Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing

  • Hyeri Kim (Department of Animal Resources Science, Dankook University) ;
  • Eun Sol Kim (Department of Animal Resources Science, Dankook University) ;
  • Jin Ho Cho (Department of Animal Science, Chungbuk National University) ;
  • Minho Song (Division of Animal and Dairy Science, Chungnam National University) ;
  • Jae Hyoung Cho (Department of Animal Resources Science, Dankook University) ;
  • Sheena Kim (Department of Animal Resources Science, Dankook University) ;
  • Gi Beom Keum (Department of Animal Resources Science, Dankook University) ;
  • Jinok Kwak (Department of Animal Resources Science, Dankook University) ;
  • Hyunok Doo (Department of Animal Resources Science, Dankook University) ;
  • Sriniwas Pandey (Department of Animal Resources Science, Dankook University) ;
  • Seung-Hwan Park (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Ju Huck Lee (Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Hyunjung Jung (Animal Nutrition & Physiology Division, National Institute of Animal Science, RDA) ;
  • Tai Young Hur (Animal Diseases & Health Division, National Institute of Animal Science, RDA) ;
  • Jae-Kyung Kim (Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute) ;
  • Kwang Kyo Oh (Microbial Safety Division, National Institute of Agricultural Sciences, Rural Development Administration) ;
  • Hyeun Bum Kim (Department of Animal Resources Science, Dankook University) ;
  • Ju-Hoon Lee (Department of Food Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Seoul National University)
  • Received : 2022.09.07
  • Accepted : 2022.12.06
  • Published : 2023.01.28
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Abstract

The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.

Keywords

Acknowledgement

This work was carried out with the support of "Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ0162982022)" Rural Development Administration, Republic of Korea and the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education(2019M3A9F3065227).

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