Maddison Wiersema
The purpose of this project was to compare the effects of housing type on the gut health of commercial laying hens. We were mainly looking at the microbes found in the gut and comparing them between the housing types: conventional cage, and aviary (cage-free). We hypothesized that hens reared in aviaries: 1) will have different microbial communities, 2) will have increased microbial diversity, 3) will have increased counts of pathogenic organisms, compared to those raised in conventional cages.
Hens from a local producer were euthanized and digesta samples were collected from the ileum (last section of the small intestine). These samples were then used for collection of DNA. The DNA was sent to a sequencing facility to be analyzed. Once the data was back, we used a variety of different computer software to further analyze the data. We first used Mothur, which is a bioinformatics processing package that is commonly used for analyzing 16s rRNA data. Results from Mothur showed that hens from the conventional cage system had a higher abundance of normal bacteria, while hens from aviary systems had a higher abundance of potentially pathogen bacteria. When looking at Alpha diversity,which includes species evenness, richness and diversity, it was concluded that the birds from conventional cages had a more even and diverse microbiome which would be considered ideal.
Next, we used SAS and R to further analyze some of the results and make sure that we were seeing significant differences. Through this, we did end up seeing significant differences between housing types as many of the bacteria were differentially expressed. We also used these statistical programs to create heat maps which allowed for easy comparisons to be made when looking at the bacteria between housing types.Overall,we saw that the conventional cage birds had a more ideal microbiome compared to birds from the aviary setting. So,regarding our hypotheses, hens in aviaries did have different microbial communities compared to hens from conventional cages, but hens from conventional cages had a more diverse intestinal microbiome. We did not have enough time to assess the number of pathogenic organisms, so next steps would be to do more research on the specific bacteria found and look at what their role is in poultry, specifically their impact on gut health and function.
Funding Organization: Egg Industry Center
Duration: 04/29/2019
Principal Investigator(s): Dr. Dawn Koltes