Microbiome cutané et maladie fongique émergente du syndrome du museau blanc chez les chauves-souris d’Amérique du Nord

Le syndrome du museau blanc (SMB), causé par le champignon Pseudogymnoascus destructans (Pd), a mis en péril les populations de chauves-souris hibernantes en Amérique du Nord. Certaines espèces sont hautement vulnérables à la maladie alors que d’autres espèces semblent être résistantes ou tolérantes à l’infection. Plusieurs facteurs physiologiques et environnementaux peuvent expliquer ces différences. Or avant 2015, peu d’études avaient porté sur le microbiome de la peau en relation avec cette maladie. La présente thèse vise à caractériser le microbiome cutané de chiroptères affectés par le SMB afin d’identifier les facteurs de vulnérabilité ou de résistance à la maladie. L’objectif principal est de déterminer comment le microbiome est affecté par la maladie ainsi que de déterminer si celui-ci à un rôle dans la protection face à l’infection fongique. Au Chapitre 1, nous avons tout d’abord exploré et comparé le microbiote cutané de petites chauves-souris brunes (Myotis lucifugus) non affectées par le SMB avec celui de chauves-souris survivantes au SMB pour tester l’hypothèse selon laquelle le microbiote cutané est modifié par la maladie. Nos résultats montrent que le site d’hibernation influence fortement la composition et la diversité du microbiote cutané. Les sites d’hibernations Pd positifs et négatifs diffèrent significativement en termes de diversité, ainsi qu’en termes de composition du microbiote. La diversité est réduite au sein du microbiote des chauves-souris survivantes au SMB et enrichi en taxons tels que Janthinobacterium, Micrococcaceae, Pseudomonas, Ralstonia et Rhodococcus. Certains de ces taxons sont reconnus pour leur potentiel antifongique et des souches spécifiques de Rhodococcus et de Pseudomonas peuvent inhiber la croissance de Pd. Nos résultats sont cohérents avec l’hypothèse selon laquelle l’infection par Pd modifie le microbiote cutané des chauves-souris survivantes et suggèrent que le microbiote peut jouer un rôle de protection face au SMB. Au Chapitre 2, nous avons étudié le microbiote d’une espèce résistante au champignon Pd en milieu contrôlé avant et après infection afin d’établir la réponse potentielle à la maladie. L’espèce étudiée est la grande chauve-souris brune (Eptesicus fuscus) dont le microbiote cutané pourrait jouer un rôle de protection contre l’infection. Nos résultats montrent que la diversité du microbiote de la grande chauve-souris brune inoculée avec Pd est plus variable dans le temps, tandis que la diversité du microbiote des chauves-souris du groupe contrôle demeure stable. Parmi les taxons les plus abondants, Pseudomonas et Rhodococcus, deux taxons connus pour leur potentiel antifongique contre Pd et d’autres champignons, sont restés stables durant l’expérience. Ainsi, bien que l’inoculation par le champignon Pd ait déstabilisé le microbiote cutané, les bactéries aux propriétés antifongiques n’ont pas été affectées. Cette étude est la première à démontrer le potentiel du microbiote cutané d’une espèce de chauves-souris pour la résistance au SMB. Au Chapitre 3, le microbiome cutané de la petite chauve-souris brune a été évalué en milieu naturel dans le contexte du SMB, à l’aide de la métagénomique, une approche haute résolution pour observer le potentiel fonctionnel du microbiome (métagénome fonctionnel). Nos résultats ont permis d’établir que le temps depuis l’infection a un effet significatif sur le métagénome fonctionnel. En effet, les chauves-souris dans la première année suivant l’infection ont un métagénome fonctionnel perturbé qui subit une perte de diversité fonctionnelle importante. Toutefois, le métagénome fonctionnel revient à une structure et composition similaire d’avant infection après 10 ans. Certaines fonctions détectées suite à l’infection sont associées à des gènes reliés au transport et à l’assimilation de métaux, des facteurs limitants pour la croissance du champignon. Ces gènes pourraient donc avoir un rôle à jouer dans la résistance ou la vulnérabilité à la maladie. Globalement, l’étude du métagénome chez la petite chauve-souris brune indique une vulnérabilité du métagénome fonctionnel au champignon, mais que celui-ci semble se rétablir après 10 ans. Une telle réponse pourrait avoir un impact sur la résilience de M. lucifugus. Cette thèse a permis d’acquérir des connaissances fondamentales sur le microbiome cutané des chauves-souris en hibernation pour mieux comprendre les communautés microbiennes de la peau dans le contexte du SMB. Le microbiome pourrait en effet jouer un rôle dans la vulnérabilité et la résistance des chauves-souris à la maladie, et il est essentiel d’adapter notre façon d’aborder la protection de ces espèces et de leur microbiome. Nous souhaitons que les travaux de cette thèse permettent de sensibiliser