Purpose: The aim of this study was to determine bacterial compositional shift occurring over the incubation time period using microbiome analysis from chicken breast samples inoculated with mixed cultures (S. Typhimurium with other bacteria from chicken rinsates) at various incubation times.
Methods: Chicken breast samples inoculated with S. Typhimurium in mixed culture were incubated at 0, 4 (reflective of the incubation times needed for MPN-qPCR-SIT), and 24 h (the incubation times needed for conventional plating, conventional MPN, and qPCR) and incubated samples were subjected to microbiome analysis.
Results: The R value from PCoA plot was 0.56 and it implied that there was significant dissimilarity among different incubation time groups in terms of phylogenetic distance. Bacterial composition of samples shifted over the incubation time period. At a phylum level, the abundance of Firmicutes and Actinobacteria significantly increased during incubation while the relative abundance of Proteobacteria decreased over the incubation time period. At a genus level, the most significant shift occurred with Enterobacteriaceae and their levels of abundance were increased from 17.99% at 0 h to 53.50 and 90.69% at 4 and 24 h incubation samples, respectively. Salmonella abundance was only 0.03% at 0 h sample but increased with the corresponding incubation times that included 4 h (0.08%) and 24 h (0.18%). The sequence identified Enterobacteriaceae appears to be reflecting the increases in artificially inoculated Salmonella.
Significance: These results indicated that enrichment procedure for a shortened time used in the MPN-qPCR-SIT can sufficiently support growth of target bacteria to ensure reliable detection and quantification. Also, Enterobacteriaceae could be used as effective indicator organisms for potential presence of Salmonella in microbiome analyses.