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About the Authors:
Richard J. Ellis
* E-mail: [email protected]
Affiliation: Specialist Scientific Support Department, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
Kenneth D. Bruce
Affiliation: Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
Claire Jenkins
Affiliation: Laboratory of Gastrointestinal Pathogens, Health Protection Agency, London, United Kingdom
J. Russell Stothard
Affiliation: Disease Control Strategy Group, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
Lilly Ajarova
Affiliation: Chimpanzee Sanctuary and Wildlife Conservation Trust (CSWCT), Entebbe, Uganda
Lawrence Mugisha
Affiliations College of Veterinary Medicine (Animal Resources and Biosecurity), Makerere University, Kampala, Uganda, Conservation & Ecosystem Health Alliance (CEHA), Kampala, Uganda
Mark E. Viney
Affiliation: School of Biological Sciences, University of Bristol, Bristol, United Kingdom
Introduction
It has become increasingly clear that the gut microbiota plays a key role in the maintenance of normal gut function, the digestion of food and much wider aspects of human health, though much remains to be discovered [1]–[6]. Analysis of the gut microbiota is rapidly increasing through the use of next generation sequencing. The gut microbiota has, however, long been recognized to contain a complex mix of mostly (in terms of biomass) bacterial taxa, the resolution of which is now rapidly increasing. Individuals begin to be colonised with microbes from birth [7], with maternal and childhood events considered to have life-long effects [8], [9]. During the first months of life the composition of individual microbiotas vary, but this stabilizes to a mix of major bacterial phyla (Firmicutes, Bacteroidetes etc. [10], [11]) as the child is weaned and by the age of three, which then persists throughout life [12]–[15]. However, the gut microbiota does undergo further maturation (in terms of the constituent species within each of the major phyla) in adulthood and alters again in old age [16]. Notwithstanding this general pattern, there is a large degree of inter-individual variation in microbiotas, such that individuals have their own “fingerprint” of microbial taxa [10]. There is both an environmental (e.g. microbial exposure, diet, infection effects [12], [13], [17]–[20]) and a genetic component [1], [14], [21], [22] controlling the composition of the microbiota. Seemingly subtle fluctuations in the intestinal ecosystem may be important in explaining differential susceptibility to pathological episodes [19]. Recent studies have examined the community composition of the gut...