Age-related differences in the respiratory microbiota of chickens

Abstract

In this era of next generation sequencing technologies it is now possible to characterise the chicken respiratory microbiota without the biases inherent to traditional culturing techniques. However, little research has been performed in this area. In this study we characterise and compare buccal, nasal and lung microbiota samples from chickens in three different age groups using 16S rRNA gene analysis. Buccal and nasal swabs were taken from birds aged 2 days (n = 5), 3 weeks (n = 5) and 30 months (n = 6). Bronchoalveolar lavage (BAL) samples were also collected alongside reagent only controls. DNA was extracted from these samples and the V2-V3 region of the 16S rRNA gene was amplified and sequenced. Quality control and OTU clustering were performed in mothur. Bacterial DNA was quantified using qPCR, amplifying the V3 region of the 16S rRNA gene. We found significant differences between the quantity and types of bacteria sampled at the three different respiratory sites. We also found significant differences in the composition, richness and diversity of the bacterial communities in buccal, nasal and BAL fluid samples between age groups. We identified several bacteria which had previously been isolated from the chicken respiratory tract in culture based studies, including lactobacilli and staphylococci. However, we also identified bacteria which have not previously been cultured from the respiratory tract of the healthy chicken. We conclude that our study can be used as a baseline that future chicken respiratory microbiota studies can build upon.

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

“…The bacterial microbiota of the chicken gut has been studied extensively, mainly because of its association with weight gain in broilers (7,8,10,41,42) and egg production in layers (2)(3)(4)43). However, chicken respiratory bacterial microbiota studies are scarce (7,(23)(24)(25), and chicken layers have been reported in only two studies (23,25). The two studies on layers have provided much-needed data on respiratory microbiota, but they were limited in terms of sample sizes, sampling time points, and use of management systems that are not widely applied in commercial settings (23,25).…”

“…However, chicken respiratory bacterial microbiota studies are scarce (7,(23)(24)(25), and chicken layers have been reported in only two studies (23,25). The two studies on layers have provided much-needed data on respiratory microbiota, but they were limited in terms of sample sizes, sampling time points, and use of management systems that are not widely applied in commercial settings (23,25). In the present study, we report the dynamics of the URT microbiota of healthy layers raised in commercial farm settings according to a standard management protocol (26).…”

“…The body site and bird's age play prominent roles in the development of bacterial microbiota in different breeds of layer and broiler chickens (7,19,23). It is therefore not surprising that a substantial amount of variation in microbially diverse populations across samples was attributable to body site and bird's age ( Fig.…”

“…Unlike the gut microbiota, the respiratory microbiota of both broilers and layers are understudied (7,(23)(24)(25). The respiratory microbiota of layers have been reported in only two studies, which showed variable results, possibly due to the effects of inadequate sample sizes and sampling time points, differences in sampling sites and techniques, layer breeds, and the use of management systems which are not widely applied in commercial settings (23,25). In broilers, a 16S rRNA-based microbiota analysis revealed wide differences between tracheal and cecal microbiota in 42-day-old birds (24).…”

BiomeSeq: A Tool for the Characterization of Animal Microbiomes from Metagenomic Data

“…Recent studies attempting to characterize the microbiomes of mammals have focused primarily on their bacterial composition, as there are well established and rapid methods of sequencing and analyzing this component (Bond et al , 2017; De Boeck et al , 2015; Gaeta et al , 2017; Glendinning et al , 2017; Johnson et al , 2018; Shabbir et al , 2015). The 16S rRNA gene is commonly used to identify and compare the bacterial genera present in a given sample (Clarridge et al , 2004).…”