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

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.

Isolation and comparative genomic analysis of reuterin-producingLactobacillus reuterifrom poultry gastrointestinal tract

“…Cluster I, corresponding to the previously defined poultry/human lineage IV, comprised all 25 L. reuteri poultry isolates of this study and all, except one (P43), poultry NCBI isolates. The same cluster also included two humans strains (SD2112 and CF48-3A) and this was also the case in all previous phylogenetic analysis of L. reuteri isolates from different hosts [2,36,38]. The fact that even with a much higher number of poultry isolates the two human isolates, respectively isolated from human breast milk in Peru (SD2112) and from the child faeces in Finland (CF48-3A), still cluster together with 29 poultry isolates, suggests that these strains could be of poultry origin.…”

“…Lactobacillus species commonly found in the caecum and colon. However, to date, only seven poultry L. reuteri strains (P43, An71, An166, 1366, JCM 1081, CSF8 and SKK-OGDONS-01) have been sequenced, and some of them included in previous phylogenetic analysis [2,5,[36][37][38].…”

Oral Delivery of Probiotics Using pH-Sensitive Phthalyl Inulin Tablets

“…In our previous result, we isolated L. reuteri LRT18 (LR) from porcine feces and it showed the highest antimicrobial activities against both pathogenic bacteria K88-positive E. coli and S. enterica subsp [5], although it was very weak against acid stress, especially in the presence of pepsin (Fig. 4).…”

“…L. reuteri LRT18 (LR, KCTC3594) used in this study was isolated from a previous study [5]. All of the materials and chemicals used in this study were purchased from Sigma-Aldrich (USA) unless otherwise stated.…”

“…In our previous study, we isolated L. reuteri LRT18 from porcine feces and selected the highest antimicrobial effect on K88positive Escherichia coli and Salmonella enterica subsp. [5].…”