Large-scale association analyses identify host factors influencing human gut microbiome composition

To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P <5 x 10(-8)) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 x 10(-20)), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 x 10(-10) <P <5 x 10(-8)) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis

Modulating the innate molecular immunity of the egg

L’œuf est un aliment riche en divers composés dont de nombreuses molécules antimicrobiennes qui sont les effectrices de son système de défense moléculaire innée et complètent l’action des immunoglobulines (IgYs) afin de protéger l’embryon. La composition en IgYs de l’œuf est sous la dépendance notamment des stimulations microbiennes de la poule. L’objectif de notre travail a été d’évaluer l’influence de ces mêmes stimulations sur le système de défense moléculaire innée du blanc d’œuf. Nous avons exploré cette hypothèse en utilisant deux approches expérimentales. La première était basée sur la comparaison de l’activité antibactérienne des blancs d’œufs de poules axéniques, de poules exemptes d’organismes pathogènes spécifiques (EOPS), et de poules conventionnelles. La seconde approche a testé les effets de deux types d’inductions du système immunitaire chez la poule: injection d’un immunostimulant, le lipopolysaccharide bactérien (LPS) et administration oral de souches vaccinales atténuées (virale, bactérienne et parasitaire). Nos résultats montrent que l’activité antibactérienne du blanc d’œuf est augmentée en fonction de la charge microbienne du milieu de vie de la poule, après stimulation de celle-ci par voie intraveineuse avec du LPS ou suite à la vaccination avec des souches atténuées virale ou bactérienne. Néanmoins cette augmentation est modérée de par son amplitude et son spectre antibactérien. Ces résultats suggèrent que les poules peuvent renforcer modérément l’activité antimicrobienne du blanc d’œuf en réponse à des stimuli microbiens de leur milieu et anticiper ainsi les besoins de l’embryon en termes de protection.The egg is a balanced source of different nutrients and contains a myriad of antibacterial peptides/proteins that ensure its chemical protection. These molecules are a part of its innate molecular defense and, in addition to the maternal immunoglobulins IgY, contribute to the protection of the forming embryo whose development occurs ex utero. It is well documented that yolk immunoglobulin deposition is induced by the environmental microbiome of the hen but no such evidence is available for antimicrobial peptides/proteins. Therefore the aim of this thesis was to assess whether the hen has the ability to stimulate the innate molecular immunity of the egg white when facing a higher environmental microbial load (commensal or pathogenic). To address these questions, we developed two main experimental approaches; the first assessed the impact of the hen environmental microbial load through the comparison of three groups of hens with different immune status:-Germ free, -Specific pathogen free (SPF), and -conventional. The second approach explored the effect of different types of immune stimulation in hens: non-infectious stimulation (systemic injection of bacterial lipopolysaccharide (LPS)); immune stimulation using attenuated live vaccines (Infectious bronchitis virus vaccine, Salmonella enterica Enteritidis vaccine and a complex of Eimeria vaccine). Our results show that the activity of egg white is increased in response to higher microbial environmental charge, after LPS systemic stimulation or after vaccinating hens with live attenuated viral and bacterial strains. However this response is moderate both in its amplitude and microbial spectrum. Altogether, it appears that hens when subjected to immune stimuli, have the ability to reinforce moderately the antibacterial activity of the egg white as an attempt to anticipate the need of protection of their embryos

Modulation de l'immunité innée moléculaire de l'oeuf

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Systemic administration of lipopolysaccharide in laying hens stimulates antimicrobial properties of egg white against Staphylococcus aureus

International audienceThe natural protective system of eggs relies on egg yolk immunoglobulins and on antimicrobial proteins/peptides mainly concentrated in the egg white. There is much evidence concerning the specific stimulation of immunoglobulins by antigens but to date, the influence of the hen milieu on the regulation of the egg innate molecular immunity has not been established. To explore the hypothesis of modulation in egg antimicrobial molecules, laying hens were immune-challenged with intravenous injections of Salmonella enterica Enteritidis lipopolysaccharide (LPS) at 24 h intervals. Eggs of the control and LPS groups were collected over a period of 21 days following the first LPS injection and the egg white activities against Staphylococcus aureus and Escherichia coli were assessed. The increase in egg white anti-S. aureus activity reached 20.9% and 23.4% (p<0.05) respectively on days 5 and 6 after the first LPS injection. Anti-E. coli activity increased moderately only on days 9 and 15 after the LPS treatment. To explore the origin of these increased antimicrobial activities, we analyzed the lysozyme and proteases inhibiting (anti-trypsin and anti-chymotrypsin) activities and the pH variations of egg whites. We recorded no significant variations between the two experimental groups for these potential modulating factors. Finally, using RT-qPCR we studied the expression of several genes coding for antimicrobial proteins and peptides involved in the immune response in the infundibulum and the magnum, Out of the 11 genes, only TLR4 in the magnum and ovocalyxin-36 in infundibulum were over-expressed respectively 24h and 8 days after the first LPS injection. The other candidate genes showed similar or down regulated expression in the LPS group as compared to the control especially during the first 24h. Our results suggest that the hen enhances the albumen antimicrobial activity of its eggs when exposed to immune stimulations or infections. This could be an attempt to preventively reinforce the protection of the embryo with nonspecific antimicrobial agents in addition to the specific antibodies exported to the egg. The origin of this stimulation of egg molecular immunity remains to be characterized amongst the numerous novel egg proteins recently identified

