Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens

• DOI: 10.1128/aem.03137-18
• Publication Date: 2019-02-26T14:10:44Z
• Authors: John M. Ngunjiri; Kara J. M. Taylor; Michael C. Abundo; Hyesun Jang; Mohamed Elaish; Mahesh KC; Amir Ghorbani; Saranga Wijeratne; Bonnie P. Weber; Timothy J. Johnson; Chang-Won Lee
• Keywords: Affect; Developmental stage

The digestive and respiratory tracts of chickens are colonized by bacteria that believed to play important roles in the overall health performance birds. Most current research on commensal (microbiota) has focused broilers gut microbiota, less attention been given layers microbiota. This bias left significant gaps our knowledge layer microbiome. study was conducted define core microbiota colonizing upper tract (URT) lower intestinal (LIT) commercial under field conditions. One hundred eighty-one were sampled from a flock >80,000 birds at nine times collect samples for 16S rRNA gene-based bacterial metabarcoding. Generally, body site age/farm stage had very dominant effects quantity, taxonomic composition, dynamics bacteria. Remarkably, ileal URT compositionally more related each other than cecum. Unique taxa dominated yet some overlapped between LIT sites, demonstrating common core. overlapping also contained various levels several genera with well-recognized avian pathogens. Our findings suggest interaction exists including potential pathogens, all stages farm sequence. baseline data generated this can be useful development effective microbiome-based interventions enhance production prevent control disease chicken layers.IMPORTANCE poultry industry is faced numerous challenges associated infectious diseases suboptimal flocks. As microbiome continues grow, it becoming clear partly influenced nonpathogenic symbionts occupy different habitats within bird. defined composition overlaps healthy, optimally performing across Consequently, set groundwork seek through modulation