Understanding the Respiratory Microbiome of Commercial Poultry (Turkeys and Chicken Layers)

PI: Timothy J. Johnson (Univ. Minnesota) and Chang Won Lee (Ohio State Univ.)

It is increasingly evident that the resident microbiota of an animal plays a critical role in animal’s susceptibility to disease. While this is evident, we are in the very early stages of fully understanding the relationships between indigenous microbiota and susceptibility or resistance to disease challenge. This is particularly true in poultry, where the respiratory microbiota as of yet remains incompletely defined. Without an understanding of the baseline microbial players in the respiratory tracts of avian species, and their succession over time, it is impossible to fully understand their role in health and disease.

The overall goal of this project is to comprehensively define the core baseline microbiota in commercial turkeys, broilers, and egg laying chickens, and understand how it changes over time. We will utilize culture-independent approaches to profile bacterial, viral, and fungal communities in the avian respiratory tract during the initial stages of bird development. In collaboration with other project participants, we will also assess the impact of various bacterial, viral, and environmental challenges on the respiratory microbiota. In addition to sampling of the respiratory microbiota, we will also sample the gastrointestinal microbiota and immune tissues from the same birds in a holistic effort to examine the relationships between the microbiota and gut and respiratory maturation.

Yearly Goals:

Year 1:

Identify flocks in Minnesota and Ohio for turkeys and chicken layers, respectively.

Develop methods for collecting biological materials from the upper respiratory tract and perform baseline sampling and bacterial and fungal microbiome analysis.

Year 2:

Develop methodologies to enrich for the viral component of the avian respiratory microbiome and the metagenomics and bioinformatics tools to determine the viral microbiome.

Year 3:

Combine the approaches developed in years 1 and 2 to perform longitudinal studies on the composition of the bacterial and viral respiratory microbiomes in flocks of commercial turkeys and chicken layers from at least3 different states.

Years 4 & 5:

Continue the longitudinal studies from previous year. Collaborate with other project PIs to analyze the respiratory microbiota in response to various pathogen and environmental challenges.


This project will enable comprehensive analyses of the complex microbiota inhabiting commercial birds during their development. This work will not only provide the first in-depth glimpse of avian respiratory microbiota across multiple types of microorganisms, but will also enable us to identify the core microbiota and the complex interactions that occur between these members during bird maturation.


wpadminProject Johnson Lee