Research Article

A Strong Impact of Genetic Background on Gut Microflora in Mice

Table 2

Identification of ARISA peak DNA.

Base pairTop BLAST hits of ARISA peak DNA1PhylumMatched from bacterial culture2

2931Lactobacillus animalis/murinusFirmicutesLactobacillus sp. 3
300FirmicutesEnterococcus gallinarum
3171Lactobacillus animalis/murinusFirmicutes
350FirmicutesEnterococcus faecalis
380FirmicutesStaphylococcus hemolyt./saprophy.
385–3901,3Lactobacillus sp.FirmicutesLactobacillus sp.3
Uncultured bacteria CD4Bacteroides sp.
400FirmicutesStaphylococcus simulins
4211Bacteroides sp.Bacteroidetes
Uncultured bacteria CD4Bacteroides sp.
4421Escherichia coli, Shigella, Salmonellaγ-ProteobacteriE. coli3
480FirmicutesLactobacillus sp.3
5171E. coli, Shigella, Salmonellaγ-ProteobacteriE. coli3
Uncultured bacteria CD4Bacteroides sp.
5861Dysgonomonas wimpennyiBacteroidetes
7101E. coli APEC, Shigella, Salmonellaγ-Proteobacteria
7921Helicobacter ganmaniε-Proteobacteria
800ActinobacteriaBifidobacterium sp.

1Eight prominent ARISA peak DNAs plus the 710 bp DNAs were cloned into plasmid and sequenced. The identity of the ARISA fragments was determined using a Basic Local Alignment Search Tool (BLAST;   http://www.ncbi.nih.gov/).
2The ARISA peak DNA size was matched to the PCR product of cultured bacterial DNA from mouse cecal content using the same primers.
3Due to the clustering of DNA products in the 385–390 bp and limitation of the cloning/sequencing vector, the specific size of the clones cannot be determined. Because multiple ribosomal intergenic spacers exist in each bacterium, single E. coli colonies produced amplicons at ~442, ~517, and ~710 bp and single colonies of Lactobacillus produced amplicons at ~293, 385–390, and ~480 bp.
4DNA sequences obtained from at least one clone each of ARISA DNA at 385–390, 421, and 517 bp were matched to an uncultured bacteria CD, LMOACA3ZDO3RM1 clone, submitted by Manichanh et al. obtained from the fecal sample of a Crohn’s disease patient [27].