The chicken tracheal microbiome: unexpected preliminary data

I wanted to post a little bit on work we have been doing to study the chicken tracheal microbiome. Mainly that we finally have some preliminary results, and they are not what we expected. Without getting into too many details, this PCoA pretty much sums it up:


The tracheal bacterial community in developing chickens looks a lot like the litter. I guess this isn’t all that surprising considering chickens breathe in the barn dust constantly. What was interesting is that the dominant OTUs contain bacteria we would expect to find in the respiratory tract (i.e., Staphylococcus, Streptococcus, E. coli, and Moraxella) — but, surprisingly the most abundant OTUs include those that are classified as Lactobacillus! The same Lactobacillus we find in the ileum and litter. So, a major component of the tracheal bacterial community in chickens (we think) appears to be some of their own gut bacteria. This could have some big implications for modulating the gut microbiome and its global effects on the animal and barn environment, even more than we thought before…


The Johnson Lab Mission

About Dr. Tim Johnson:cropped-photo-on-9-28-16-at-9-06-pm.jpg

Dr. Timothy Johnson is an Associate Professor of microbiology at the University of Minnesota in the College of Veterinary Medicine. Dr. Johnson received his PhD in Molecular Pathogenesis from North Dakota State University in 2004, followed by postdoctoral studies at Iowa State University’s College of Veterinary Medicine. Dr. Johnson joined the University of Minnesota’s Department of Veterinary and Biomedical Sciences in 2007. He has since developed a research and outreach program focused on the genetic mechanisms enabling the spread of antibiotic resistance in Enterobacteriaceae. In tandem, his work focuses on the identification of antibiotic alternatives that manipulate the animal microbiome allowing for enhanced growth and reduced disease. Dr. Johnson has received new investigator awards from the Plasmid Biology Society and American Association for Avian Pathologists for his research accomplishments. He also currently serves as Director of Research and Development at the Mid-Central Research and Outreach Center’s Poultry Research Laboratory in Willmar, MN.

Dr. Johnson’s research occurs in two locations, one lab on the University of Minnesota – Saint Paul campus and a second lab at the Minnwest Technology campus in Willmar, MN.

Our research mission:

  1. Understand the ways that antibiotic resistance spreads through human and animal populations
  2. Identify alternatives to antibiotics that can be used to enhance performance and reduce disease in agricultural animals
  3. Determine the microbial community structures of a healthy microbiome in production animals, and the primary on-farm drivers of microbiome modulation

Our outreach mission:

  1. Provide rapid response capability to the poultry industry of Minnesota
  2. Develop the next line of novel tools for research and diagnostics in poultry
  3. Reach the next generation of scientists in rural Minnesota
  4. Train the future workforce of scientists in rural Minnesota agriculture