Microbial environment and immune challenge modulate the molecular innate defence of the hen egg

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Microbial environment of the hen modulates the innate immune defence of the egg against bacteria

International audienceThe egg is a complex formation that allows the development of an embryo ex utero by providing essential nutrients and a molecular protective system. In addition to immunoglobulins, molecular defences of the egg are also composed of antimicrobial peptides/proteins that are predominantly localized in egg white (EW). The present study investigated whether this innate antimicrobial protection is stimulated by the degree of contamination of the hen milieu by using two experimental models. Firstly, we compared the global antimicrobial activity of EW issued from hens reared in extreme bacterial environments: bacterial free (axenic, Ax), specific pathogen free (SPF) and standard (ST) conditions. EW issued from the ST and SPF groups demonstrated a greater inhibitory effect against Staphylococcus aureus as compared to those of Ax groups (9.8% and 4% respectively, P<0.05). The second approach explored the effect of an immune challenge in hens on the antimicrobial potential of EW. EW from hens stimulated with Salmonella Enteritidis lipopolysaccharide showed greater antimicrobial activity against Staphylococcus aureus (14.8%, P<O.OOI) than those of control hens. These results suggest that hens can reinforce the antimicrobial activity of the EW in response to immune stimulations induced by microbial contamination and anticipate the needs of the embryo in terms of protection. Further quantitative analyses of magnum gene expression and EW concentration of antimicrobial protein candidates were carried out to explore putative mechanisms of regulation

Passive maternal exposure to environmental microbes selectively modulates the innate defences of chicken egg white by increasing some of its antibacterial activities.

International audienceBackground Egg defence against bacterial contamination relies on immunoglobulins (IgY) concentrated in the yolk and antimicrobial peptides/proteins predominantly localized in the egg white (EW). Hens contaminated with pathogenic microorganisms export specific IgYs to the egg (adaptative immunity). No evidence of such regulation has been reported for the antimicrobial peptides/proteins (innate immunity) which are preventively secreted by the hen oviduct and are active against a large range of microbes. We investigated whether the egg innate defences can be stimulated by the environmental microbial contamination by comparing the antimicrobial activity of EW of hens raised in three extreme breeding conditions: Germ-free (GF), Specific Pathogen Free (SPF) and Conventional (C) hens. Results The difference in the immunological status of GF, SPF and C hens was confirmed by the high stimulation of IL-1β, IL-8 and TLR4 genes in the intestine of C and SPF groups. EW from C and SPF groups demonstrated higher inhibitory effect against Staphylococcus aureus (13 to 18%) and against Streptococcus uberis (31 to 35%) as compared to GF but showed similar activity against Salmonella Enteritidis, Salmonella Gallinarum, Escherichia coli and Listeria monocytogenes. To further investigate these results, we explored putative changes amongst the three main mechanisms of egg antimicrobial defence: the sequestration of bacterial nutrients, the inactivation of exogenous proteases and the direct lytic action on microorganisms. Lysozyme activity, chymotrypsin-, trypsin- and papain-inhibiting potential of EW and the expression of numerous antimicrobial genes were not stimulated suggesting that these are not responsible for the change in anti-S. aureus and anti-S. uberis activity. Moreover, whereas the expression levels of IL-1β, IL-8 and TLR4 genes were modified by the breeding conditions in the intestine of C and SPF groups they were not modified in the magnum where egg white is formed. Conclusions Altogether, these data revealed that the degree of environmental microbial exposure of the hen moderately stimulated the egg innate defence, by reinforcing some specific antimicrobial activities to protect the embryo and to insure hygienic quality of table eggs

