Identification of bacterial isolates from commercial poultry feed via 16S rDNA

Abstract

The study’s objective was to identify typical aerobic isolates from commercial, corn-soybean meal poultry diets utilizing 16S rDNA, assign them their corresponding taxonomy, and compare the data with the previously published WGS analysis of these same isolates. Ten grams of a commercial corn-soybean meal poultry diet was homogenized in 100 mL of tryptic soy broth for 2 min, serially diluted, plated onto tryptic soy agar (TSA), and incubated aerobically for 24 h at 37 °C. Subsequently, 20 unique colonies were streaked for isolation on TSA and incubated aerobically for 24 h at 37 °C. This process was repeated three consecutive times for purification of isolates until only 11 morphologically distinct colonies were obtained. DNA was extracted using Qiagen’s DNeasey® Blood and Tissue Kit. The 16S rRNA V4 region was targeted using an Illumina MiSeq and analyzed via QIIME2-2020.2. Alpha diversity and Beta diversity metrics were generated, and taxa were aligned using Silva in Qiime2-2020.2. Twenty-five distinct genera were identified within the 11 different colonies. Because 16S rDNA identification can provide an understanding of pathogen associations and microbial niches within an ecosystem, the information may present a potential method to establish and characterize the hygienic indicator microorganisms associated with poultry feed.

KEYWORD:

• S: Poultry feed
• poultry diet
• 16S rDNA sequencing
• aerobic isolates
• hygienic indicator microorganisms

Acknowledgements

The author DKD would like to acknowledge the Graduate College at the University of Arkansas for its continued support through the Distinguished Academy Fellowship and the continued support from the Cell and Molecular Biology Program and Department of Food Science at the University of Arkansas.

Declarations

Ethics approval

This study does not contain any research with human participants or animals performed by any of the authors.

Consent for publication

I, Steven C. Ricke, hereby declare that I participated in the study and in the development of the manuscript titled “Identification of Bacterial Isolates from Commercial Poultry Feed via 16S rDNA”. I have read the final version and give my consent for the article to be published in Journal of Environmental Science and Health, Part B.

Disclosure statement

The authors declare that they have no competing interests.

Availability of data and materials

All data are fully available.

Author’s contributions

The author SCR conceived of the presented idea, developed the theory, supervised the project, and helped with writing the manuscript. ACM carried out the experiment. EGO wrote the manuscript. DKD verified the analytical methods, performed the computations, and helped with writing the manuscript.

Additional information

Funding

This project was not funded by any external grants and was solely supported by Dr. Steven Ricke’s research funds at the Center for Food Safety.