<p>Consumption of soy foods has been shown to provide beneficial health outcomes such as reduction of menopause symptoms, reduced risk of breast cancer and prostate cancer, improved cardiovascular health, and improved bone health. The mechanism hypothesized to be driving these outcomes is the conversion of the soy isoflavone daidzein into the metabolite equol by bacteria in the gut microbiome. Equol is an exclusively microbially produced metabolite with a high binding affinity to mammalian estrogen receptors. Not all humans harbor equol-producing microbes in their gut, and less than half of the population can be classified as equol producers. To date, soy feeding research published suffers from confounding factors that make assessing the causal impact of equol production in health difficult due to: (i) large interpersonal variation of the human microbiome and human genomes and that (ii) all lab-raised rodent models harboring natural microbiomes are highly efficient equol producers. In this study, we sought to establish a gnotobiotic mouse model harboring synthetic bacterial communities with divergent equol-producing capacities by designing two communities: the Equol(-) community and Equol(+) community. The Equol(-) community was designed to include ten bacterial strains commonly found within a human microbiome without equol-producing capacity<em>.</em> To create the Equol(+) community, the equol-producing bacteria <em>Adlercreutzia equolifaciens</em> was added to the Equol(-) community<em>.</em> Female and male germ-free C57BL/6 mice were colonized with either the Equol(-) or Equol(+) community for 4 weeks. Daidzein was administered by dietary supplementation (1.5% wt/wt daidzein) in a semi-purified diet containing fermentable fiber starting two weeks prior to bacterial colonization. As expected, equol was detected in the serum of mice colonized with the Equol(+) community, but not detectable in those colonized with the Equol(-) community. There were no sex differences detected in equol production. 16S rRNA gene sequencing of mouse cecal content revealed that ~50-80% of the strains from each community colonized within the mice at detectable levels. Strain-specific qPCR improved the detection of strains not observed consistently through 16S rRNA gene sequencing. Our results demonstrated that this model is reliable in producing the expected equol producing and non-equol producing phenotypes when colonized with the Equol(+) and Equol(-) communities, respectively. This model system can be utilized in a broad range of future studies to conclusively determine the causal impact of endogenous equol production in many areas, such as cardiometabolic health and bone health.</p>

Yes / Background: The changes that occur in the microbiome of aging individuals are unclear, especially in light of the imperfect correlation of frailty with age. Studies in older human subjects have reported subtle effects, but these results may be confounded by other variables that often change with age such as diet and place of residence. To test these associations in a more controlled model system, we examined the relationship between age, frailty, and the gut microbiome of female C57BL/6 J mice. Results: The frailty index, which is based on the evaluation of 31 clinical signs of deterioration in mice, showed a near-perfect correlation with age. We observed a statistically significant relationship between age and the taxonomic composition of the corresponding microbiome. Consistent with previous human studies, the Rikenellaceae family, which includes the Alistipes genus, was the most significantly overrepresented taxon within middle-aged and older mice. The functional profile of the mouse gut microbiome also varied with host age and frailty. Bacterial-encoded functions that were underrepresented in older mice included cobalamin (B12) and biotin (B7) biosynthesis, and bacterial SOS genes associated with DNA repair. Conversely, creatine degradation, associated with muscle wasting, was overrepresented within the gut microbiomes of the older mice, as were bacterial-encoded β-glucuronidases, which can influence drug-induced epithelial cell toxicity. Older mice also showed an overabundance of monosaccharide utilization genes relative to di-, oligo-, and polysaccharide utilization genes, which may have a substantial impact on gut homeostasis. Conclusion: We have identified taxonomic and functional patterns that correlate with age and frailty in the mouse microbiome. Differences in functions related to host nutrition and drug pharmacology vary in an age-dependent manner, suggesting that the availability and timing of essential functions may differ significantly with age and frailty. Future work with larger cohorts of mice will aim to separate the effects of age and frailty, and other factors. / This work was supported by the Canadian Institutes of Health Research (CIHR) through an Emerging Team Grant to RGB, CIHR Operating Grants to Langille et al. Microbiome 2014, 2:50 Page 10 of 12 http://www.microbiomejournal.com/content/2/1/50 SEH (MOP 126018) and RAR (MOP 93718), and a CIHR Fellowship to MGIL. Infrastructure was supported by the Canada Foundation for Innovation through a grant to RGB. RGB also acknowledges the support of the Canada Research Chairs program.

