In recent articles (Rogers et al., 2009, Rogers et al., 2010), we discussed a fundamental shift in the way in which polymicrobial infections can be viewed. In these articles, we used chronic bacterial infections of the lower airways, and specifically those that occur in cystic fibrosis (CF) patients, as a model system. These infections are of course critical in clinical terms for these patients; respiratory failure due to a combination of these chronic infections with the host immune response that they elicit remains the leading cause of mortality in CF. Given the importance of maintaining lung health in these patients, the CF airways are the focus of a wide range of scientific and clinical studies. In particular, research momentum has built in relation to identifying the microbes present in the CF lung. Already, many important insights have been gained through the application of increasingly sophisticated culture-independent analytical methodologies to identify all microbial nucleic acids (Bittar et al., 2008, Ecker et al., 2008, Rogers et al., 2004, Sibley et al., 2008b) and those from viable or metabolically active microbes (Rogers et al., 2005, Rogers et al., 2008) in the CF lung. In doing so, the data generated have revealed microbial assemblages of far greater diversity and in turn complexity than has previously been recognised in this context. These studies, which have served to highlight the inadequacy of traditional culture-based diagnostic microbiology to fully characterise such infections (Rogers et al., 2009), have also led to a significant shift in our view of what the word "infection" represents for these and other chronic diseases, with potentially important implications for their optimal treatment. In this article we contrast the information we and others have accrued from chronic lung infections with data generated from studies examining the microbial communities present in the gut. In doing so we highlight parallels between these two contexts and discuss how these commonalities can inform clinical thinking.