feeding trials tilapia was fed 16 and trout six different diets. Microbial diversity was lower in the GIT of tilapia as compared to trout and no significant shifts in community structure were detected in both species. With a high-throughput DNA sequencing technique, we followed a metagenomic approach to classify the autochthonous microbiota of tilapia and trout on a phylogenetic level. Pyrosequencing was used to define a core microbiota that would enable comparative feeding studies to be carried out. The proposed microbiota of tilapia consisted of genera from the Proteobacteria (5), Firmicutes (1), Actinobacteria (1), Fusobacteria (1) and Cyanobacteria (2). The microbiota of trout comprised genera of the Proteobacteria (3), Firmicutes (3) and Actinobacteria (1). Three genera from the Proteobacteria were common in tilapia and trout, confirming the dominance of this group in the GIT of freshwater fish. The variability and distribution of Lactobacillus in the GITs of both species was determined. Culturing of lactic acid bacteria (LAB) from the GIT of tilapia proves to be difficult and this was confirmed by the low-abundance of particularly Lactobacillus. A number of other LAB genera were identified that confirmed LAB as part of the autochthonous microbiota in freshwater cultured fish. The detection of secondary bacterial fish pathogens as part of the resident microbiota was also established. The use of 454 pyrosequencing in this study, gave a deeper insight into the structure of bacterial communities in the GITs of tilapia and trout. This research is novel and based on our knowledge, the first study to determine the core microbiota in two South African aquaculture species. Data based on community diversity and structure can be used as a basis for further studies. One important study would be to determine the effect environmental stressors would have on the core microbiota. / AFRIKAANSE OPSOMMING: Volgens `n 2010-verslag van die FAO (Food and Agriculture Organization) is 85% van die wêreld se visbronne oorbenut. Dit beklemtoon die belangrikheid van kommersiële akwakultuur as `n alternatief tot visvangste. Internasionaal neem die groeitempo van akwakultuur produksie af, alhoewel groei in Afrika tussen 1970 en 2008 jaarliks met `n gemiddeld van 12.6% toegeneem het. In 2008 was lande suid van die Sahara verantwoordelik vir 0.50% van die wêreld se akwakultuur produksie. Die Suid-Afrikaanse akwavoer industrie het die behoefte raakgesien vir akwakultuur navorsing in alternatiewe voerbestanddele om 'n meer volhoubare toekoms te verseker. Die roetine gebruik van antibiotika in visboerderye het bygedra tot die ontstaan van weerstandbiedende organismes, en daarom is nuwe strategieë nodig. Tans is alternatiewe voeding en die praktiese vervanging van antibiotiese stowwe belangrike uitdagings in akwakultuur. Die gebruik van plantaardige proteïne in viskos word verkies bo dierlike proteïene soos vismeel. Deur die ontwikkeling van volhoubare viskos, wat beide voedingswaarde en voordele vir die gesondheid van visse inhou, moet die mikrobiota in die spysverteringskanaal (SVK) van die gasheer oorweeg word. Die SVK van visse is `n oop sisteem en dien sodoende as `n infeksie kanaal vir patogeniese bakterieë. `n Vergelykende studie is uitgevoer om SVK mikrobiota struktuur te bepaal in Mosambiek tilapia (Oreochromis mossambicus) en reënboogforêl (Oncorhynchus mykiss). Tilapia en forêl is twee belangrike varswater spesies in Suid-Afrikaanse akwakultuur. Tilapia is `n warmwater herbivoor met `n lang, gekronkelde SVK. In teenstelling is forêl `n kouewater vis met `n kort SVK, wat uit verskillende segmente bestaan. Tilapia is in hersirkulasie waterstelsels met `n lae pH gekweek terwyl forêl in deurvloei waterstelsels met `n hoër pH gekweek is. Tilapia diëte het plantaardige proteïne bevat tewyl forêl diëte proteïne vanaf dier-afkoms bevat het. Om die rol van SVK bakterieë beter te verstaan is populasie struktuur bepaal langs die lengte