American Gut: an Open Platform for Citizen Science Microbiome Research

Author:

McDonald Daniel1ORCID,Hyde Embriette1,Debelius Justine W.1,Morton James T.1,Gonzalez Antonio1,Ackermann Gail1,Aksenov Alexander A.23,Behsaz Bahar4,Brennan Caitriona1,Chen Yingfeng5,DeRight Goldasich Lindsay1,Dorrestein Pieter C.23,Dunn Robert R.6,Fahimipour Ashkaan K.7,Gaffney James1,Gilbert Jack A.891011,Gogul Grant1,Green Jessica L.7,Hugenholtz Philip12,Humphrey Greg1,Huttenhower Curtis1314,Jackson Matthew A.15,Janssen Stefan1ORCID,Jeste Dilip V.1617,Jiang Lingjing1,Kelley Scott T.5ORCID,Knights Dan1819,Kosciolek Tomasz1,Ladau Joshua20,Leach Jeff21,Marotz Clarisse1,Meleshko Dmitry22,Melnik Alexey V.23,Metcalf Jessica L.23,Mohimani Hosein24,Montassier Emmanuel1825ORCID,Navas-Molina Jose1,Nguyen Tanya T.1617,Peddada Shyamal26,Pevzner Pavel2427,Pollard Katherine S.20,Rahnavard Gholamali1314ORCID,Robbins-Pianka Adam28,Sangwan Naseer10,Shorenstein Joshua1,Smarr Larry42729,Song Se Jin1ORCID,Spector Timothy15,Swafford Austin D.27,Thackray Varykina G.30,Thompson Luke R.3132,Tripathi Anupriya1,Vázquez-Baeza Yoshiki1,Vrbanac Alison1,Wischmeyer Paul3334,Wolfe Elaine1,Zhu Qiyun1,Knight Rob1427,

Affiliation:

1. Department of Pediatrics, University of California San Diego, La Jolla, California, USA

2. Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA

3. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA

4. Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA

5. Department of Biology, San Diego State University, San Diego, California, USA

6. Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA

7. Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA

8. Department of Surgery, University of Chicago, Chicago, Illinois, USA

9. Institute for Genomic and Systems Biology, University of Chicago, Chicago, Illinois, USA

10. Department of Biosciences, Argonne National Laboratory, Chicago, Illinois, USA

11. Marine Biology Laboratory, University of Chicago, Chicago, Illinois, USA

12. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia

13. Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA

14. The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

15. Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom

16. Departments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA

17. Sam and Rose Stein Institute for Research on Aging and Center for Healthy Aging, University of California San Diego, La Jolla, California, USA

18. Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA

19. Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA

20. The Gladstone Institutes, University of California, San Francisco, California, USA

21. Human Food Project, Terlingua, Texas, USA

22. St. Petersburg State University, Center for Algorithmic Biotechnology, Saint Petersburg, Russia

23. Department of Animal Science, Colorado State University, Fort Collins, Colorado, USA

24. Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA

25. Université de Nantes, Microbiotas Hosts Antibiotics and Bacterial Resistances (MiHAR), Nantes, France

26. Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

27. Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA

28. Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA

29. California Institute for Telecommunications and Information Technology (Calit2), University of California San Diego, La Jolla, California, USA

30. Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA

31. Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA

32. Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA

33. Department of Anesthesiology and Surgery, Duke University School of Medicine, Durham, North Carolina, USA

34. Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA

Abstract

We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

Publisher

American Society for Microbiology

Subject

Computer Science Applications,Genetics,Molecular Biology,Modeling and Simulation,Ecology, Evolution, Behavior and Systematics,Biochemistry,Physiology,Microbiology

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