les acteurs de la conservation à l’existence et à l’importance potentielle du microbiome pour la santé de son hôte. Cette thèse fait également état de l’avancement des méthodes d’analyses qui permettront d’être de plus en plus précis et d’appliquer les connaissances du microbiome en biologie de la conservation.White-nose syndrome (WNS) caused by the fungus Pseudogymnoascus destructans (Pd) has put hibernating bat populations at risk in North America. Some species are highly vulnerable to the disease while other species appear to be resistant or tolerant. Several physiological and environmental factors can explain these differences. However, before 2015, few studies have focused on the skin microbiome in relation to this disease. The present thesis aims to characterize the cutaneous microbiome of bats affected by WNS in order to identify the factors of vulnerability or resistance to the disease. The main objective is to determine how the microbiome can protect against the Pd fungus, or conversely how the microbiome is altered by the fungal infection. In Chapter 1, we first explored and compared the skin microbiota of little brown bats (Myotis lucifugus) unaffected by WNS with that of WNS survivors to test the hypothesis that the skin microbiota is modified by the disease. Our results show that the hibernation site strongly influences the composition and diversity of the skin microbiota. The Pd positive and negative sites differ significantly in terms of diversity, as well as in terms of the composition of the microbiota. Diversity is reduced within the microbiota of bats surviving WNS and enriched in taxa such as Janthinobacterium, Micrococcaceae, Pseudomonas, Ralstonia, and Rhodococcus. Some of these taxa are recognized for their antifungal potential and specific strains of Rhodococcus and Pseudomonas may inhibit the growth of Pd. Our results are consistent with the hypothesis that Pd infection modifies the skin microbiota of surviving bats and suggest that the microbiota may play a protective role against WNS. In Chapter 2, we studied in a controlled environment the microbiota of a species that exhibits evidence of resistance with mild WNS symptoms, before and after infection, to establish the potential response to the disease. The species studied is the big brown bat (Eptesicus fuscus), whose skin microbiota could play a protective role against infection. Our results show that the diversity of the microbiota of big brown bats inoculated with Pd is more variable over time, while the diversity of the microbiota of the control bats remains stable. Among the most abundant taxa, Pseudomonas and Rhodococcus, two taxa known for their antifungal potential against Pd and other fungi, remained stable during the experiment. Thus, although inoculation with the Pd fungus destabilized the skin microbiota, bacteria with antifungal properties were not affected. This study is the first to demonstrate the potential of the skin microbiota of a bat species for resistance to WNS. In Chapter 3, the skin microbiome of the little brown bat was evaluated in the natural environment in the context of WNS, using metagenomics, a higher-resolution approach to observe the functional potential of the microbiome (functional metagenome). Our results established that the time since infection has a significant effect on the functional metagenome. Indeed, bats in the first year after infection have a disrupted functional metagenome that undergoes a significant loss of functional diversity. However, the functional metagenome returns to a similar structure and composition to that observed before infection after 10 years. Certain functions detected following infection are associated with genes linked to the transport and assimilation of metals, known limiting factors for the growth of the fungus. These genes could therefore have a role to play in resistance or vulnerability to the disease. Overall, this metagenomics study indicates functional metagenome vulnerability to the fungus, although the original functional metagenome is reestablished after 10 years. Such diversified response could impact M. lucifugus resilence. This thesis provides fundamental knowledge on the skin microbiome of hibernating bats to better understand the microbial communities of the skin in the context of WNS. The microbiome could indeed play a role in the vulnerability and resistance of bats to disease and it is essential to adapt our way of approaching the protection of these species and their microbiomes. We hope that the results of this thesis will raise awareness among conservation stakeholders about the existence and potential importance of the microbiome for the health of its host. This thesis also reports on the advancement of analytical methods that will make it possible to be more and more precise and to apply knowledge of the microbiome in conservation biology

