Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System

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.

Probiotics Strains Modulate Gut Microbiota and Lipid Metabolism in Mule Ducks

“…The decrease in Firmicutes (order Clostridiales ) associated with the increase in Bacteroidetes (order Bacteroidiales ) and Proteobacteria has already been highlighted in a previous study in the lab [ 30 ]. Furthermore, in Pekin ducks, the most abundant bacteria (more than 95%) over the first 36 days were also Firmicutes, in particular, the Clostridiales order, as in our study [ 29 ]. Interestingly, in our work, at Eof point, a strong increase in the abundance of Lactobacillus, as described in geese and ducks, was observed but not linked to the supplementation of probiotics [ 8 - 10 ].…”

“…The rapid evolution of the diversity of intestinal microbiota during the early stages of development demonstrated by Best et al . [ 29 ] and Rey et al . [ 30 ] in ducks and the strong effect of strain inoculation in newborn chickens on the composition of microbiota [ 31 , 32 ] suggest that supplementation in ducklings will be more efficient in modulating microbiota and host physiology immediately after hatching.…”

Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water

“…The early consequences directly involve infant gut function and immune system, and they are even associated with the signatures of the late gut microbiota as well as health and fitness of a host. These findings, therefore, give rise to great interest in gut microbiota of ontogenetic development in vertebrates such as birds, broilers, pig, and fish (Jami et al, 2013 ; Waite et al, 2014 ; Bakke et al, 2015 ; Corrigan et al, 2015 ; Niu et al, 2015 ; Best et al, 2016 ).…”

Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

“…In recent years, more and more studies focus on the gut microbes, which play an important role in our lives. Previous studies have demonstrated that diets 3 , 4 , breeding patterns, ages, and feed additives can impact the poultry gut microbes with respect to diversity, composition, and community structure 5 , 6 . Firmicutes, Bacteroidetes and Proteobacteria are the dominant phyla in poultry gut lumen.…”