Bovine respiratory disease (BRD) is the leading cause of morbidity in feeder and stocker cattle, resulting in large impacts on economics of stocker and feedlot operations. One of the most effective means of controlling BRD is the mass administration of antimicrobials (AM) at arrival or “metaphylaxis”, potentially leading to increased antimicrobial resistance (AMR). Mannheimia haemolytica (MH), the most commonly isolated bacterial pathogen in BRD cases in feedlot cattle, has been shown to have integrative-conjugative elements (ICE), which are mobile genetic elements that have the ability to integrate themselves in the host genome. Notably, these ICE have been shown to contain multiple antimicrobial resistance genes (ARG) conferring resistance to antimicrobial classes used for BRD treatment. ICE have also been shown to be transferred between different genera. Since these ICE contain genes for resistance to multiple AM classes, administration of one AM could increase pressure for bacteria to transfer ICE for resistance to multiple drug classes; therefore, mass administration of AM may lead to increased isolation of multidrug resistant (MDR) MH and increase presence of resistance genes in the metagenome. Many NGS studies to date have used low numbers of cattle or pooled samples due to cost. Pooling is an acceptable strategy to increase number of units sampled, however sequencing depth per individual sample is decreased, and there is little evidence comparing pools to individual samples. In a trial involving high risk stocker cattle, tulathromycin metaphylaxis was associated with increased isolation of MDR MH, and this was associated with ICE related genes. Using pooled DNA extracted from NPS in these animals, which were shown to be acceptable for group level comparisons, metaphylaxis also increased ARG richness and diversity in these heifers; however, BRD treatment and time had a greater effect on the mircrobiome and resistome. Further work is needed to improve MH strain classification. These finding highlight the complexity of AMR research, because though tulathromycin had a clear effect on odds of isolation of MDR MH, metaphylaxis’ effects on the resistome and microbiome were more complex, and time and BRD contributed to greater change.

Development of type 2 diabetes (T2D) is preceded by prediabetes, which is a metabolically "atypical" state associated with chronic low-grade inflammation, overweight and obesity, lack of exercise, and detrimental changes to the gut microbiome. Dietary intake and exercise are modifiable lifestyle factors for reducing T2D risk; however, several questions remain unanswered related to the efficacy and role of prebiotics and exercise, and their respective influences on gut microbiome composition, intestinal permeability, insulin sensitivity and metabolic flexibility. Sedentary to recreationally active overweight and obese adults 40-75 years old at-risk for T2D were recruited (n=22) and randomized to either supplementation with inulin, a prebiotic dietary fiber, (10g/d) or maltodextrin while consuming a controlled diet for six weeks. At baseline and week 6, participants completed a stool collection, a 4-sugar probe test, an intravenous glucose tolerance test (IVGTT), and high-fat meal challenge with skeletal muscle biopsies to evaluate changes in the gut microbiome composition, intestinal permeability, insulin sensitivity and metabolic flexibility, respectively. There were no baseline group differences (all p>0.05). Following the intervention, Bifidobacteria operational taxonomic units increased in the intervention group ([placebo: Δ 9.5 ± 27.2 vs inulin: 96.3 ± 35.5][p=0.03]). There were no other group differences over time in any other outcome variables with the exception of changes in metabolic flexibility. Secondarily, a systematic review of literature was conducted to determine the influence of exercise engagement on gut microbiome composition. Overall, exercise interventions appeared to diversify taxa within the Firmicutes phylum, and specifically in several taxa associated with butyrate production and gut barrier function. Due to unclear risk of bias in all studies and low quality of evidence, additional research is needed using well- designed trials. In summary, the respective influences of prebiotics and exercise on human gut microbiome composition and their subsequent effects on metabolic function and disease risk are not well understood. / PHD / Type 2 diabetes (T2D) is common in the United States. Prediabetes occurs before T2D, and goes frequently undiagnosed, yet lifestyle changes (e.g. dietary changes and exercise engagement) may prevent or delay the development of T2D. Gut bacteria is a newer area of research that may have an important role in disease prevention. Several dietary supplements, such as pre- and probiotics, and their influence on gut bacteria have been studied, but the effectiveness of the prebiotic inulin for delaying or preventing T2D is unknown. Additionally the effects of exercise on gut bacteria and its role for T2D prevention is still not well understood. To address these questions, sedentary to recreationally active overweight and obese adults 40-75 years old at increased risk for T2D were recruited (n=22) and randomly assigned to either supplementation with inulin (10g/d) or maltodextrin and all consumed a six week standardized diet. At baseline and week 6, all participants completed a stool collection, a 4-sugar probe test, a high-fat challenge (HFC), and intravenous glucose tolerance test (IVGTT), and changes were evaluated in the gut microbiome, intestinal permeability, and indicators of metabolism, respectively. At week 6 Bifidobacteria, which is associated with improved gut health, increased in the inulin group ([placebo: Δ 9.5 ± 27.2 vs inulin: 96.3 ± 35.5][p=0.03]). There were no other differences over time for any other measurements with the exception muscle metabolism meal response. A systematic review of currently available research was also conducted to determine the influence of exercise engagement on gut microbiome composition. Overall, exercise engagement appeared to increase bacteria that is associated with better gut health. These findings are preliminary, and most evidence is from animal studies. Therefore, more research is needed to confirm these changes in humans. In summary, the roles of prebiotics and exercise on gut bacteria and human health are not well understood.

