The intestinal microbiome (IM) or the community of commensal and pathogenic microbes that inhabit the intestinal tract of fish has long been of interest in aquaculture because of its hypothesized role in nutrient digestion and fish immunity. Artificial improvement to the IM of fish with pre- and probiotics has been shown to have benefits in some studies; however, the mechanisms behind these supplements are poorly understood because of a lack of knowledge on the basic structure of the IM of fish. The research described here aims to characterize the IM of the highly studied and commercially important Icatlurid catfish, channel catfish Ictalurus punctatus and blue catfish I. furcatus. In this study we evaluated differences between the homeostatic IM, across genotype (Objective 1) and developmental ontogeny (Objective 2), using high-throughput sequencing of 16S rRNA gene amplicons. We compared the IM of four selected strains of blue catfish and three selected strains of channel catfish at 193 days post-hatch (DPH) in Objective 1 (n = 40); while the influence of developmental ontogeny was evaluated by observing the IM of a single family of channel catfish at 3, 65, 125, and 193 DPH Objective 2 (n = 20). The bacterial phyla Fusobacteria, Firmicutes, and Proteobacteria were detected in all fish strains and developmental time points; however, at the genus level the abundances of different bacteria varied among experimental units, as well as being rather variable between individuals. At 3 DPH (n = 5) the IM of channel catfish sac-fry larvae showed the most variation between individuals; with bacteria from the genus Bradyrhizobium dominating the IM of two sac-fry (84% and 88%), and Flavobacterium, Lactobacillus, Comamonadaceae dominating the IM of the remaining three sac-fry analyzed (86%, 99%, and 97% respectively). The dominant bacteria in the gut of all other fish analyzed (n = 55), was Cetobacterium somerae (mean ± SD, 41.4% ± 36%), a commensal microbe that is known to produce vitamin B12. Statistical differences in the abundance of three different bacteria within the order Clostridiales (P ≤ 0.039) were detected in Objective 1, with more of these OTUs inhabiting the gut of channel catfish than that of blue catfish. Statistical differences in the abundance of Edwardsiella, a genus of bacteria known to cause disease in catfish, were detected across the two species of Ictalurid catfish in Objective 1 (P = 0.038), and across developmental ontogeny in Objective 2 (P = 0.021); however, these bacteria were detected at low abundance (0.002% - 0.004%). Comparisons of beta diversity showed significant differences between many strains of Ictalurids, with a highly significant difference between channel catfish and blue catfish (P = 0.001); however, few differences were detected when comparing beta diversity across the four time points over the first 193 DPH in Objective 2, with only 3 DPH and 125 DPH showing significant differences (P = 0.022). Overall these data suggest host-genotype, and to a lesser extent developmental ontogeny, influence the structure of the IM of Ictalurid catfish. As the first study to be conducted on the IM of these fish species, these results have performance implications on the culture of these commercially important catfish, while also enhancing our basic knowledge on the dynamics of the fish microbiome.

The composition and metabolic activity of the microbiome affect many aspects of health, and there is current interest in dietary constituents that may affect this system. The purpose of this study was to evaluate the effects of a mix of probiotics, a mix of prebiotics and a bioactive protein fraction on the microbiome, when fed to mice individually and in combination. Mice were fed the total western diet (TWD) supplemented with prebiotics, probiotics, and Tri-Factor (bioactive proteins) individually and in combination for four weeks. Subsequently, effects on the composition of gut microbiome, gut short chain fatty acids (SCFAs) concentration, gut inflammation and integrity of the mucosal barrier were analyzed. Ruminococcus gnavus was increased in mice gut microbiome after feeding prebiotics. Bifidobacterium longum was increased after feeding probiotics. Probiotic was associated with higher level of Clostridium neonatale. The treatments affected beta-diversity with exception of Tri-Factor, but not alpha diversity of microbiome. All treatments were associated with lower plasma zonulin, compared to the control group, indicating an effect on gut permeability. There were no treatment effects on cecal or fecal SCFAs, and the treatments did not affect gut inflammation as measured by fecal calprotectin.

The FGLa/ASTs are one family of allatostatin peptides and share an amidated C-terminal sequence (FGL-amide). The inhibitory effect of FGLa/ASTs on juvenile hormone (JH) biosynthesis in Diploptera punctata led to their discovery, but there is a lack of allatostatic function across most insect species that suggests this function may not be their primary role. Rather, the FGLa/ASTs are implicated as brain/gut peptides, modulating gut physiology. This thesis demonstrates the pleiotropic nature of FGLa/ASTs in Locusta migratoria and emphasizes the role of FGLa/ASTs as brain/gut peptides involved in homeostatic processes. FGLa/AST-like immunoreactivity (FLI) is associated with the corpus cardiacum (CC) and corpus allatum (CA). FGLa/ASTs increase adipokinetic hormone release from the CC and alter JH biosynthesis from the CA, suggesting roles in energy utilization and in growth and metamorphosis. Each region of the gut exhibits FLI. The gut is dually innervated: neurons in the abdominal ganglia of the central nervous system (CNS) innervate the posterior gut and some contain FLI, while neurons within the stomatogastric nervous system (STNS) that innervate the anterior gut do not seem to contain FLI, indicating that source of FLI on the gut are cells within the CNS, which may release FGLa/ASTs at the gut to alter aspects of gut physiology. FGLa/ASTs are involved in peristalsis, neural control of foregut contractions, and ileal K+ transport. In particular, FGLa/ASTs inhibit contractions of each gut region and also modulate the rhythmic motor output of a central pattern generator within the ventricular ganglion of the STNS. FGLa/ASTs also inhibit ileal K+ efflux, suggesting a diuretic action and implicating FGLa/ASTs in fluid and ion homeostasis. This work provides a comprehensive picture of how FGLa/ASTs play an integral role in nutrient processing, energy mobilization, and growth and metamorphosis to contribute to the overall maintenance of homeostasis. This reinforces the role of FGLa/ASTs as brain/gut peptides and emphasizes their involvement in the flexibility of nervous communication and integration of the endocrine system with the CNS to achieve homeostasis.

