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Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity

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Abstract

After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.

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Acknowledgements

This work was supported by the Strategic Initiative for Microbiomes in Agriculture and Food; Ministry of Agriculture, Food, and Rural Affairs, Republic of Korea (No. 914005-04); and 2016 Research Grant from Kangwon National University (No. 520160476). Jun-Yeong Lee, Geon Goo Han, and Gwi-Deuk Jin were supported by Brain Korea 21 Plus program.

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  1. Eun Bae Kim and Yun-Jaie Choi have equal contributions.

Authors and Affiliations

  1. Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea

    Jun-Yeong Lee, Geon Goo Han, Jaeyun Choi & Yun-Jaie Choi

  2. Department of Animal Life Science, Kangwon National University, Chuncheon, Republic of Korea

    Gwi-Deuk Jin, Byung Jo Chae & Eun Bae Kim

  3. Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Republic of Korea

    Sang-Kee Kang

  4. Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea

    Yun-Jaie Choi

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  1. Jun-Yeong Lee
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Correspondence to Eun Bae Kim or Yun-Jaie Choi.

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Porcine feces were collected from several swine farms in accordance with institutional policies and regulations for the care and use of laboratory animals (Laboratory Animal Center, Seoul National University, Korea). All of the experimental protocols were reviewed and approved by the Institutional Animal Care and Use Committee at Seoul National University (SNU-140522-3) and Kangwon National University (KW-140509-1).

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Lee, JY., Han, G.G., Choi, J. et al. Pan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity. Microb Ecol 74, 709–721 (2017). https://doi.org/10.1007/s00248-017-0977-z

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