I'm not sure if it has differentiation, but lifestyle factors could have an impact. If, for example, in more developed countries there's a great emphasis on (especially) childhood cleanliness, it may be affecting the development of "good" bacteria:
http://www.bbc.com/future/story/20151118-can-you-be-too-clea...
Another lifestyle example could be the prevalence of C-section births in more developed countries: