Large Overlap Between the Intestinal and Reproductive Tract Microbiomes of Chickens

The work described in the manuscript strongly implies that material from the gut travels the full length of the poultry reproductive tract. This is possibly the result of chicken physiology which includes the cloaca, a cavity to which both the intestinal and reproductive tract open into. As the cloaca is common to birds, reptiles, amphibians, most fish, and monotremes, our finding may be relevant to many vertebrates. Importantly, these results indicate that mere presence in, and ascending of the oviduct are not virulence characteristics specific to pathogens as commonly thought, but are the result of chicken physiology and characterize all gut bacteria. Furthermore, as a vertical transmission route from the hen to the chick has been suggested, our work starts laying a mechanistic foundation to this route, by describing the movement of gut bacteria to the oviduct, where they may be enclosed in the developing egg. Last, as our results show that gut material travels the full length of the oviduct, fertilization in poultry occurs in the presence of at least bacterial products if not live bacteria, therefore food additives and diet possibly have a much more direct effect on reproduction and egg formation than previously considered.