Understanding how barn sanitation practices impact the chicken gut microbiome and the significance of variations in early life gut microbial community structure on microbial functionality
Notice bibliographique
Résumé
Chemical disinfectants are widely used by Canadian broiler producers for barn sanitation, although little is known regarding their effects on chicken performance and the gut microbiome, which had been well recognized to have great importance to the host health. In this thesis, studies were conducted in commercial barns to evaluate the impacts of barn sanitation practices on chicken performance, the gut microbiome, and immune responses. The significance of variations in early-life gut microbial structure were also assessed with regards to their effects on the microbial population, microbial functional capacity, as well as indices of host immune response. To determine the impact of barn sanitation practices on the chicken performance and the gut microbiome, barn cleaning with chemical disinfectants versus water-wash was conducted as a cross-over experiment. At the end of the production cycle, the flock mean body weight and mortality rate were comparable between the barn sanitation treatment groups. The barn water-wash resulted in a modest but significant effect on the structure of broiler cecal microbiota, with notable reductions in cecal Campylobacter jejuni occurrence and abundance. In addition, chickens from the barn water-wash group had increased level of cecal acetate, butyrate and total short-chain fatty acids that were negatively correlated with C. jejuni abundance. To further assess the effects of the barn sanitation practices on chicken gut microbial functional capacity, particularly on microbial metabolism and antibiotic resistance, cecal content samples were subjected to shotgun metagenomic sequencing. At day 7, the gut microbiome of chickens from the chemically disinfected barns had decreased capacity of amino acid production with increased stringent response compared to the water-wash group. Similarly at day 30, the gut microbiome of chickens reared in chemically disinfected barns exhibited decreased abundance of the genetic pathways encoding amino acid and short-chain fatty acid biosynthesis due to decreased cecal Helicobacter pullorum population. Our data suggested that the use of chemical disinfectants in barn cleaning were more effective in controlling persistent antibiotic resistance genes. Finally, a study was conducted to investigate distinct cecal early-life microbial structures identified among commercial broiler chickens in gut microbial interaction, functionality, as well as host immune status. Week-old commercial broiler chickens were screened and chickens with distinct cecal Bacteroides composition were identified. Compared to the Bacteroides-under-representative group, the chickens with Bacteroides-over-representative cecal microbiota had increased microbial genetic potential of complex polysaccharide degradation and short-chain fatty acid production in the gut, which was supported by increased cecal short-chain fatty acid concentrations. In addition, chickens with high cecal Bacteroides had lower expression of interleukin-1β gene and higher expression interleukin-10 gene and tight-junction protein claudin-1 gene. The results indicated that elevated cecal Bacteroides may be beneficial to commercial broiler chickens in suppressing gut inflammation coincided with the increment of short-chain fatty acid production. Collectively, this thesis provides insights into the role of barn sanitation practices during poultry production in the microbiome of commercial broiler chickens, and exhibits the significance of variations in early-life gut microbial community structure in microbial functionality and host immune status.
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Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,001 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,001 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,001 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».