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

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Collection period

2016-03-01
2016-11-30

Date completed

2017

Date updated

Time period coverage

Geographic coverage

Minnesota, USA

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Journal Title

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Title

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

Published Date

2018-01-16

Group

Author Contact

Johnson, Timothy J
tjj@umn.edu

Type

Dataset
Genomics Data

Abstract

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.

Description

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

Referenced by

Johnson, T.J., Youmans, B.P., Noll, S., Cardona, C., Evans, N.P. Karnezos, T.P... & Lee, C-W. (2018). A consistent and predictable commercial broiler chicken bacterial microbiota in antibiotice-free production displays strong correlations with performance. Applied and Environmental Microbiology, pii: AEM.00362-18.
https://doi.org/10.1128/AEM.00362-18

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Funding information

USDA-AFRI Grant nos. 2016-67015-24911 and 2015-68004-23131

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Suggested 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 (DRUM), https://doi.org/10.13020/D63T10.
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File View/OpenDescriptionSize
chunk1.tarChunk1 of raw sequencing reads (please see sample key)1.86 GB
chunk2.tarChunk2 of raw sequencing reads (please see sample key)1.86 GB
chunk3.tarChunk3 of raw sequencing reads (please see sample key)1.86 GB
chunk4.tarChunk4 of raw sequencing reads (please see sample key)1.85 GB
chunk5.tarChunk5 of raw sequencing reads (please see sample key)1.86 GB
chunk6.tarChunk6 of raw sequencing reads (please see sample key)1.86 GB
chunk7.tarChunk7 of raw sequencing reads (please see sample key)1.86 GB
chunk8.tarChunk8 of raw sequencing reads (please see sample key)1.85 GB
chunk9.tarChunk9 of raw sequencing reads (please see sample key)1.86 GB
chunk10.tarChunk10 of raw sequencing reads (please see sample key)1.86 GB
chunk11.tarChunk11 of raw sequencing reads (please see sample key)1.86 GB
chunk12.tarChunk12 of raw sequencing reads (please see sample key)1.86 GB
chunk13.tarChunk13 of raw sequencing reads (please see sample key)1.46 GB
Sample_metasheet_for_DRUM.xlsxDescription of files with metadata104.97 KB
chunk14.tarNegative controls of the study56.37 MB
Readme.txtReadme9.23 KB

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