AN EXAMINATION OF THE MICROBIOME OF BROILER CHICKENS IN VARYING STATES OF STRESS AND NECROTIC ENTERITIS CHALLENGE
Type of DegreeMaster's Thesis
Restriction TypeAuburn University Users
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The gut influences and is in turn shaped by its microbial communities, with the host’s environment and its history molding those populations in ways unique to the specific location and stimulus received. For domestic chickens these influential factors can vary with the minutest changes ranging from what the bird has been fed to how its grandparents were raised or even how its egg was stored and handled before hatching. To further explore these influences three trials were conducted to collect gut samples at various days post hatch and observe changes in composition of the microbial communities therein. The experiments consisted of three separate trials: An exploratory study establishing the influence of different flocks of origin by placing birds from 2 separate hatcheries (hatchery A, hatchery B) either in homogenous or mixed groups on floor pens or in battery cages. Midgut (defined as the area between the duodenal loop and Meckel’s diverticulum) and ceca samples were collected via necropsy on day 0, 5, and 14 for battery cage birds, and day 0,5,14, 16, 21, 28, and 48 for floor raised birds. A trial observing the influence of environmental stressors by placing birds in normal and less than optimal lighting and/or temperatures during rearing in floor pens or battery cages. Samples of the crop, midgut and the ceca were taken via necropsy at day 0,5,14, 28 and 36. A final study was conducted to record differences in gut communities during times of disruptive stressors and sickness in challenged vs unchallenged birds in normal/low lighting in floor pen/battery cages. Challenge was achieved by dosing challenge birds with 1 ml coccidiosis vaccine at 10x the recommended dose then inoculating with 107 CFU/ml C. perfringens at days 18, 19, and 20. Samples of the crop, midgut, and the ceca were taken at day 0 and 21. All samples were extracted of DNA and Illumina sequenced. Raw sequence reads were run through the bioinformatic pipeline program QIIME, and the resulting data was used to generate alpha and beta analyses as well as general classification. Overall birds from different origins were characterized both by distinctly different microbiomes when raised homogenously, and by exerting influence over each other when raised together. Birds raised together showed characteristics of the group possessing more diverse day 0 microbiome, with midgut more closely resembling hatchery B and ceca resembling hatchery A . Possible influence of parental microbiome was observed, with hatchery A being known to have fed all vegetarian diets to breeders. Chicks from that location were slower to adopt Bacteroides a classification of bacterium that are known to be prevalent in diets high in animal protein and fat, when fed a diet containing animal protein compared to hatchery B chicks. Birds raised in less than optimal temperature and lighting conditions were not significantly different in diversity, however midgut samples from birds in high temperature/low light and low temperature/low light pens had a higher proportional prevalence of Lactobacillus when compared to high temperature/high light and low temperature/high light pens, with low temperature/high lighting level pens having the lowest Lactobacillus prevalence. Due to sample contamination it is unclear to what extent bacterial challenge influences the populations in low light vs normal lighting reared birds. However the continued trend of higher proportional Lactobacillus prevalence in low light pens was observed. Based on observations, mixing day old chicks from a flock with known superior microbial communities with chicks from an flock with weak or non-beneficial microbial communities may have a net positive effect on the new flock overall. Lighting seems to have some influence on microbes generally considered to be beneficial, with Lactobacillus being consistently more prevalent in low light situations. The effects of mixed flock brooding has many implications to the ability to somewhat correct for poor quality chicks or chicks from low production flocks. Further exploration as to whether this effect is only observed between distinct hatchery locations or is observable between individual flocks is recommended. Investigating a potential link between lighting and Lactobacillus presence is highly recommended, as little research was found as to the effect of light on Lactobacillus in poultry or even in general.