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

Abstract

The digestive and respiratory tracts of chickens are colonized by bacteria that are believed to play important roles in the overall health and performance of the birds. Most of the current research on the commensal bacteria (microbiota) of chickens has focused on broilers and gut microbiota, and less attention has been given to layers and respiratory microbiota. This research bias has left significant gaps in our knowledge of the layer microbiome. This study was conducted to define the core microbiota colonizing the upper respiratory tract (URT) and lower intestinal tract (LIT) in commercial layers under field conditions. One hundred eighty-one chickens were sampled from a flock of Ͼ80,000 birds at nine times to collect samples for 16S rRNA gene-based bacterial metabarcoding. Generally, the body site and age/farm stage had very dominant effects on the quantity, taxonomic composition, and dynamics of core bacteria. Remarkably, ileal and URT microbiota were compositionally more related to each other than to that from the cecum. Unique taxa dominated in each body site yet some taxa overlapped between URT and LIT sites, demonstrating a common core. The overlapping bacteria also contained various levels of several genera with well-recognized avian pathogens. Our findings suggest that significant interaction exists between gut and respiratory microbiota, including potential pathogens, in all stages of the farm sequence. The baseline data generated in this study can be useful for the development of effective microbiome-based interventions to enhance production performance and to prevent and control disease in commercial chicken layers. IMPORTANCE The poultry industry is faced with numerous challenges associated with infectious diseases and suboptimal performance of flocks. As microbiome research continues to grow, it is becoming clear that poultry health and production performance are partly influenced by nonpathogenic symbionts that occupy different habitats within the bird. This study has defined the baseline composition and overlaps between respiratory and gut bacteria in healthy, optimally performing chicken layers across all stages of the commercial farm sequence. Consequently, the study has set the groundwork for the development of interventions that seek to enhance production performance and to prevent and control infectious diseases through the modulation of gut and respiratory bacteria.

Microbiome and biological blood marker changes in hens at different laying stages in conventional and cage free housings

“…Previous studies have shown that early exposures of chickens to stress (i.e., in commercial hatcheries) have prolonged effects later in life and that chickens negatively respond to stress at different maturities ( Ericsson et al., 2016 , Hedlund et al., 2019 ). Likewise, age and body site drive major shifts in the chicken gut and lung microbiota ( Awad et al., 2016 , Ngunjiri et al., 2019 ). However, changes in biological markers of stress and disease susceptibility as well as shifts in the mature hen microbiome between early, peak, and late laying stages have not been previously investigated.…”

“…The chicken gut and lungs are 2 of the primary barriers between pathogens and the host ( Bingula et al., 2017 ). Factors such as age may influence the composition of these commensal communities ( Awad et al., 2016 , Kers et al., 2018 , Ngunjiri et al., 2019 ). The overgrowth of pathogenic bacteria in these sites is detrimental to both chicken health and consumers.…”

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

“…In early life it is generally observed that the caeca contain high abundances of Enterobacteriales [9,10] and over the first few weeks of life these decline and members of the Clostridiales come to predominate [9][10][11][12][13][14][15][16], with some studies also showing a large increase in Bacteroidetes [12,17,18]. However, the results from some studies do not entirely follow this pattern [19,20] and variability in microbiota composition between flocks can be high [21,22]. Several studies have also examined samples from the small intestine which are less rich and diverse than caecal samples and contain a high abundance of Lactobacilli [12,14,17,18,20,[23][24][25].…”

Characterization of the upper respiratory tract microbiome of turkeys

“…Results of the study on the digestive system of chickens and turkeys demonstrated that age and environment appear to play a key role in the initial stages of turkey bacterial microbiome maturation [17,29]. In other studies, significant differences in the richness and diversity of respiratory track communities were observed between age groups but in the nasal cavity of chickens [15]. However, the tracheal community composition shifted very gradually as the chicken aged.…”

“…The growing number of studies on the avian microbiome demonstrates the influence of the gastrointestinal and respiratory microbiome on the proper development and efficiency of poultry production. In recent years the studies on the bacterial microbiome of poultry have primarily focused on chickens [12][13][14][15]. Particularly focused on the composition and diversity of intestinal microbiome of chickens [11,16].…”