van die SVK. Geoutomatiseerde ribosomale intergeniese spasie analise (ARISA) is `n herhaalbare DNS vingerafdruk tegniek wat die intergeniese spasies gebied (ITS) in bakterieë teiken. Analise gebaseer op operasionele taksonomiese eenhede (OTEs) is gebruik om die mikrobiota van SVK segmente statisties te vergelyk. Die SVK kompartemente in forêl het ook duidelike bakteriële populasie strukture getoon. `n Groot variasie tussen identiese segmente van verskillende vise is waargeneem en individuele mikrobiota kon nie uitgesonder word nie. ARISA is gebruik om die effek van plantaardige dieet formulasies op die SVK mikrobiota te toets. Die SVK van visse speel `n rol in voedselvertering, terwyl die natuurlike SVK bakterieë `n belangrike rol speel in siektebeheer en die benutting van voedingstowwe. Twee voedingsproewe is op tilapia en forêl uitgevoer, met onderskeidelik 16 en 6 verskillende diëte,. Mikrobiese diversiteit was laer in die tilapia SVK in vergeleke met die SVK van forêl en geen beduidende verskuiwings in populasie struktuur is in beide visse waargeneem nie. `n Hoë deurvloei DNS-volgorde bepalings tegniek, gekombineer met `n metagenomiese benadering is gebruik om die mikrobiota van tilapia en forêl op `n taksonomiese vlak te bepaal. “Pyrosequencing” is gebruik om `n kern microbe populasie te identifiseer ten einde vergelykende studies te vergemaklik. Die voorgestelde kern mikrobiota in tilapia het bestaan uit genera van die Proteobakterieë (5), Firmikute (1), Aktinobakterieë (1), Fusobakterieë (1) en Sianobakterieë (2). Die voorgestelde kern mikrobiota van forêl het bestaan uit genera van die Proteobakterieë (3), Firmikutes (3) en Aktinobakterieë (1). Drie genera van die Proteobakterieë het algemeen in tilapia en forêl voorgekom, wat die oorheersing van hierdie groep in die SVK van varswatervisse bevestig. Die veranderlikheid en verspreiding van Lactobacillus in die SVKs van beide visse is bepaal. Dit is moelik om melksuurbakterieë (MSB) uit die SVK van tilapia te isoleer en `n lae voorkoms van Lactobacillus is waargeneem. Ander MSB genera is ook geïdentifiseer wat MSB as deel van die plaaslike mikrobiota in varswater gekweekte visse bevestig. Verder is daar ook vasgestel dat sekondêre patogene deel uitmaak van die plaaslike mikrobiota. In hierdie studie het 454 “pyrosequencing” `n dieper insig gegee oor die struktuur van bakterie-populasies in die SVK van tilapia en forêl. Hierdie navorsing is oorspronklik en volgens die literatuur die eerste studie wat `n kern mikrobe populasie in twee Suid-Afrikaanse akwakultuur spesies waargeneem het. Data wat gebasseer is op populasie diversiteit en struktuur kan gebruik word as basis vir verdere studies. Een so `n studie kan die effek van omgewings stresfaktore op die kern mikrobiota in hierdie vise bepaal.

Variations in drug metabolism may alter drug efficacy and cause toxicity; better understanding of the mechanisms and risks shall help to practice precision medicine. At the 21st International Symposium on Microsomes and Drug Oxidations held in Davis, California, USA, in October 2-6, 2016, a number of speakers reported some new findings and ongoing studies on the regulation mechanisms behind variable drug metabolism and toxicity, and discussed potential implications to personalized medications. A considerably insightful overview was provided on genetic and epigenetic regulation of gene expression involved in drug absorption, distribution, metabolism, and excretion (ADME) and drug response. Altered drug metabolism and disposition as well as molecular mechanisms among diseased and special populations were presented. In addition, the roles of gut microbiota in drug metabolism and toxicology as well as long non-coding RNAs in liver functions and diseases were discussed. These findings may offer new insights into improved understanding of ADME regulatory mechanisms and advance drug metabolism research. (C) 2017 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.

