People with the genetic disease Cystic Fibrosis suffer from decreased lung and pancreatic functions, the former of which is often attributed to the thickened lung mucous that prevents expulsion of inhaled bacteria.  Many research groups are using DNA sequencing methods to characterize the communities of bacteria that live in CF lungs, and a smaller number of research groups have addressed the issue of intestinal bacterial communities that could be affected by the pancreatic deficiencies.  Typically researchers are only looking at lungs or guts, but a recent paper looks at the bacteria in both organs soon after birth of individuals with CF.  (Madan et al.: http://mbio.asm.org/content/3/4/e00251-12).

Although lungs and intestines typically had different genera of bacteria present, there was overlap between them: Streptococcus and Veillonella species in particular were found in both environments.
In addition, genera that were present in the intestines were later found to be present in the lung samples, suggesting either a common source seeding these two organs, or direct transmission from feces to air to lung (it's okay to cringe, but surely this happens all the time).  Also of interest was their finding that breast feeding had an (albeit slight) effect on the bacterial community composition in the lungs, which made me think of the known link between breast feeding and decreased risk of asthma.

The data presented in this paper were indeed interesting, but I would have liked to see healthy controls included.  Would we have seen the same results if looking at a healthy population of infants?  Surely it is much more difficult to recruit these individuals for the research, but given they were only sampling the oropharyngeal tract and feces, it wouldn't have been too invasive.  And although I could complain about the use of these sampling sites to represent the lungs and intestines, I'll hold my breath today. 

The main point here is this: bacterial communities that inhabit the human body are coming from somewhere, and that somewhere is likely to be very similar for the lungs, the skin, the intestines, etc.  What is it about these body sites that selects for the distinct bacterial communities that exist there?  Or is there no selection but merely a "first come, first serve" colonization process?  I am skeptical of the latter, considering the well known associations between particular bacteria and body site.  If we could only figure out how to keep the good guys and tell the bad guys to go away.  The only problem is....sometimes they might be the same guy!