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PhD student, University of Alberta


Which microbes are normal inhabitants of the chicken gut and how do they benefit chickens?

Bacteria are generally associate to disease occurrence, but many species colonize the chicken gastrointestinal tract without causing harm. In fact, the presence of commensal bacteria in the gut can positively influence host immune development, health, and disease resistance. This beneficial relationship is specific and established by long-term co-adaptation processes, suggesting that microorganisms in the gut are required for proper bird development, performance, and health. While aiming at reducing the exposure to pathogens, current production practices, such as high sanitation and antibiotic use, can inadvertently minimize chicken exposure to healthy microbes. We hypothesize that proper colonization of the gut with commensal bacteria can improve chicken’s ability to deal with immune challenges, therefore reducing the need of antibiotics use. We will analyse and compare the microbial composition of extensively and conventional raised chickens across Alberta, and of wild Red Jungle Fowl birds. The Jungle Fowl is the closest wild relative of the chicken, therefore its microbiome may resemble chicken’s native microbiome. We will expose chickens to cultures of microbes obtained from i) conventionally raised broilers, ii) extensively raised broilers, iii) wild jungle fowl, iv) a mix of conventionally raised broilers and wild jungle fowls. Then, we will evaluate how seeding microbes obtained from birds from different systems can influence gut colonization, performance, immunological profile, and inflammatory responses. We aim to determine whether the microbes of domestic birds have co-evolved over the recent genetic selection, or whether the microbes from wild birds are more capable of colonizing the chicken gut. Our goal is to identify and create a culture collection of microorganisms that could potentially reduce performance losses and diseases outbreaks in the poultry industry. The proposed approach differs from consumption of probiotics, which disappear from the gut when administration ceases. We aim to develop tools to support an one-time exposure to native microorganisms that will be best able to colonize the chicken gut, providing added protection to the host, and potentially reducing the dependence on antibiotics as growth promoters.


Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota.

Abstract: The gastrointestinal tract is populated by a complex and vast microbial network, with a composition that reflects the relationships of the symbiosis, co-metabolism, and co-evolution of these microorganisms with their host. The mechanism that underlies such interactions between the genetics of the host and gut microbiota remains elusive.To understand how genetic variation of the host shapes the gut microbiota and interacts with it to affect the metabolic phenotype of the host, we compared the abundance of microbial taxa and their functional performance between two lines of chickens (fat and lean) that had undergone long-term divergent selection for abdominal fat pad weight, which resulted in a 4.5-fold increase in the fat line compared to the lean line. Our analysis revealed that the proportions of Fusobacteria and Proteobacteria differed significantly between the two lines (8 vs. 18% and 33 vs. 24%, respectively) at the phylum level. Eight bacterial genera and 11 species were also substantially influenced by the host genotype. Differences between the two lines in the frequency of host alleles at loci that influence accumulation of abdominal fat were associated with differences in the abundance and composition of the gut microbiota. Moreover, microbial genome functional analysis showed that the gut microbiota was involved in pathways that are associated with fat metabolism such as lipid and glycan biosynthesis, as well as amino acid and energy metabolism. Interestingly, citrate cycle and peroxisome proliferator activated receptor (PPAR) signaling pathways that play important roles in lipid storage and metabolism were more prevalent in the fat line than in the lean line.Our study demonstrates that long-term divergent selection not only alters the composition of the gut microbiota, but also influences its functional performance by enriching its relative abundance in microbial taxa. These results support the hypothesis that the host and gut microbiota interact at the genetic level and that these interactions result in their co-evolution.

Pub.: 30 Nov '16, Pinned: 28 Aug '17

Effects of feeding Original XPC™ to broilers with a live coccidiosis vaccine under industrial conditions: Part 2. Cecal microbiota analysis.

Abstract: Biological supplements in poultry feed are of continued interest due to the improvements in growth performance, protection from pathogen invasion, and benefits in overall host health. The fermentation metabolites of Diamond V Original XPC™ (XPC) have previously been shown to improve commercial performance and reduce Salmonella in poultry. The current study sought to characterize the cecal microbiota using culture-independent analysis based on 16S rRNA gene in Coccivac-D sprayed broilers supplemented with XPC and/or Salinomycin (SAL). Ross 708 male broilers (n = 640) were assigned to one of 4 treatments: Cocci-vaccine (T1), Cocci-vaccine + XPC (T2), Cocci-vaccine + SAL (in the grower diet only) (T3), and Cocci-vaccine + SAL (in the grower diet only) + XPC (T4). Analysis with a PCR-based denaturing gradient gel electrophoresis (DGGE) indicated a shift in the microbial populations present at the various sampling ages - 16, 28, and 42 days. Phylogenetic analysis indicated further consistency in microbial communities directly related to bird age. Identification of microbial communities present and the assessment of their respective quantities using an Illumina MiSeq indicated treatment with XPC had no significant impact on microbial diversity (Chao1 index, observed operational taxonomic unit (OTU) and phylogenetic diversity (PD) whole tree). Sampling age revealed significantly greater diversity at 16 and 28 d (P < 0.05) as compared to the 42 d for the Shannon diversity index, while showing significantly decreased richness and diversity in the 42 d sampling age (Chao1 and observed OTU; P < 0.05). The results of the current study indicate that the chicken intestinal microbiota are impacted more by temporal changes rather than by the feed additive studied.

Pub.: 25 Mar '17, Pinned: 28 Aug '17