Il tratto gastro intestinale infantile al momento del parto è considerato virtualmente sterile e viene rapidamente colonizzato da microrganismi di origine materna e/o ambientale nei primi giorni di vita. Studi accoppiati di microbiologia classica e molecolare hanno dimostrato come la cavità amniotica sia popolata da microrganismi alcuni dei quali appartenenti a taxa non ancora coltivati e caratterizzati. Lo scopo del presente lavoro di tesi è stato quello di valutare la composizione del microbiota infantile durante i primi due anni di vita, in particolare, di popolazioni parzialmente “trascurate”. La tesi è suddivisibile in tre tematiche principali: presenza di popolazioni idrogenotrofiche, la distribuzione della famiglia delle Lachnospiraceae in soggetti sani prima del secondo anno di vita, e la possibile correlazione tra gli archaea metanogeni e la dieta in modello animale. Le tecniche impiegate nel presente lavoro di tesi sono state la PCR-DGGE e la PCR quantitativa (qPCR) e il sequenziamento Illumina. Le principali conclusioni derivabili dai tre studi sono correlate alla necessità di sviluppare nuove coppie di primers che meglio possano descrivere la complessa ecologia delle comunità microbiche intestinali. L’ambizioso obiettivo potrà considerarsi raggiunto quando si potranno identificare e stimare in modo preciso e corretto anche le popolazioni batteriche poco abbondanti nel microbiota intestinale infantile. / At birth, the gastrointestinal tract is virtually sterile, but is rapidly colonized during the first days of life until a relatively stable state is reached. Several studies using both bacterial culture techniques and bio-molecular methods revealed that the amniotic cavity harbors microorganisms and, among them, uncultivated and uncharacterized taxa. The aim of the present PhD thesis was to evaluate the composition of some neglected populations inhabiting the infant gut microbiota until the second year of life. The PhD thesis is composed of three main chapters related to the presence of hydrogenotrophic populations, the occurrence of the Lachnospiraceae family in healthy subjects before the second year and the possible linkage between methanogens and diet in a piglet’s model. PCR-DGGE, the quantitative PCR (qPCR) and the Illumina deep sequencing have been the prevalent molecular techniques used in this work. Main conclusions obtained from these studies were mainly linked to the need of new primer sets that better describe the ecological complexity of the gut microbial community. This ambitious objective will be reached when it is possible to properly identify and quantify less represented bacterial populations within the infant gut ecosystem.

Une consommation de fibres alimentaires adéquate semble protéger du risque de développer un diabète de type 2 dont a contrario la prévalence ne cesse de progresser à travers le monde. Parmi les mécanismes d'action pouvant expliquer comment les fibres contribuent à l'homéostasie du glucose et à la sensibilité à l'insuline, l'implication du microbiote intestinal semble aujourd'hui très probable. Cependant il n'est pas toujours aisé de différencier ses effets de ceux pouvant découler d'une réduction de l'indice glycémique voir de ceux induits par des micronutriments parfois associés aux fibres. Les travaux de cette thèse ont permis de confirmer que les fructo-oligosaccharides (FOS), fibres prébiotiques peu visqueuses, peuvent améliorer la sensibilité à l'insuline de différents modèles animaux d'obésité induite par le régime alimentaire. La réduction de la sensibilité à l'insuline induite par le surpoids n'est pas complètement contrebalancée par les FOS mais leurs effets sont visibles même sans perte de poids associée. D'autre part une corrélation directe entre les modifications de la composition et des activités du microbiote intestinale induites par les FOS et le métabolisme de l'hôte a pu être mise en évidence. Au-delà d'une augmentation des bifidobactéries déjà bien documentée, les travaux de cette thèse ont révélé la modulation par les FOS d'autres clusters bactériens plus prépondérants au sein de l'écosystème digestif comme ceux des Clostridium leptum et Clostridium coccoides – Eubacterium rectale. En