Functional characterization of a microbial consortium for the competitive exclusion of Salmonella in chickens

Authors: HARRIS, DYLAN - Oak Ridge Institute For Science And Education (ORISE); WICKWARE, CARMEN - Oak Ridge Institute For Science And Education (ORISE); Anderson, Christopher; Looft, Torey

Submitted to: Conference Research Workers Disease Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 12/6/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: OBJECTIVES: Salmonella is one of the leading causes of intestinal disease globally with poultry being a major source for human infection. While undefined communities of bacteria, particularly from the cecal contents of healthy birds, have been shown to limit the ability of Salmonella to colonize young birds, a fully defined consortium has potential, as it would improve efficacy and reproducibility. This project sought to construct a defined consortium of commensal bacteria derived from the chicken gut microbiome to reduce and prevent the colonization of Salmonella within young birds. An animal study was performed using this defined consortium of 15 commensal bacteria, and when compared to a negative control, showed inhibition of Salmonella. However, the consortium exhibited reduced inhibition against Salmonella when compared to the administration of an undefined cecal content control. To examine the functional capacity of the bacteria within the consortium, predicted functions of individual consortium members were compared against Salmonella Heidelberg (SH2813) to evaluate competition potential and examine any redundancy or gaps in function to refine and increase the competitive nature of the consortium. METHODS: To examine potential functions within the consortium, individual members of the consortium were sequenced via Oxford Nanopore with basecalling performed via Guppy’s Super accurate model. Each member’s genome was assembled using Flye, Minasm+Minipolish, and Raven. Trycycler was used to obtain a consensus whole-genome sequence for each consortium member through the reconciliation and alignment of the sequences generated by the three assemblers. Genome annotation was performed with Distilled and Refined Annotation of Metabolism (DRAM) and Anvi’o was used to visualize the functional characteristics of assembled genomes under a pangenomic comparison. Potential functions were compared to the available genome for SH2813 along with other Salmonella spp. RESULTS: Pangenomic comparisons between consortium members and Salmonella spp. showed some overlap in terms of gene clusters, but most organisms appeared unique in terms of gene content. Functional genomic comparisons of the consortium members to Salmonella spp. revealed overlap in predicted function amongst many of the consortium members in terms of carbohydrate metabolism with some members contributing more functionality than others. Gaps in metabolic pathways that Salmonella may be utilizing were also revealed such as TMAO reductase and thiosulfate reduction. CONCLUSIONS: While administration of undefined cecal contents had a much stronger effect on the overall inhibition of Salmonella colonization, the consortium still managed to inhibit Salmonella over time. The delay in Salmonella inhibition in animals colonized by the consortium suggests some niches within the community are not being occupied by consortium members. Functional genomic comparison shows that there are gaps within the metabolic network that could be filled by adding strains to the consortium to improve inhibition of Salmonella such as non-pathogenic TMAO reductase and thiosulfate reductase producers. Further characterization of the functional capacity of our consortium members will inform key additions of new consortium members to compete with Salmonella and reduce its colonization in poultry.