Human beings contain complex societies of indigenous microbes, yet little i
s known about how resident bacteria shape our physiology. We colonized germ
free mice with Bacteroides thetaiotaomicron, a prominent component of the n
ormal mouse and human intestinal microflora. Global intestinal transcriptio
nal responses to colonization were observed with DNA microarrays, and the c
ellular origins of selected responses were established by laser-capture mic
rodissection. The results reveal that this commensal bacterium modulates ex
pression of genes involved in several important intestinal functions, inclu
ding nutrient absorption, mucosal barrier fortification, xenobiotic metabol
ism, angiogenesis, and postnatal intestinal maturation. These findings prov
ide perspectives about the essential nature of the interactions between res
ident microorganisms and their hosts.