modulant ces populations, les FOS influencent le métabolisme des acides biliaires et le niveau d'hydroxylation d'acides gras monoinsaturés. / An adequate intake of dietary has proven to protect against the risk to develop type 2 diabetes, for which the prevalence is currently increasing all around the world. Among the different mechanisms that could explain how dietary fibres can contribute to insulin sensitivity and glucose homeostasis, involvement of the gut microbiota seems more than likely. However it is not always possible to differentiate the effects that linked to the microbiota from those induced a reduction of the glycaemic index or those induced by some micronutrients sometimes closely associated to dietary fibres. The experiments conducted during this PhD validate that fructo-oligosaccharides (FOS), poorly viscous prebiotic fibres, can enhance insulin sensitivity if different animal models of diet-induced obesity. Reduction of insulin sensitivity resulting from overweight status is not completely solved by FOS but their effect is not linked to weight loss. Moreover, a direct correlation between the modifications of the composition and activities of the intestinal microbiota triggered by FOS and metabolism of the host has been highlighted. This work reveals that more than a single increase of Bifidobacteria already well documented, FOS can alter other bacterial clusters more predominant within the digestive ecosystem like Clostridium leptum and Clostridium coccoides – Eubacterium rectale. By modulating these populations, FOS will alter the metabolism of biliary acids and the level of monounsaturated fatty acids hydroxylation.

It is well established that replacing dietary saturated fatty acids with unsaturated fatty acids reduces cardiovascular disease (CVD) risk. Although epidemiological and clinical evidence indicate health benefits of consuming various fatty acid classes including n-9, n-6, and short- and longer-chain n-3 fatty acids, current dietary recommendations fall short of providing the optimal amounts of these fatty acids in daily diets. In addition, significant knowledge gaps remain in our understanding of the effects of, and mechanisms underpinning the action of, the various fatty acid classes on risk factors for CVD. The objective of this research was to contribute to the evaluation of health benefits of using different dietary oils, and determine how these benefits may play a role in improving public health and decreasing CVD risk. Additionally, this research examined effects of diet-gene interactions, endogenous fatty acid ethanolamides (FAEs) on body fat mass distribution as well as changes in the composition of gut microbiota following consumption of dietary oil treatments. The Canola Oil Multicenter Intervention Trial (COMIT) was conducted as a 5-phase randomized, controlled, double-blind, cross-over clinical trial. Each 4-wk treatment period was separated by 4-wk washout intervals. A total of 130 volunteers with abdominal obesity consumed each of 5 identical weight-maintaining, fixed-composition diets with one of the following treatment oils (60 g/3000 kcal) in the form of beverages: 1) conventional canola oil (Canola; n-9 rich), 2) high–oleic acid canola oil with docosahexaenoic acid (CanolaDHA; n-9 and n-3 rich), 3) a blend of corn and safflower oil (25:75) (CornSaff; n-6 rich), 4) a blend of flax and safflower oils (60:40) (FlaxSaff; n-6 and short-chain n-3 rich), and 5) high–oleic acid canola oil (CanolaOleic; highest in n-9). At endpoints, plasma fatty acid levels reflected the differences in fatty acid composition of five dietary treatments. All diets lowered total cholesterol (TC) compared with baseline. TC was lowest after the FlaxSaff phase and highest after CanolaDHA. The CanolaDHA treatment improved HDL-C, triglycerides, and blood pressure thereby reducing Framingham risk scores compared with other oils varying in unsaturated fatty acid composition. Homozygotes minor allele carriers of rs174583 (TT) on FADS2 gene showed lower (P<0.01) plasma EPA and DPA levels across all diets, but no differences were observed in DHA concentrations after the CanolaDHA feeding. In addition, plasma FAE levels were positively