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The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level
  1. Wiley Barton1,2,3,
  2. Nicholas C Penney4,5,
  3. Owen Cronin1,3,
  4. Isabel Garcia-Perez4,
  5. Michael G Molloy1,3,
  6. Elaine Holmes4,
  7. Fergus Shanahan1,3,
  8. Paul D Cotter1,2,
  9. Orla O'Sullivan1,2
  1. 1Alimentary Pharmabiotic Centre Microbiome Institute, University College Cork, National University of Ireland, Cork, Ireland
  2. 2Teagasc Food Research Centre, Cork, Ireland
  3. 3Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
  4. 4Section of Biomolecular Medicine, Division of Computational Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
  5. 5Division of Surgery, Department of Surgery and Cancer, Imperial College London, London, UK
  1. Correspondence to Professor Fergus Shanahan, APC Microbiome Institute, University College Cork, National University of Ireland, Cork, T12 DC4A Ireland; f.shanahan{at}


Objective It is evident that the gut microbiota and factors that influence its composition and activity effect human metabolic, immunological and developmental processes. We previously reported that extreme physical activity with associated dietary adaptations, such as that pursued by professional athletes, is associated with changes in faecal microbial diversity and composition relative to that of individuals with a more sedentary lifestyle. Here we address the impact of these factors on the functionality/metabolic activity of the microbiota which reveals even greater separation between exercise and a more sedentary state.

Design Metabolic phenotyping and functional metagenomic analysis of the gut microbiome of professional international rugby union players (n=40) and controls (n=46) was carried out and results were correlated with lifestyle parameters and clinical measurements (eg, dietary habit and serum creatine kinase, respectively).

Results Athletes had relative increases in pathways (eg, amino acid and antibiotic biosynthesis and carbohydrate metabolism) and faecal metabolites (eg, microbial produced short-chain fatty acids (SCFAs) acetate, propionate and butyrate) associated with enhanced muscle turnover (fitness) and overall health when compared with control groups.

Conclusions Differences in faecal microbiota between athletes and sedentary controls show even greater separation at the metagenomic and metabolomic than at compositional levels and provide added insight into the diet–exercise–gut microbiota paradigm.

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  • Contributors WB prepared DNA samples for metagenomic sequencing. OOS and WB processed and analysed the metagenomic data. EH, IGP and NCP performed metabolomic processing and statistical analysis thereof. FS, PDC, OOS and WB devised experimental design and approach. FS, PDC, OC, OOS, MGM, EH, NCP and WB wrote manuscript. Results discussed by all authors.

  • Funding This research was funded by Science Foundation Ireland in the form of a centre grant (APC Microbiome Institute Grant Number SFI/12/RC/2273). Research in the Cotter laboratory is funded by SFI through the PI award, ‘Obesibiotics’ (11/PI/1137). OOS and WB are funded by Science Foundation Ireland through a Starting Investigator Research Grant award (13/SIRG/2160). Nicholas Penney is funded by the Diabetes Research and Wellness Foundation through the Sutherland-Earl Clinical Research Fellowship 2015. The centre is supported by the NIHR Imperial Biomedical Research Centre based at Imperial College Healthcare National Health Service (NHS) Trust and Imperial College London.

  • Disclaimer The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health.

  • Competing interests FS is a founder shareholder in Atlantia Food Clinical Trials, Tucana Health and Alimentary Health. He is director of the APC Microbiome Institute, a research centre funded in part by Science Foundation Ireland (APC/SFI/12/RC/2273) and which is/has recently been in receipt of research grants from Abbvie, Alimentary Health, Cremo, Danone, Janssen, Friesland Campina, General Mills, Kerry, MeadJohnson, Nutricia, 4D pharma and Second Genome, Sigmoid pharma.

  • Ethics approval Cork Clinical Research Ethics Committee.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement In conformation of data accessibility protocol, metagenomic raw sequence data from this study are deposited in EMBL BNucleotide Sequence Database (ENA) (, accession number PRJEB15388.