Epidemiological and ecological modelling reveal diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study

Abigail L. Coughtrie; Denise E. Morris; Rebecca Anderson; Nelupha Begum; David W. Cleary; Saul N. Faust; Johanna M. Jefferies; Alex R. Kraaijeveld; Michael V. Moore; Mark A. Mullee; Paul J. Roderick; Andrew Tuck; Robert N. Whittaker; Ho Ming Yuen; C. Patrick Doncaster; Stuart C. Clarke

Inferences from this study should be understood in the context of a number of methodological constraints. The characteristics of the 21% (n = 2103) of responders may differ from those of non-responders. The study focused on a limited number of species, and did not account for species such as Group A Streptococci which may play an important role within this sample site as well as other non-culturable species. Furthermore, the swab samples used were not optimised for the detection of viral species. The questionnaire used for the study was designed for simplicity and ease of completion. This meant that information was not collected on a number of important factors, including smoking status, siblings, and attendance at nursery or day-care facilities. Samples assessed by real-time PCR were limited by the number of species that were targeted as well as the non-random nature of their selection. The ecological models ignore acquired or specific host immunity, which can influence the ecology of the respiratory tract (53) . The combined analysis of bacterial and viral species, and the combined analysis of all RTI, may also be simplistic. Neutral theory assumes no variation in the total number of species within a community whilst niche theory ignores dispersal (54, 55) . The quantification of nestedness provides only a single measure of matrix temperature per classification of samples, ruling out significance testing.