There is a rising global prevalence of type 2 diabetes (T2D), which poses both health and economic burdens. Effective research on T2D and clinical interventions can decrease the impact of these burdens and fill knowledge gaps in their efficacy, safety, and long-term outcomes. This comprehensive literature-based review examines the role of the gut microbiome in T2D and treatments, such as metformin and scutellaria radix-coptidis rhizoma (SC) herb couple, for gut microbiome (GM) modulation and improvement in T2D. For the purposes of this thesis, the GM is defined as a healthy nondiabetic GM, whereas dysbiosis, a deviation from a healthy GM maybe associated with the pathogenesis of T2D in terms of glucose metabolism, insulin sensitivity and inflammatory pathways and dysbiosis has been observed in individuals with a diagnosis of T2D. Microbial metabolites, such as short chain fatty acids and bile acids, and inflammatory processes have been associated with diabetes-related outcomes. Metformin, a traditional first line antidiabetic agent, as well as the traditional Chinese medicine herb couple, SC, modulate the composition of the GM in alleviating T2D. Based on the current body of knowledge, we propose to further investigate the effect of metformin and SC on the GM in T2D alleviation and measure the composition of the GM before and after an interventional clinical trial period. Investigating the effects of these study drugs and their relation to the GM may provide new insights on the pathogenesis and management of T2D.

Les produits cosmétiques sont des substances utilisées pour entretenir ou modifier l'aspect des parties superficielles du corps humain (telles que la peau, les ongles ou les cheveux). Dans de nombreux pays d’Afrique et d’Asie et dans certaines communautés africaines immigrantes, plusieurs femmes et parfois des hommes utilisent des produits contenant des agents actifs tels que le mercure, l’hydroquinone et le propionate de clobétasol pour éclaircir leur peau. Ces principaux agents sont toxiques et leur présence dans les cosmétiques est règlementée, voire interdite, dans plusieurs pays. Dans notre étude, nous avons déterminé les concentrations de ces ingrédients dans plusieurs produits utilisés en Afrique de l’Ouest et au Canada. Nous avons également exploré l’effet de ces produits sur le microbiome cutané. Nos résultats révèlent que 68 à 84% des crèmes et 7.5 à 65% des savons dépassent les normes lorsqu’on considère l’interdiction de mercure, d’hydroquinone et de propionate de clobétasol et les concentrations déclarées sur les étiquettes ne sont pas souvent fiables. Selon la diversité de Shannon, il semble y avoir plus d’équitabilité, et donc moins de dominance dans le groupe des femmes utilisant les crèmes éclaircissantes que dans le groupe des femmes qui ne les utilisent pas. Par ailleurs, nous n’avons pas trouvé de différences significatives au niveau du microbiome cutané du groupe avec crèmes et sans crèmes au niveau du phylum et du genre. Cependant, d’autres méthodes plus approfondies avec plus d’échantillonnage pourraient révéler à des échelles plus fines (espèces, souches, etc.) l’effet de ces produits sur le microbiome cutané. / Cosmetics are substances used to maintain or change the appearance of external parts of the human body (such as skin, nails or hair). In many countries of Africa and Asia and in some immigrant African communities, many women and sometimes men use products containing active agents such as mercury, hydroquinone and clobetasol propionate to lighten their skin. These main active agents are toxic and their presence in cosmetics is regulated or even banned in several countries. In our study, we determined the concentrations of these ingredients in many products used in West Africa and Canada. In addition, we also explored the effect of these products on the skin microbiome. Our results reveal that 68 to 84% of cream and 7.5 to 65% of soaps exceed the standards when considering mercury, hydroquinone and clobetasol propionate ban in lightening products and concentrations of the three compounds declared on labels of soaps and creams usually did not correspond to concentrations actually measured. According to Shannon diversity index, there seems to be more evenness, less dominance in group of African women with creams than in those without cream. Moreover, we have not found significant differences in the skin microbiome of the group with creams and the one without creams at the phylum and genus level. However, additional detailed studies with more sampling methods could reveal at finer scales (species, strains, etc.) the effect of these products on the human skin microbiome.