Modulation des propriétés antibactériennes du blanc d’œuf par la poule en réponse à différents stimuli microbiens

L’objectif de cette étude est d’évaluer l’influence de stimulations microbiennes de poules sur le système de défense innée du blanc d’oeuf en utilisant deux modèles expérimentaux. Le premier est basé sur la comparaison de l’activité antibactérienne des blancs d’oeufs de poules axéniques élevées en conditions stériles (Ax), de poules exemptes d’organismes pathogènes spécifiques (EOPS) et de poules conventionnelles (C). Le second modèle compare des oeufs de poules contrôles ou immunostimulées par injection de lipopolysaccharide bactérien (LPS). Les résultats ont montré que les blancs d’oeufs des groupes C et EOPS ont une activité inhibitrice renforcée vis-à-vis de Staphylococcus aureus comparée à ceux du groupe Ax. De même, une meilleure activité antimicrobienne contre ce pathogène est observée pour les blancs d’oeufs du groupe LPS par rapport à ceux du groupe contrôle. En revanche, l’activité anti-Escherichia coli n’est pas modifiée ni par le degré de contamination du milieu des poules (Ax vs EOPS vs C) ni par l’injection de lipopolysaccharide (LPS vs contrôle). L’analyse de l’expression de gènes codants pour des protéines/peptides antimicrobiens de l’oeuf et les mesures des activités du lysozyme et d’antiprotéases dans le blanc n’ont pas permis d’expliquer les stimulations de l’activité antimicrobienne du blanc d’oeuf. Ces résultats suggèrent que les poules peuvent renforcer modérément l’activité antimicrobienne du blanc d’oeuf en réponse à des stimuli microbiens de leur milieu et anticiper les besoins de l’embryon en termes de protection. Les mécanismes moléculaires à l’origine de cette modulation demeurent néanmoins inconnus à ce jour

Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models

Summary: The intestinal microbiota is a fundamental factor that broadly influences physiology. Thus, studies using transgenic animals should be designed to limit the confounding effects of microbiota variation between strains. Here, we report the impact on intestinal microbiota of co-housed versus F2-generation littermates, two commonly used techniques to standardize microbiota in animal models. Our results establish that while fecal microbiota is partially normalized by extended co-housing, mucosal communities associated with the proximal colon and terminal ileum remain stable and distinct. In contrast, strain inter-crossing to generate F2 littermates allows robust microbiota standardization in fecal, colon, and ileum sampling locations. Using reciprocal inter-crosses of P1 parents, we identify dissymmetry in F2 community structures caused by maternal transmission, in particular of the Verrucomicrobiaceae. Thus, F2 littermate animals from a unidirectional P1 cross should be used as a standard method to minimize the influence of the microbiota in genotype-phenotype studies. : Standardization of the microbiota in mouse models ensures reproducibility of findings and avoids erroneous conclusions. Here, Robertson et al. demonstrate that the use of F2-generation littermates is the superior method for standardization of the gut microbiota between experimental groups to minimize the influence of the microbiota in genotype-phenotype studies. Keywords: microbiota, microbiota standardization, intestinal, co-housing, littermates, mous

Thermal manipulation of the embryo modifies the physiology and body composition of broiler chickens reared in floor pens without affecting breast meat processing quality

Selection in broiler chickens has increased muscle mass without similar development of the cardiovascular and respiratory systems, resulting in limited ability to sustain high ambient temperatures. The aim of this study was to determine the long-lasting effects of heat manipulation of the embryo on the physiology, body temperature (Tb), growth rate and meat processing quality of broiler chickens reared in floor pens. Broiler chicken eggs were incubated in control conditions (37.8 degrees C, 56% relative humidity; RH) or exposed to thermal manipulation (TM; 12 h/d, 39.5 degrees C, 65% RH) from d 7 to 16 of embryogenesis. This study was planned in a pedigree design to identify possible heritable characters for further selection of broiler chickens to improve thermotolerance. Thermal manipulation did not affect hatchability but resulted in lower Tb at hatching and until d 28 post-hatch, with associated changes in plasma thyroid hormone concentrations. At d 34, chickens were exposed to a moderate heat challenge (5 h, 32 degrees C). Greater O-2 saturation and reduced CO2 partial pressure were observed (P 0.17). In conclusion, TM of the embryo modified the physiology of broilers in the long term as a possible adaptation for heat tolerance, without affecting breast meat quality. This study highlights the value of 2 new heritable characters involved in thermoregulation for further broiler selection