Repetitive sequence-based PCR (rep-PCR) is a distinctive typing approach that is used to
differentiate between bacterial strains. This method is also useful for studying bacterial diversity
from different sources. In this study, four rep-PCR which are enterobacterial repetitive intergenic
consensus PCR (ERIC-PCR), BOX-PCR, repetitive extragenic palindromic PCR (REP-PCR)
and polytrinucleotide (GTG)5-PCR were evaluated for differentiation of eighteen Escherichia
coli isolates to correct source based on part of intestine and age. These isolates were recovered
earlier from ileal and caecal mucosal contents of chickens at different age. The purpose of this
study was to investigate the efficacy of four rep-PCR methods and composite of rep-PCR
patterns to differentiate E. coli isolates to original sources of part of intestines and age based on
the D index (discriminatory power determined based on Simpson’s index of diversity calculated
at similarity coefficient of 90%). The (GTG)5-PCR had the highest D index (0.9804) for part of
intestine and age factors. The similar D index was observed in the composite of rep-PCR
patterns. The lowest D index was observed in ERIC- and BOX-PCR at 0.9020 and 0.8039 for
part of intestine and age factors, respectively. (GTG)5-PCR was also the most discriminative rep-
PCR observed due to its ability to cluster 14I 3E and 14I 2X isolates, and 14C 1E and 14C 3E
isolates correctly in part of intestine and age factors. It was concluded that (GTG)5-PCR is a
promising tool for discriminating E. coli isolates extracted from chicken intestines.
Objective: While some oral carcinomas appear to arise de novo, others develop within long-standing conditions of the oral cavity that have malignant potential, now known as oral potentially malignant disorders (OPMDs). The oral bacteriome associated with OPMD has been studied to a lesser extent than that associated with oral cancer. To characterize the association in detail we compared the bacteriome in whole mouth fluid (WMF) in patients with oral leukoplakia, oral cancer and healthy controls. Methods: WMF bacteriome from 20 leukoplakia patients, 31 patients with oral cancer and 23 healthy controls were profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Sparse Partial Least Squares Regression Discriminant Analysis model was used to identify bacterial taxa that best discriminate the studied groups. Results: We found considerable overlap between the WMF bacteriome of leukoplakia and oral cancer while a clearer separation between healthy controls and the former two disorders was observed. Specifically, the separation was attributed to 14 taxa belonging to the genera Megaspheara, unclassified enterobacteria, Prevotella, Porphyromonas, Rothia and Salmonella, Streptococcus, and Fusobacterium. The most discriminative bacterial genera between leukoplakia and oral cancer were Megasphaera, unclassified Enterobacteriae, Salmonella and Prevotella.Conclusion: Oral bacteria may play a role in the early stages of oral carcinogenesis as a dysbiotic bacteriome is associated with oral leukoplakia and this resembles that of oral cancer more than healthy controls. Our findings may have implications for developing oral cancer prevention strategies targeting early microbial drivers of oral carcinogenesis.