Fluorescent hybridisation combined with flow cytometry and hybridisation of total RNA to analyse the composition of microbial communities in human faeces using 16S rRNA probes.
To determine the structure of human faecal microbiota, faecal samples from 23 healthy individuals were analysed with a similar set of probes targeting six phylogenetic groups using rRNA dot-blot hybridisation and whole cell fluorescent in situ hybridisation (FISH) combined with flow cytometry. When microbiota compositions derived by each method were compared, the results were not statistically different for Clostridium coccoides, Fusobacterium prausnitzii, Bifidobacterium spp. and Enterobacteria. Conversely, the proportions were significantly different for Bacteroides and Atopobium (P<0.05). The metabolic state of these bacteria within the colon could explain the discrepancy observed between the rRNA level and the actual cell proportion. However, both approaches supplied consistent and complementary information on the structure of the faecal microbiota. FISH combined with flow cytometry appears best suited to future high throughput analysis.
Rigottier-Gois
Lionel
L
Institut National de la Recherche Agronomique, Unité d'Ecologie et de Physiologie du Système Digestif, bât. 405, Domaine de Vilvert, 78352 Jouy en Josas Cedex, France. gois@diamant.jouy.inra.fr
Bourhis
Anne-Gaëlle
AG
Gramet
Geneviève
G
Rochet
Violaine
V
Doré
Joël
J