associated with plasma fatty acid profiles. Minor allele A carriers of rs324420 of FAAH gene showed a higher (P<0.05) plasma FAE levels compared with major allele C carriers across all diets, and showed higher (P=0.0002) docosahexaenoylethanolamide levels in response to the CanolaDHA diet. Impacts of consuming 60 g of five dietary oil treatments on gut microbiota composition were relatively minor at the phylum level and mainly at the genus level, while BMI contributed to a significant shift at the phylum level. In conclusion, consumption of a novel DHA-enriched canola oil improved blood lipid profile and largely reduced CVD risk. Diet-gene interactions might help identify sub-populations who appear to benefit from increased consumption of DHA and oleic acid. The metabolic and physiological responses to dietary fatty acids may be influenced via circulating FAEs, while the altered microbiota profile by shifts in MUFA and/or PUFA may be associated with specific physiological effect. Personalized diets varying in unsaturated fatty acids composition based on specific lifestyles, environmental factors, psychosocial factors, and genetic make-ups will become the future “healthy eating” recommendations to prevent CVD risk. / May 2016

Orientador: Thais Borges Cesar / Banca: Paula Garcia Chiarello / Banca: Renata Maria Galvão de Campos Cintra / Banca: Anderson Marliere Navarro / Banca: Katia Sivieri / Resumo: Introdução: Aos compostos do suco de laranja 100% puro (SL) são atribuídos várias propriedades biológicas, como atividade antioxidante, anti-hipertensiva, redutora do colesterol e glicemia sanguíneos, e atualmente estudos in vitro têm mostrado que o suco de laranja pode ter ação seletiva sob a microbiota intestinal. Objetivo: Investigar o impacto do consumo diário de suco de laranja sobre a microbiota intestinal e no perfil glicídico e lipídico em mulheres. Métodos: Foram avaliadas 10 mulheres por período de 120 dias, distribuídos em três etapas: (1ª): dieta livre de citrus 30º dia (30 dias); (2ª) ingestão de 300 mL/dia de SL 90º dia (60 dias); (3ª) dieta livre de citrus 120º dia (30 dias). Avaliação dietética e antropometria foram realizadas quinzenalmente durante o período experimental. Foram colhidas amostras de sangue, urina e fezes, no início do estudo e a cada 30 dias, até o final do experimento. Foi realizado: analise dos parâmetros bioquímicos; identificação dos metabólitos urinários por UHPLC-UV-VIS; e análise da composição da microbiota por sequenciamento de gene RNAr 16S. Resultados: A avaliação da composição corporal e a excreção urinária não mostraram alterações durante as etapas experimentais. Os parâmetros bioquímicos mostraram diminuição da glicose (-6,25%), da insulina (-32,7%) e da resistência à insulina (-43,8%), além do colesterol total (-13,9%), LDL (-16%) e triglicerídeos (-30%) com a ingestão de SL (90º dia). Após a parada do consumo de SL (120º dia), o... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Introduction: 100% pure orange juice (OJ) compounds are assigned to various biological properties, such as antioxidant, antihypertensive, blood cholesterol lowering and glycemia activity. Currently, in vitro studies have shown that orange juice can present selective action of intestinal microbiota. Objective: To investigate the impact of daily consumption of orange juice on the intestinal microbiota and on the lipid and glucose profile in women. Methods: Ten women were evaluated for 120 days at three differen stages: (1st) citrus-free diet 30th day (30 days); (2nd) intake of 300 mL / day SL 90th day (60 days); (3rd) citrus-free diet 120th day (30 days). Dietary assessment and anthropometry were performed biweekly during the experimental stages. Samples of blood, urine and feces were taken at the beginning of the study, and every 30 days until the end of the experiment. It was carried out: analysis of the biochemical parameters; identification of urinary metabolites by UHPLC-UV-VIS; and analysis of the composition of the microbiota by 16S rRNA gene sequencing. Results: Changes during the experimental stages were not found in evaluation of body composition and urinary excretion. Biochemical parameters showed a decrease in glucose (-6.25%), insulin (-32.7%) and insulin resistance (-43.8%), total cholesterol (-13.9%), LDL (-16%) and triglycerides (-30%) with ingestion of OJ (90th day). After stopping OJ intake (120th day), the biochemical parameters returned to the initial values... (Complete abstract click electronic access below) / Doutor

