Poultry gastrointestinal microbiome changes during ontogenesis

Microorganisms which inhabit gut play great role in providing with nutrients, antibiotics, hormones and vitamins necessary for poultry health and performance. Therefore study of gut microbiome changes during ontogenesis seems to be essential. The structure of gut microflora in poultry embryos is of particular interest and debated because of very few publications on the problem. Despite embryo intestine is commonly considered sterile there are several reports on gut colonization by microorganisms in embryos during ontogenesis. Using T-RFLP (Terminal Restriction Fragment Length Polymorphism) analysis to generate a fingerprint of a microbial community we compared gut flora in chick embryos on days 6 and 17 to those in 26-day, 150-day and 300-day old Hisex White layers. Unlike accepted view, a high biodiversity was seen in embryo gut with Enterobacteriaceae ( Escherichia coli mainly) predominated. Clostridia, Bacteroides, Negativicutes, Actinomycetales, Bifidocteriales were also found in contrast to earlier reports of their presence only in chicks at hatching and in adult poultry gut. Moreover, in the embryo gut we found the causal agents of dangerous animal disease, Burkholderia sp., Pseudomonas sp., Salmonella sp., Klebsiella sp. and Rickettsiales bacteria. Interestingly, the embryo gut biodiversity on day 6 was higher as compared to day 17 (75±2.75 phylotypes vs 30±1.20 phylotypes). In the layers aged 26, 150 and 300 days the diversity was much higher (over 175±8.12 phylotypes) as compared to embryos due to new members involved into gut bacterial community. Moreover, the poultry aged 300 days was lower both in the total diversity and in the percentage of unidentified microorganisms when compared to 26-day and 150-day old hens. In the adults, the predominating microbial taxa changed, in particular, Clostridia and Negativicutes became more abundant whereas Bacillales and Bifidobacteriales were depressed. Our findings indicate gut colonization by Lactobacilales and pathogenic Listeria sp., Pantoea sp., Enterobacter sp., Mycoplasma sp., Acinetobacter sp., Pasteurellaceae, Campylobacteraceae, Fusobacteria which occurred during ontogenesis. Thus the gut microbiome formation starts in embryo which is important for hatching and growing healthy poultry.