Cystic fibrosis (CF) is most often thought of as a disease of the lung, and most microbiome studies of CF patients begin and end with the respiratory tract. But CF also causes profound complications in the gut and pancreas, problems that can seriously impact growth and nutrition. A study in mBio this week treats the lungs and guts of infants with CF as co-evolving ecosystems, comparing and contrasting the ways in which the bacterial communities in these niches evolve and interact.
Madan et al. studied respiratory and intestinal samples taken from infants with CF every three months from birth to 21 months, using 454 pyrosequencing of 16S genes to tease apart the identities of the bacteria living in those organs. They showed that most of the bacteria in both tracts fell into 8 distinct genera, and although the lung community was distinct from the gut community, there was some overlap between the two systems. This core microbiota is dominated by species of Veillonella and Streptococcus.
They also examined how these microbiomes changed with the introduction of breast milk, formula, and solid foods to the babies' diets. They were able to link changes in diet to changes in the lungs - something that hasn't really been looked at before in infants with CF - and found that what goes on in the gut determines the microbial development in the lungs. Changes in diet resulted in distinct changes in the flora of the lungs - a finding that suggests a tight link between nutrition and the development of respiratory tract.
The authors also note that clusters of bacteria, including potential pathogens like Enterococcus, were present early in life in the gut and then detected later in the respiratory tract, which not only highlights the interrelatedness of the two organ systems, say the authors - it's also important from a clinical standpoint, as it suggests interventions with oral probiotic therapy might eventually be used to inoculate the lungs with desirable strains or eradicate undesirables.