Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expressions

Authors: WARD, TONYA - University Of Minnesota; WEBER, BONNIE - University Of Minnesota; MENDOZA, KRISTELLE - University Of Minnesota; DANZEISEN, JESSICA - University Of Minnesota; LLOP, KATHARINE - University Of Minnesota; LANG, KEVIN - University Of Minnesota; CLAYTON, JONATHAN - University Of Minnesota; GRACE, ELICIA - University Of Minnesota; BRANNON, JEANINE - University Of Minnesota; RADOVIC, IGOR - University Of Minnesota; BEAUCLAIRE, MACI - University Of Minnesota; HEISEL, TIMOTHY - University Of Minnesota; KNIGHTS, DAN - University Of Minnesota; CARDONA, CAROL - University Of Minnesota; Kogut, Michael - Mike; JOHNSON, CASEY - University Of Delaware; NOLL, SALLY - University Of Minnesota; ARSENAULT, RYAN - University Of Delaware; REED, KENT - University Of Minnesota; JOHNSON, TIMOTHY - University Of Minnesota

Submitted to: mBio
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/17/2019
Publication Date: 10/15/2019
Citation: Ward, T.L., Weber, B.P., Mendoza, K.M., Danzeisen, J.L., Llop, K., Lang, K., Clayton, J.B., Grace, E., Brannon, J., Radovic, I., Beauclaire, M., Heisel, T.J., Knights, D., Cardona, C., Kogut, M.H., Johnson, C., Noll, S.L., Arsenault, R., Reed, K.M., Johnson, T.J. 2019. Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expressions. mBio. 10(5). Article e02171-19. https://doi.org/10.1128/mbio.02171-19.
DOI: https://doi.org/10.1128/mbio.02171-19

Interpretive Summary: The development of the immune response in chicks is influenced by the animal’s gut. This is because the gut is exposed not only to nutrients, but also many bacteria that live in the gut. What has been found over the last 20 years is that bacteria that do not cause disease but normally grow in the gut can work together to make animals’ immune systems work better and prevent bad germs from growing. This paper shows that the growth of certain bacteria control specific components of the chick’s local immune environment in the gut. This paper would be beneficial to turkey growers, microbiologists, and nutritionists and will help make better animal feeds that encourage the growth of the normal bacteria in the gut and help the development of a healthy immune system.

Technical Abstract: The microbiome is important to all animals, including poultry, where it plays a critical role in health and performance. Low-dose antibiotics have historically been used to modulate food production animals and their microbiome. Identifying alternatives to antibiotics that confer similar modulatory properties has been elusive. The purpose of this study was to determine if host specific probiotics could recapitulate the effects of low-dose antibiotics on host response and the microbiome. Over the first thirteen days of life, turkey poults were supplemented continuously with a low-dose antibiotic (bacitracin methylene disalicylate, 50 g/ton), or oral supplementation of a prebiotic with or without two different poultry-specific probiotics (n=80 per group). Gastrointestinal bacterial and fungal communities of poults were characterized by the 16S rRNA gene and ITS2 amplicon sequencing. Localized host gene expression was assessed using RNA-Seq, kinase activity by turkey-specific kinome peptide arrays, and performance parameters were assessed. We found that development of the early-life microbiome of turkey poults was tightly ordered in a tissue- and timespecific manner. Low-dose antibiotic and turkey-specific probiotic supplementation, not generic probiotic supplementation, elicited similar shifts in overall microbiome composition during development when compared to controls. Treatment-induced bacterial changes were accompanied by parallel shifts in the fungal community, ileum host gene expression, and enhanced weight gain. To our knowledge, this study provides novel evidence for coordinated interkingdom relationships between host, bacteria, and fungi occurring at the gut level. Therefore, alternative approaches to low-dose antibiotic use in poultry are feasible and can be optimized utilizing the indigenous poultry microbiome. Similar approaches may also be beneficial for humans.