Pollution of the environment by human and animal faecal pollution affects the safety of
shellfish, drinking
water and recreational beaches. To pinpoint the origin of contaminations, it is essential to define the differences between human microbiota and that of farm animals. A strategy based on real-time quantitative
PCR (qPCR)
assays was therefore developed and applied to compare the composition of
intestinal microbiota of these two groups. Primers were designed to quantify the
16S rRNA gene from dominant and subdominant
bacterial groups. TaqMan((R)) probes were defined for the qPCR technique used for dominant microbiota. Human faecal microbiota was compared with that of farm animals using faecal samples collected from rabbits,
goats, horses, pigs, sheep and cows. Three dominant
bacterial groups (
Bacteroides/Prevotella,
Clostridium coccoides and
Bifidobacterium) of the human microbiota showed differential population levels in animal species. The
Clostridium leptum group showed the lowest differences among human and farm animal species. Human subdominant
bacterial groups were highly variable in animal species.
Partial least squares regression indicated that the human microbiota could be distinguished from all farm animals studied. This culture-independent comparative assessment of the faecal microbiota between humans and farm animals will prove useful in identifying biomarkers of human and animal faecal contaminations that can be applied to
microbial source tracking methods.