A health at every size intervention improves intuitive eating and diet quality in Canadian women

Background & aims: Health at Every Size® (HAES®) interventions focus on healthy lifestyle by promoting behavioral changes related to diet and physical activity while emphasizing self-acceptance and well-being through an empowerment and intuitive approach. The purpose of this study was to investigate the effects of a HAES® program on intuitive eating and diet quality in women. Methods: The HAES® intervention, offered by professionals from Health and Social Services Centers in Quebec (Canada), was composed of thirteen 3-h weekly meetings and a 6-h intensive day. For this study, 216 women (1.9% normal-weight, 21.1% overweight, 77.0% obese) who took part to the HAES program were compared to 110 women (3.9% normal-weight, 23.3% overweight, 72.8% obese) from a control group (waiting list). Intuitive eating was assessed using the Intuitive Eating Scale and diet quality was evaluated through the calculation of the Healthy Eating Index (HEI) from a validated web-based self-administrated food frequency questionnaire. Measurements were performed at baseline, post-intervention, and at one-year follow-up. Results: Women who participated in the HAES® program significantly increased their intuitive eating score compared to women in the control group at post-intervention and at follow-up (group by time interaction, p = 0.0002). A significant improvement in diet quality was also observed in the HAES® group in comparison with the control group at post-intervention (group by time interaction, p = 0.0139). The intuitive eating score and the HEI score were positively associated in the HAES® group at post-intervention (r = 0.20, p = 0.0237) and one-year follow-up (r = 0.22, p = 0.0359), but no such associations were noted in the control group (post-intervention, r = 0.04, p = 0.70; one-year follow-up, r = -0.15, p = 0.30). Conclusions: The HAES® program seems effective in improving intuitive eating and also favours improvements in diet quality. However, the association between intuitive eating and diet quality remains unclear, being positive and significant only after the HAES® intervention

Assessing nutritional value of ready-to-eat breakfast cereals in the province of Quebec (Canada) : a study from the Food Quality Observatory

Objective: The Food Quality Observatory was created in the province of Quebec (Canada) in 2016. In this study, the Observatory aimed to generate a methodology to (1) test the use of sales data combined with nutrient values to characterise the nutritional composition of ready-to-eat (RTE) breakfast cereals offered and purchased in the province of Quebec (Canada) and (2) verify the extent to which a front-of-pack label based on the percentage of daily value (DV) for total sugar, as a strategy to improve the food supply, would be distributed in this food category. Design: Nutritional information were obtained by purchasing each RTE breakfast cereal available in the Greater Montreal area. Cereals were then classified according to their processing type. Setting: The nutritional values of 331 RTE breakfast cereals available in Quebec were merged with sales data covering the period between May 2016 and May 2017. A total of 306 products were successfully cross-referenced. Results: Granola and sweetened cereals were the most available (36·6 % and 19·6 %, respectively) and purchased (19·8 % and 40·9 % of sales, respectively). When compared with other types of cereals, granola cereals had a higher energy, fat, saturated fat, protein content and a lower Na content. A larger proportion of chocolate (65 %) and sweetened cereals (49 %) were above 15 % of the DV for sugar. Conclusions: This study showed that the methodology developed generates important data to monitor nutritional quality of the food supply and ultimately contribute to improve the nutritional quality of processed foods

