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

posted on 2023-11-30, 08:15 authored by Timothy J. Johnson, Bonnie P. Youmans, Sally Noll, Carol Cardona, Nicholas Evans, Peter Kernezos, John Ngunjiri, Michael Abundo, Chang-Won Lee

Defining the baseline bacterial microbiome is critical towards understanding its relationship with health and disease. In broiler chickens, numerous studies have aimed at defining the core microbiome, yet the core and its possible relationships with health and disease have been difficult to define due to lack of study power. Here, the most comprehensive microbiome-based effort to date in commercial broilers was undertaken. The primary goals of this study included understanding what constitutes core 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 549 flocks within that system, the baseline bacterial microbiome was defined. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiome, irrespective of flock. The tracheal bacterial microbiome of broilers was comprehensively defined for the first time, and interestingly, Lactobacillus was the dominant bacterial taxa 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 representing targets for future probiotic development, many negatively associated potential pathogens were identified in the absence of clinical disease, indicating subclinical dynamics occurring that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives for sustainable poultry production.

This dataset includes forward and reverse raw sequencing reads for 2,309 broiler chicken gut, respiratory, and litter samples surveyed using 16S amplicon profiling.

Resources in this dataset:


National Institute of Food and Agriculture, 2016-67015-24911

National Institute of Food and Agriculture, 2015-68004-23131


Data contact name

Johnson, Timothy J.

Data contact email


University of Minnesota

Temporal Extent Start Date


Temporal Extent End Date



  • Not specified

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

Minnesota; broiler chickens; microbiome; statistics; poultry; United States; data collection; genomics; gastrointestinal system; barns; geography; birds; flocks; Lactobacillus; tissues; probiotics; antibiotics; poultry production; funding; microorganisms; computer software; issues and policy; Biological Sciences; Business and Industry

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Johnson, Timothy J; Youmans, Bonnie P; Noll, Sally; Cardona, Carol; Evans, Nicholas; Kernezos, Peter; Ngunjiri, John; Abundo, Michael; Lee, Chang-Won. (2018). A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance. Retrieved from the Data Repository for the University of Minnesota,