Intestinal Enterobacteriaceae and Escherichia coli populations in Japanese adults demonstrated by the reverse transcription-quantitative PCR and the clone library analyses

A primer set specific for Escherichia coli/Shigella 16S rRNA was developed and used for RT-qPCR analysis of fecal samples from 35 healthy adult volunteers in combination with the previously reported primer set specific for Enterobacteriaceae. Enterobacteriaceae and E. coli were present in the 29 out of 35 volunteers tested as intestinal commensals at the average population levels of 107.1 ± 0.9 and 106.8 ± 0.7 cells g− 1 of stools (mean ± standard deviation), respectively. Among the 7 volunteers, the significant deviation between the count of Enterobacteriaceae and that of E. coli was observed, suggesting non-E. coli/Shigella species were predominant in their Enterobacteriaceae populations. The clone library analysis revealed that the non-E. coli/Shigella populations included Citrobacter freundii, Citrobacter koseri, Enterobacter cloacae, Klebsiella oxytoca, Klebsiella pneumoniae/variicola and Morganella morganii. These data suggested that the RT-qPCR method with the primer sets specific to both Enterobacteriaceae and E. coli/Shigella enabled the accurate enumeration of intestinal E. coli populations and the other Enterobacteriaceae species populations.

► A new primer set specific for Escherichia coli/Shigella 16S rRNA was developed.
► We enumerated Enterobacteriaceae and E. coli counts in the intestine by RT-qPCR.
► We revealed diversity of Enterobacteriaceae populations in the intestines.