Towards the modulation of the microbiome to control Campylobacter in broiler chickens

Campylobacter is the leading cause of bacterial gastroenteritis in humans worldwide. Chicken meat is an important source of Campylobacter for humans. However, the interactions between Campylobacter and the microbiome associated with broiler chickens are little understood. Therefore, a series of studies were designed to fill that knowledge gap with the long-term goal of modulating the microbiome to deter Campylobacter colonization in broiler chickens. Chapter I reviewed the current literature on Campylobacter in broiler chickens. Chapter II documented a protocol for a systematic review on the efficacy of prebiotics and probiotics against foodborne pathogens in poultry. Chapter III evaluated the performance of commonly used bacterial differential abundance tests on cecal microbiome data using a parametric simulation. Chapter IV described a survival analysis assessing the association between cecal microbiome during the first two weeks of age and the time-to-peak Campylobacter colonization in broiler chickens under commercial settings, employing random survival forest and supervised principal component analysis. Chapter V explored the association of microbiome and Campylobacter in broiler litter in two studies. A matched case-control study interrogated the relationship between microbiome composition and the isolation of Campylobacter in litter of commercial broiler houses, whereas a cohort study explored the relationship between Campylobacter and the longitudinal changes in the litter microbiome throughout the broiler production cycle. Chapter VI integrated the data from Chapters IV and V, while acknowledging the interdependence of the litter and cecal microbiome in broiler chickens due to their coprophagic behavior. Chapter VI made use of inverse probability weighting modelling to tackle the time-varying confounding in interconnected processes. Methods for bacterial differential abundance that take into account the specific characteristics of microbiome data showed a better performance than methods designed for RNA-seq. Campylobacter dynamics in ceca and litter are related to each other and to the associated microbiomes in broiler chickens. Moreover, associations of Bifidobacterium in litter, Negativibacillus, DTU089, GCA-900066575, and Oscillibacter in ceca with Campylobacter counts at a harvest age common for small broilers, were detected. In conclusion, modulation of the litter and/or cecal microbiome could potentially hinder Campylobacter colonization in broilers, helping decrease the burden of campylobacteriosis in humans.

Author dc:creator

• Valeris Chacin, Robert Jose

Language dc:language.iso

en

Handle dc:identifier.uri

https://hdl.handle.net/11299/278101

OAI identifier oai:identifier

oai:conservancy.umn.edu:11299/278101