Intakes of total, free, and naturally occurring sugars in the french-speaking adult population of the province of Québec, Canada : the PREDISE study

The objective of this study was to characterize the intakes of different types of sugars in an age- and sex-representative sample of French-speaking adults from five regions of the Province of Québec, Canada, enrolled in the cross-sectional PREDISE (PRÉDicteurs Individuels, Sociaux et Environnementaux) study (n = 1147, 18–65 years old; 50.2% women). Because only total sugar content of foods and beverages is available in the Canadian Nutrient File (CNF) 2015, the initial step of this study was thus to build a database of free and naturally occurring sugars content of each food item and recipe included in the R24W, which is an automated, self-administered, web-based, 24-h dietary recall validated to estimate nutrient intakes in French-speaking adults of the Province of Québec. Total sugars were manually differentiated into free and naturally occurring sugars using a systematic algorithm based on previously published systematic algorithms. The World Health Organization (WHO)’s free sugar definition was used to differentiate total sugars into free and naturally occurring sugars. Dietary intake estimates were assessed using three 24-h dietary recalls completed with the R24W. Mean total, free, and naturally occurring sugar intakes were 116.4 g (19.3% of daily energy intake (%E)), 72.5 g (11.7%E), and 44.0 g (7.5%E), respectively. Over half (57.3%) of the overall sample did not meet the WHO’s recommendation to consume less than 10%E from free sugars. Women had a higher %E from naturally occurring sugars than men and being younger was associated with a greater %E from free sugars. Sugar intakes among French-speaking adults from the Province of Québec were mainly in the form of free sugars, with the majority of the population exceeding the WHO recommendation regarding free sugar intake. This suggests that public health efforts towards reducing free sugar intake in this population are relevant and necessary, considering that overconsumption of free sugars negatively influences health outcomes

Supplemental Information 6: Data S1.

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing–loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (kcat/KM) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing–loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research

Conservation of resources theory and research use in health systems

<p>Abstract</p> <p>Background</p> <p>Health systems face challenges in using research evidence to improve policy and practice. These challenges are particularly evident in small and poorly resourced health systems, which are often in locations (in Canada and globally) with poorer health status. Although organizational resources have been acknowledged as important in understanding research use resource theories have not been a focus of knowledge translation (KT) research. What resources, broadly defined, are required for KT and how does their presence or absence influence research use?</p> <p>In this paper, we consider conservation of resources (COR) theory as a theoretical basis for understanding the capacity to use research evidence in health systems. Three components of COR theory are examined in the context of KT. First, resources are required for research uptake. Second, threat of resource loss fosters resistance to research use. Third, resources can be optimized, even in resource-challenged environments, to build capacity for KT.</p> <p>Methods</p> <p>A scan of the KT literature examined organizational resources needed for research use. A multiple case study approach examined the three components of COR theory outlined above. The multiple case study consisted of a document review and key informant interviews with research team members, including government decision-makers and health practitioners through a retrospective analysis of four previously conducted applied health research studies in a resource-challenged region.</p> <p>Results</p> <p>The literature scan identified organizational resources that influence research use. The multiple case study supported these findings, contributed to the development of a taxonomy of organizational resources, and revealed how fears concerning resource loss can affect research use. Some resources were found to compensate for other resource deficits. Resource needs differed at various stages in the research use process.</p> <p>Conclusions</p> <p>COR theory contributes to understanding the role of resources in research use, resistance to research use, and potential strategies to enhance research use. Resources (and a lack of them) may account for the observed disparities in research uptake across health systems. This paper offers a theoretical foundation to guide further examination of the COR-KT ideas and necessary supports for research use in resource-challenged environments.</p