The mammalian gut microbiota is considered to be determined mostly by diet, while the effect of genotype is still controversial. Here, we examined the effect of genotype on the gut microbiota in normal populations, exhibiting only natural polymorphisms, and evaluated this effect in comparison to the effect of sex. DNA fingerprinting approaches were used to profile the gut microbiota of eight different recombinant inbred mouse lines of the collaborative cross consortium, whose level of genetic diversity mimics that of a natural human population. Analyses based on automated ribosomal internal transcribed spacer analysis demonstrated significant higher similarity of the gut microbiota composition within mouse lines than between them or within same-gender groups. Thus, genetic background significantly impacts the microbiota composition and is a stronger determinant than gender. These findings imply that genetic polymorphisms help shape the intestinal microbiota of mammals and consequently could affect host susceptibility to diseases.

Gill bacterial communities of Chama pacifica, an Indo-Pacific invasive oyster to the eastern Mediterranean Sea, were compared with those of Chama savignyi, its northern Red Sea congeneric species. Summer and winter bacterial populations were characterized and compared using 16S rDNA clone libraries, and seasonal population dynamics were monitored by automated ribosomal intergenic spacer analysis (ARISA). Clone libraries revealed a specific clade of bacteria, closely related to marine endosymbionts from the Indo-Pacific, found in both ecosystems, of which one taxon was conserved in oysters from both sites. This taxon was dominant in summer libraries and was weakly present in winter ones, where other members of this group were dominant. ARISA results revealed significant seasonal variation in bacterial populations of Mediterranean Sea oysters, as opposed to Red Sea ones that were stable throughout the year. We suggest that this conserved association between bacteria and oyster reflects either a symbiosis between the oyster host and some of its bacteria, a co-invasion of both parties, or both.

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Ileal and colon-involving CD sustain distinct microbiotas, suggesting that different mechanisms underlie the two major manifestations of CD. The potential contribution of Fusobacterium to inflammation in ileal CD should be further investigated.