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Lactobacillus reuteri  is a natural inhabitant of selected animal and human gastrointestinal tract (GIT). Certain strains have the capacity to transform glycerol to 3-hydroxypropionaldehyde (3-HPA), further excreted to form reuterin, a potent antimicrobial system. Reuterin-producing strains may be applied as a natural antimicrobial in feed to prevent pathogen colonization of animals, such as in chicken, and replace added antimicrobials. To date, only seven  L. reuteri  strains isolated from chicken have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate  L. reuteri  strains from chicken GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy strains were isolated from faces, crops and ceca of six chicken from poultry farms and samples from slaughterhouse. Twenty-five strains were selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated into a phylogenetic tree of 40 strains from different hosts. Phylogenetic analysis based on gene content as well as on core genomes showed grouping of the selected 25  L. reuteri  chicken isolates within the poultry/human lineage VI. Strains harboring  pdu-cob-cbi-hem  genes (23/25) produced between 156 mM ± 11 and 330 mM ± 14 3-HPA, from 600 mM of glycerol, in the conditions of the test. All 25 chicken strains were sensitive to cefotaxime (MIC between 0.016 and 1 μg/mL) and penicillin (MIC between 0.02 and 4 μg/mL). Akin to the reference strains DSM20016 and SD2112, the novel isolates were resistant to penicillin, possibly associated with identified point mutations in  ponA ,  pbpX ,  pbpF  and  pbpB . All strains resistant to erythromycin (4/27) carried the  ermB  gene, and it was only present in chicken strains. All strains resistant to tetracycline (5/27) harbored  tetW  gene. This study confirms the evolutionary history of poultry/human lineage VI and identifies  pdu-cob-cbi-hem  as a frequent trait but not always present in this lineage.  L. reuteri  chicken strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of chicken.

Isolation and Comparative Genomic Analysis of Reuterin-Producing Lactobacillus reuteri From the Chicken Gastrointestinal Tract