The FGLa/ASTs are one family of allatostatin peptides and share an amidated C-terminal sequence (FGL-amide). The inhibitory effect of FGLa/ASTs on juvenile hormone (JH) biosynthesis in Diploptera punctata led to their discovery, but there is a lack of allatostatic function across most insect species that suggests this function may not be their primary role. Rather, the FGLa/ASTs are implicated as brain/gut peptides, modulating gut physiology. This thesis demonstrates the pleiotropic nature of FGLa/ASTs in Locusta migratoria and emphasizes the role of FGLa/ASTs as brain/gut peptides involved in homeostatic processes. FGLa/AST-like immunoreactivity (FLI) is associated with the corpus cardiacum (CC) and corpus allatum (CA). FGLa/ASTs increase adipokinetic hormone release from the CC and alter JH biosynthesis from the CA, suggesting roles in energy utilization and in growth and metamorphosis. Each region of the gut exhibits FLI. The gut is dually innervated: neurons in the abdominal ganglia of the central nervous system (CNS) innervate the posterior gut and some contain FLI, while neurons within the stomatogastric nervous system (STNS) that innervate the anterior gut do not seem to contain FLI, indicating that source of FLI on the gut are cells within the CNS, which may release FGLa/ASTs at the gut to alter aspects of gut physiology. FGLa/ASTs are involved in peristalsis, neural control of foregut contractions, and ileal K+ transport. In particular, FGLa/ASTs inhibit contractions of each gut region and also modulate the rhythmic motor output of a central pattern generator within the ventricular ganglion of the STNS. FGLa/ASTs also inhibit ileal K+ efflux, suggesting a diuretic action and implicating FGLa/ASTs in fluid and ion homeostasis. This work provides a comprehensive picture of how FGLa/ASTs play an integral role in nutrient processing, energy mobilization, and growth and metamorphosis to contribute to the overall maintenance of homeostasis. This reinforces the role of FGLa/ASTs as brain/gut peptides and emphasizes their involvement in the flexibility of nervous communication and integration of the endocrine system with the CNS to achieve homeostasis.

La nutrition postnatale précoce conditionne la santé du futur adulte du fait de son rôle déterminant dans l’implantation du microbiote intestinal et le développement de la physiologie de l’hôte. L’objectif de mon travail de thèse a été d’évaluer les conséquences de la réintroduction de matière grasse laitière associée ou non au probiotique Lactobacillus fermentum dans des préparations pour nourrissons, sur le microbiote, la physiologie intestinale et le métabolisme de l’adulte, en utilisant le miniporc Yucatan comme modèle de l’Homme. Nos travaux ont montré un renforcement des défenses non spécifiques intestinales chez le jeune et une amélioration des fonctions endocrine et immunitaire intestinales de l’adulte soumis à un régime hyper-énergétique, réduisant ainsi le risque de développer une inflammation et des désordres métaboliques. Ces effets ont été associés à une modification de la digestion des préparations chez le jeune et à une modulation de la composition et de l’activité métabolique du microbiote intestinal. Des effets spécifiques de la matière grasse laitière et de L. fermentum, et d’autres complémentaires, ont été observés, suggérant des mécanismes d’action différents. Les modifications induites par la composition des préparations pour nourrissons étaient site- et âge-spécifiques, le comportement du microbiote caecal se rapprochant du microbiote fécal. En conclusion, l’optimisation des préparations pour nourrissons pourrait passer par l’ajout de matière grasse laitière et du probiotique L. fermentum. / Early postnatal nutrition programs adult health owing to its crucial role in gut microbiota colonization and host physiology development. The objective of my thesis was to investigate the consequences of dairy lipid addition with or without probiotic Lactobacillus fermentum in infant formulas on adult gut microbiota, physiology and metabolism, using Yucatan minipig as a model for humans. We demonstrated increased non-specific intestinal defences in piglets and improved intestinal endocrine and immune functions in adults submitted to a high-energy diet, which may protect them from inflammation and metabolic disorders. These effects were associated in piglets to changes in digestion and gut microbiota composition and metabolism. We observed specific and complementary effects of dairy lipids and L. fermentum, suggesting different mechanisms of action. The infant formula composition had site- and age-specific effects, the caecal microbiota being closer to the faecal one. To conclude, the addition of dairy lipids and L. fermentum in infant formulas is an effective way to improve infant formulas.