A consistent and predictable commercial broiler chicken bacterial microbiota in antibiotic-free production displays strong correlations with performance

Timothy J. Johnson, Bonnie P. Youmans, Sally Noll, Carol Cardona, Nicholas P. Evans, T. Peter Karnezos, John M. Ngunjiri, Michael C. Abundo, Chang Won Lee

Research output: Contribution to journalArticlepeer-review

76 Scopus citations


Defining the baseline bacterial microbiome is critical to understanding its relationship with health and disease. In broiler chickens, the core microbiome and its possible relationships with health and disease have been difficult to define, due to high variability between birds and flocks. Presented here are data from a large, comprehensive microbiota-based study in commercial broilers. The primary goals of this study included understanding what constitutes the core bacterial microbiota in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system and metadata from these and an additional 512 flocks within that system, the baseline bacterial microbiota was defined using 16S rRNA gene sequencing. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiota, irrespective of flock. The tracheal bacterial microbiota of broilers was comprehensively defined, and Lactobacillus was the dominant bacterial taxon in the trachea. Numerous bacterial taxa were identified, which were strongly correlated with broiler chicken performance across multiple tissues. While many positively correlated taxa were identified, negatively associated potential pathogens were also identified in the absence of clinical disease, indicating that subclinical dynamics occur that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives, such as probiotics, for sustainable poultry production.

Original languageEnglish (US)
Article numbere00362-18
JournalApplied and environmental microbiology
Issue number12
StatePublished - Jun 1 2018

Bibliographical note

Funding Information:
Bioinformatics were supported using tools available from the Minnesota Supercomputing Institute. This project was supported by Agriculture and Food Research Initiative Competitive Grants (2016-67015-24911 and 2015-68004-23131) from the USDA National Institute of Food and Agriculture. We are grateful for Carrie Cremers for assistance in this study.

Publisher Copyright:
© 2018 American Society for Microbiology.


  • Antibiotic free
  • Broilers
  • Chickens
  • Microbiome
  • Performance
  • Poultry


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