Essential oils have different effects on human pathogenic and commensal bacteria in mixed faecal fermentations compared to pure cultures

A static batch culture system inoculated with human faeces was used to determine the influence of essential oil compounds (EOC) on the mixed faecal microbiota. Bacteria were quantified using qPCR of 16S rRNA genes. Incubation for 24 h of diluted faeces from 6 individuals caused enrichment of Bifidobacterium spp., but proportions of other major groups were unaffected. Thymol and geraniol at 500 ppm suppressed total bacteria, resulting in minimal fermentation. Thymol at 100 ppm had no effect, nor did 100 or 500 ppm eugenol or nerolidol except for a slight suppression of Eubacterium hallii. Methylisoeugenol at 100 or 500 ppm suppressed the growth of total bacteria, accompanied by a large fall in the molar proportion of propionate formed. The relative abundance of Faecalibacterium prausnitzii was unaffected except at 500 ppm thymol. The ability of the EOC to control numbers of the pathogen, Clostridium difficile, was investigated in a separate experiment, in which the faecal suspensions were amended by the addition of pure culture of C. difficile. Numbers of C. difficile were suppressed by thymol and methylisoeugenol at 500 ppm and to a lesser extent at 100 ppm. Eugenol and geraniol gave rather similar suppression of C. difficile numbers at both 100 and 500 ppm. Nerolidol had no significant effect. It was concluded from these and previous pure-culture experiments that thymol and geraniol at around 100 ppm could be effective in suppressing pathogens in the small intestine, with no concern for beneficial commensal colonic bacteria in the distal gut.