Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota

A cultivation-independent approach, polymerase chain reaction-denaturing gr adient gel electrophoresis (PCR-DGGE), was used to characterize changes in fecal bacterial populations resulting from consumption of a low residue die t or oral administration of a broad-spectrum antibiotic. C57BL/6NHsd mice w ere weaned to either a standard nonpurified diet (LC-diet) or a low residue diet (LR-diet) and at 17 wk of age were randomly assigned to receive drink ing water with or without 25 ppm cefoxitin for 14 d. On d 1, 2, 7 and 14, m icrobial DNA was extracted from feces, and the V3 region of the 16S rDNA ge ne was amplified by PCR and analyzed by DGGE. The diversity of fecal microb ial populations, assessed using Shannon's index (H'), which incorporates sp ecies richness (number of species, or in this case, PCR-DGGE bands) and eve nness (the relative distribution of species), was not affected by cefoxitin . However, use of Sorenson's pairwise similarity coefficient (C-s), an inde x that measures the species in common between different habitats, indicated that the species composition of fecal bacterial communities was altered by cefoxitin in mice fed either diet. Dietary effects on fecal microbial comm unities were more pronounced, with greater H' values (P < 0.05) in mice fed the LR-diet (1.9 +/- 0.1) compared with the LC-diet (1.6 +/- 0.1). The C-s values were also greater (P < 0.05) in fecal bacterial populations from mi ce fed the LR-diet (C-s = 69.8 +/- 2.0%) compared with mice fed the LC-diet (C-s = 50.1 +/- 3.8%), indicating greater homogeneity of fecal bacterial c ommunities in mice fed the LR-diet. These results demonstrate the utility o f cultivation-independent PCR-DGGE analysis combined with measurements of e cological diversity for monitoring diet- and antibiotic-induced alterations of the complex intestinal microbial ecosystem.