The evolving focus of cystic fibrosis microbiome research

For more than two decades, culture-independent microbiome analysis has been employed in efforts to improve clinical outcomes for those with CF and to gain a better fundamental understanding of polymicrobial infections. The use of these techniques began during the 1990s in response, at least in part, to growing concerns over the emergence of new infectious syndromes. Pathogens such as Burkholderia cepacia and rapidly growing nontuberculous mycobacteria were increasingly associated with sudden and profound deterioration in lung function in persons with CF (PwCF) and the potential for other “novel” species to contribute to clinical outcomes was a growing worry. In particular, there was hope that understanding the impact of “non-traditional” taxa might help to explain the unpredictable nature of pulmonary exacerbations.

The considerable body of respiratory microbiome research that followed resulted in the CF lung becoming one of a small number of clinical contexts through which the ecology of polymicrobial infections was explored...