Comme de nombreuses espèces naturelles, l’abeille européenne (Apis mellifera) est confrontée à une pression croissante de facteurs biotiques et abiotiques : environnement, diversité génétique, parasitisme, etc. Chacun de ces facteurs peut potentiellement influencer les communautés de micro-organismes qui constituent le microbiote de l’abeille et évoluent avec elle. L’objectif de cette thèse était de comprendre la dynamique et la structuration du microbiote intestinal de la lignée évolutive M de l’abeille européenne en fonction de facteurs biogéographiques, génétiques et temporels des colonies d’abeilles. Cette analyse a été réalisée dans sept conservatoires de cette lignée évolutive, répartis au Portugal (A. m. iberiensis), en Espagne et en France (A. m. mellifera), selon un gradient Nord-Sud et Est-Ouest. Dans un premier temps, mon travail a permis de décrire un facteur jusqu’ici mal connu : l’humidité dans les ruches. Celle-ci s’est révélée stable, entre 50 et 60 % d’humidité relative toute l’année, suggérant une hygrorégulation par les colonies d’abeilles, quelle que soit la période de l’année et la dynamique populationnelle au sein des nids (ici, la ruche). Par la suite, nous avons développé un protocole permettant le suivi spatio-temporel de la charge virale des abeilles par cytométrie en flux. Son application sur nos abeilles a montré que le temps influence moins la charge virale que le lieu géographique. Enfin, une analyse métagénomique sur un gène ciblé (ARNr 16s) a confirmé l’effet de la localisation géographique des ruches, cette fois sur la structuration des communautés bactériennes peuplant les intestins des abeilles qui appartiennent à la lignée évolutive M. Par ailleurs, cette dernière analyse a montré l’importance de prendre en compte l’interaction entre les facteurs, qui peuvent avoir plus d’impact pris ensemble que séparément. Enfin, des perspectives sont envisagées, telles que la réalisation d’un réseau d’inter-actants permettant de comprendre la part de chaque facteur sur les communautés bactériennes mais également les pathogènes. / Like many natural species, the European bee (Apis mellifera) faces a threat of biotic and abiotic factors: environment, genetic diversity, parasitism, etc. Each of these factors can potentially influence the communities of microorganisms that constitute the bee's microbiota and evolve with it. The aim of this work was to understand the dynamics and structure of the gut microbiota of the M evolutionary line of A. mellifera according to biogeographic, genetic and temporal factors of bee colonies. This analysis was carried out in the conservatories of this evolutionary line, located in Portugal (A. m. iberiensis), Spain and France (A. m. mellifera) along a North-South and East-West gradient. First, my work has described a hitherto barely understood factor: humidity in hives. It appeared to be stable in our beehives, between 50 and 60% relative humidity all year long, which suggests a hygroregulation by honeybee colonies whatever the periode of year and the populational dynamics inside the nest (i.e. the beehive). We developed a protocol allowing spatio-temporal monitoring of the viral load of bees by flow cytometry. After using it on our colonies, we showed that time influences less viral load than geographical location. Finally, a metagenomic analysis on a target gene (16s rRNA) confirmed the importance of the geographical location of beehives, this time on the structuring of bacterial communities living in guts of honeybees belonging to the M evolutive lineage. In addition, this last analysis has shown the importance to take into account the interaction between factors, which can have a bigger effect when taken together. Finally, perspectives are envisaged, such as the realization of a network of interactants allowing to understand the part of each factor on the bacterial but also pathogens’ communities.