Schwab, C. | Search bioRxiv

bioRxiv2019

Microbiability of meat quality and carcass composition traits in swine

The impact of gut microbiome composition was investigated at different stages of production (Wean, Mid-test, and Off-test) on meat quality and carcass composition traits of 1,123 three-way-crossbred pigs. Data were analyzed using linear mixed models which included the fixed effects of dam line, contemporary group and gender as well as the random effects of pen, animal and microbiome information at different stages. The contribution of the microbiome to all traits was prominent although it varied over time, increasing from weaning to Off-test for most traits. Microbiability estimates of carcass composition traits were greater compared to meat quality traits. Adding microbiome information did not affect the estimates of genomic heritability of meat quality traits but affected the estimates of carcass composition traits. High microbial correlations were found among different traits, particularly with traits related to fat deposition with decrease in genomic correlation up to 20% for loin weight and belly weight. Decrease in genomic heritabilities and genomic correlations with the inclusion of microbiome information suggested that genomic correlation was partially contributed by genetic similarity of microbiome composition.

genomics↗

bioRxiv2019

Isolation and comparative genomic analysis of reuterin-producing Lactobacillus reuteri from poultry gastrointestinal tract

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 poultry, and replace added antimicrobials. To date, only seven L. reuteri strains isolated from poultry have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate L. reuteri strains from poultry GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy reuterin-producing strains were isolated from poultry crop, faeces and caeca and twenty-five selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated in 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 poultry isolates within the poultry/human lineage VI. Strains harbouring 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 poultry strains were sensitive to cefotaxime (MIC between 0.016 and 1 g/mL) and penicillin (MIC between 0.02 and 4 g/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 poultry 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 poultry strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of poultry.

genomics↗