Les diatomées sont des algues microscopiques qui contribuent à hauteur de 25% environ à la production primaire planétaire. Les diatomées sont très souvent entourées d’une flore bactérienne, avec laquelle de nombreuses interactions ont été documentées. Les génomes de diatomées contiennent par ailleurs de nombreux gènes dont l’origine prédite est bactérienne.Nous avons étudié Asterionella formosa, une diatomée pennée présente dans de nombreux lacs et cours d’eau à l'aide de données omiques. L’utilisation de la métagénomique a permis de reconstruire 30 génomes bactériens, utilisés pour prédire d'éventuelles interactions avec la diatomée. Le séquençage de la sous-unité 16S de l’ARN ribosomique a montré que les différentes espèces bactériennes avaient une abondance variable au cours des phases de croissance de la diatomée, et que certaines étaient plus souvent au contact de la diatomée que libres dans le milieu. Le génome d'A. formosa a ensuite été séquencé à l'aide de la technologie Pacbio et comparé à ceux d'espèces proches. Enfin, l’impact des bactéries sur les diatomées a été abordé sous l’angle de l’évolution et des transferts horizontaux de gènes, qui ont été prédits à partir des données transcriptomiques d’une centaine de diatomées marines.Ce travail représente une première étape dans l'étude de la communauté bactérienne associée à A. formosa. Des expériences complémentaires incluant l’utilisation de transcriptomique ou métabolomique sont maintenant envisageables. Les données collectées et/ou analysées dans ce travail contribuent d'ores et déjà à l’effort global de caractérisation génomique des diatomées. / Diatoms are ubiquitous microalgae that contribute approximately 25% to the primary production worldwide. Many interactions, either positive, neutral or negative, have been documented between diatoms and bacteria. Diatom genomes also harbor numerous genes of putative bacterial origin.We are studying Asterionella formosa, a freshwater pennate diatom. We characterized the community using a combination of omics and laboratory techniques. We reconstructed of the genome of the diatom as well as 30 individual genomes from co-cultured bacterial species and investigated metabolisms that could support diatom-bacteria interactions. 16S rRNA sequencing revealed that the abundance of some bacterial species was highly variable over the course of A. formosa growth. Some species seemed preferentially attached to the diatom while others were mainly free-living. Then, the reference sequence of the A. formosa genome was improved by additional long-read (Pacbio) sequencing. Last, relationships between diatoms and bacteria were investigated at a broader evolutionary scale, by looking at horizontal gene transfers using transcriptomic data of a hundred marine diatoms.This work is a first step in the study of the dynamic and complex bacterial community associated with the diatom A. formosa. The accurate identification and the reconstruction of the genome of these bacteria will enable further in silico predictions based on metabolic networks and new omics experiments using transcriptomic or metabolomic. This work already contributes to a global effort to study diatoms by the means of genomics.

