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

There are likely to be both niche and neutral processes involved in microbial community formation in the upper respiratory tract, with speciation and the environment playing key . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/099069 doi: bioRxiv preprint roles (50, 51) . The evidence that niche processes tend towards dominance hierarchies rather than resource segregation suggests that the microbial species compete for similar resources; moreover, communities may have fragile coexistence equilibria, with some dominant competitors functioning as keystone species capable of triggering cascades of extinctions (15) . Further development of ecological methodologies will allow predictions of microbial variation as a result of infection, season and increasing age. Monitoring communities in states of health and disease is important for generating knowledge that will be useful in clinical practice (52) .