Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR

Type Article
Date 2009-06
Language English
Author(s) Furet Jean-Pierre1, Firmesse Olivier1, Gourmelon MicheleORCID2, Bridonneau Chantal1, Tap Julien1, Mondot Stanislas1, Dore Joel1, Corthier Gerard1
Affiliation(s) 1 : INRA, Unite Ecol & Physiol Syst Digestif, U910, F-78350 Jouy En Josas, France.
2 : IFREMER, Microbiol Lab, EMP, MIC, Plouzane, France.
Source Fems Microbiology Ecology (0168-6496) (Wiley-blackwell Publishing, Inc), 2009-06 , Vol. 68 , N. 3 , P. 351-362
DOI 10.1111/j.1574-6941.2009.00671.x
WOS© Times Cited 262
Keyword(s) quantitative PCR, faecal microbiota, human, farm animals
Abstract 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.
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