Nous avons collecté et comparé les microbiotes et les microbiomes intestinaux de plusieurs dizaines de lézards de l’espèce Podarcis sicula, vivant dans des populations continentales et insulaires croates. L’une de ces populations présentait la particularité d’avoir subi un changement de régime alimentaire récent, une transition d’un régime insectivore vers un régime omnivore (à 80% herbivores) sur une période de 46 ans. Les analyses de diversité menées sur la région V4 de l’ARN ribosomique 16S de ces communautés microbiennes ont révélé que la diversité spécifique (diversité alpha) des microbiotes de lézards omnivores (enrichis en archées méthanogènes) excède celle des microbiotes de lézards insectivores. Les communautés microbiennes des lézards apparaissent en outre faiblement structurées : 5 entérotypes peuvent être identifiés au niveau du phylum, et 3 phyla majoraires (les Bactéroidètes, les Firmicutes et les Protéobactéries) sont présents dans cette espèce. Cependant, ni le régime alimentaire, l’origine spatiale ou temporelle, et le sexe des lézards ne se traduisent par des différences significatives et majeures dans les microbiotes. Des analyses linéaires discriminantes avec effet de la taille des OTUs et des reads des microbiomes fonctionnellement annotés indiquent plutôt que le changement de régime alimentaire de Podarcis sicula est associé à des changements ciblés dans l’abondance de certains composants du microbiote et du microbiome de ces lézards, nous conduisant à formuler l’hypothèse de changements ciblés des communautés microbiennes dans cet holobionte non-modèle, par opposition à des transformations plus radicales. Sur un plan plus théorique, cette thèse propose également des modèles de réseaux (réseaux de similarité de reads et graphes bipartis) susceptibles d’aider à approfondir les analyses des microbiomes. / We collected and compared intestinal microbiota and microbiomes from several Podarcis sicula lizards, which live in Croatian continental and insular populations. One of these populations has recently changed its diet over an 46 years timespan, switching from an insectivorous diet to an omnivorous one (up to 80% herbivorous). Diversity analyses of these microbial communities, based on the V4 region of their 16S rRNA, showed that the microbiota taxonomic diversity (or alpha diversity) is higher in omnivorous lizards (enrichment in methanogenic archaea) than in insectivorous ones. Besides, microbial communities seem weakly structured: 5 enterotypes are detected at the phylum level, and 3 major phyla (Bacteroidetes, Firmicutes and Proteobacteria) are present. However, neither diet, spatial or temporal origin, nor lizard gender correlate with significant differences in microbiota. Linear discriminant analyses with size effect, based on OTUs and functionally annotated reads from the microbiomes, suggest that Podarcis sicula diet change is associated to targeted changes of the abundance of some enzymes in the microbiomes. Such a result leads us to propose a hypothesis of targeted changes in the microbial communities of this non-model holobiont, instead of more radical transformations. On a more theoretical level, this thesis also proposes network models (Reads similarity networks and bipartite graphs) that can help improving microbiome analyses.

Le développement des plantes est conditionné par leurs interactions avec le microbiote racinaire, dont le fonctionnement repose sur des fonctions élémentaires partagées par plusieurs taxons, au sein de groupes fonctionnels. Certains de ces groupes incluent des PGPR (Plant Growth-Promoting Rhizobacteria), qui stimulent la croissance des plantes grâce à différentes fonctions phytobénéfiques. L'inoculation d'une PGPR peut avoir un impact sur la physiologie de la plante et sur les autres partenaires microbiens de la racine. D'ailleurs, une PGPR inoculée peut modifier la structure génétique du microbiote racinaire global, sans que l'on sache comment cet impact se concrétise au niveau de groupes fonctionnels particuliers. L'hypothèse de cette thèse est que les PGPR inoculées peuvent modifier la structure de communautés microbiennes fonctionnelles importantes pour le développement de la plante. Ces travaux ont évalué l'impact de l'inoculation de la PGPR Azospirillum lipoferum CRT1 sur la taille et/ou la diversité des diazotrophes, des producteurs d'1-aminocyclopropane-1-carboxylate (ACC) désaminase et des producteurs de 2,4-diacétylphloroglucinol (ainsi que de la communauté bactérienne totale) dans la rhizosphère du maïs cultivé en champ sous différents intrants azotés. Nos travaux ont montré que diazotrophes et producteurs d'ACC désaminase pouvaient être co-sélectionnés dans la rhizosphère du maïs, et que l'inoculation modifiait la composition taxonomique de ces groupes fonctionnels. En conclusion, l'inoculation de PGPR module la sélection rhizosphérique de taxons telluriques portant des fonctions phytobénéfiques, ce qui pourrait contribuer aux effets phytobénéfiques observés / Plant development is influenced by interactions established with root microbiota. Microbiota functioning relies on individual functions carried out by functional groups, which often contain multiple microbial taxa. Some of these groups include plant growth-promoting rhizobacteria (PGPR), which stimulate plant growth thanks to several plant-beneficial functions. PGPR inoculation may impact plant physiology and microbial partners of roots, and inoculated PGPR can modify the genetic structure of the root microbiota. However, it is not known how this impact materializes at the level of particular microbial functional groups. The hypothesis of this thesis is that inoculated PGPR will also modify the structure/composition of microbial functional groups important for plant development. This work assessed the impact of inoculation with the PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of diazotrophs, 1-aminocyclopropane-1-carboxylate (ACC) deaminase producers and 2,4-diacetylphloroglucinol producers (as well as the total bacterial community) colonizing the maize rhizosphere in three fields and under different nitrogen fertilization regimes. Our work showed that diazotrophs and ACC deaminase producers could be co-selected in maize rhizosphere and that PGPR inoculation modified the taxonomic composition of functional groups. To conclude, PGPR inoculation modulates rhizospheric selection of microbial members of functional groups important for plant growth, which may mediate some of the plant-beneficial effects of PGPR inoculants

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