Purpose: This study is to identify host-specific genetic markers within 16S rDNAs of Faecalibacterium-like bacteria and to evaluate their uses in tracking the source of fecal contamination in food.
Methods: To identify host-specific genetic markers, a collection of over 20,000 16S rDNA sequences of Faecalibacterium-like bacteria, reportedly associated with different host species, was obtained from the Ribosomal Database Project and subject to the comparative analysis via bioinformatics methods, including phylogenic assay and multiple alignments. Based on the newly identified and potentially host-specific genetic markers, polymerase reaction assays (PCR) were developed for the evaluation of each genetic marker’s host specificity, using the pooled fecal samples from different animal hosts (dairy cattle, beef cattle, chicken, dog, horse, human, goose, pig, sheep, and turkey) .
Results: Five intervening sequences (IVSs) within the variable region 1 of 16S rDNAs, associated with different Faecalibacterium-like bacteria, have been identified by bioinformatics analysis and appear to be host specific as demonstrated by the PCR assays. The IVS-1, -2, and -3 were found to present only in poultry (chicken and turkey) feces, while the IVS-4 and -5 only in cattle and pig feces. In addition, two genetic markers, specific for horse and dog feces respectively, were accidently identified by this study.
Significance : This is the first study on the host specificity of commensal bacteria’s ribosomal IVSs, which may prove to be useful genetic markers for identification of the source of fecal contamination in food.