Abstract
Little to no research has been conducted on the gut microbiome of the Pekin duck, yet over 24.5 million ducks are raised for human consumption each year in the United States alone. Knowledge of the microbiome could lead to an understanding of the effects of growing conditions such as the use of prebiotics, probiotics, and enzymes in feeding practices, the use of antibiotics, and the sources of pathogenic bacteria in diseased ducks. In order to characterize changes in the caecal microbiome that occur as ducks develop through a typical industry grow-out period, a 16S rRNA community analysis of caecal contents collected over a 6-week period was conducted using a next generation sequencing approach. Transitions in the composition of the caecal microbiome occurred throughout the lifespan, with a large shift during days 4 through 10 posthatch. Two major phyla of bacteria were found to be present within the caeca of aviary raised ducks, with the relative abundance of each phylum varying by age of the duck. Proteobacteria is dominant for the first 3 days of age, and Firmicutes increases and dominates beginning at day 4. Barn raised ducks contained a significant population of Bacteroidetes in addition to Proteobacteria and Firmicutes at later developmental time points, though this phylum was absent in aviary raised ducks. Genera containing pathogens of anseriformes most often found in industry settings were either absent or found as normal parts of the caecal microbial populations. The high level differences in phylum abundance highlight the importance of well-designed sampling strategies for microbiome based studies. Results showed clear distinctions between Pekin Duck caecal contents and those of Broiler Chickens and Turkey in a qualitative comparison. These data provide a reference point for studies of the Pekin Duck through industry grow-out ages, provide a foundation for understanding the types of bacteria that promote health, and may lead to improved methods to increase yields and decrease instances of disease in agricultural production processes.
Highlights
Investigation of microbes associated with host organisms has become an increasingly important approach to better understand the host organisms, the microbial communities, and the interactions that occur between hosts, their microbes, and environment (Gilbert et al, 2016)
Microbial communities associated with caecal contents of Pekin ducks were analyzed in order to understand the structure of and changes associated with the development of ducks through a typical industry growth period
Two studies were conducted in a controlled aviary setting—Aviary Study 1 was designed as a broad overview of the 36-day developmental cycle; Aviary Study 2 was designed to focus on the first 10 days of duck development. These data were compared to Barn Study 3, a parallel study that occurred in a production barn environment (Schenk et al, 2016) in order to examine differences in microbial community structure and developmental changes that could occur in different environments
Summary
Investigation of microbes associated with host organisms has become an increasingly important approach to better understand the host organisms, the microbial communities, and the interactions that occur between hosts, their microbes, and environment (Gilbert et al, 2016). Microbiome of Developing Pekin Ducks of the gut of many organisms, in particular mammals, has been found to protect against pathogens, impact digestion, influence immune system function, and affect the health of individuals (e.g., Turnbaugh et al, 2006; Cho and Blaser, 2012; Flint et al, 2012; D’Argenio and Salvatore, 2015; Gilbert et al, 2016). Studies of commercial avian species have revealed changes in the microbiome associated with species, age, diet, host site, and commercial environmental conditions (van der Wielen et al, 2002; Lu et al, 2003; Gong et al, 2007; Wei et al, 2013; Choi et al, 2014; Stanley et al, 2014; Vasaï et al, 2014; Roto et al, 2015). The majority of bacteria associated with avian species has been found in the intestinal caeca, where a relatively lower oxygen partial pressure and decreased enzyme and bile salt concentrations create conditions suitable for a variety of bacteria (Gabriel et al, 2006)
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