Longitudinal analysis of microbial interaction between humans and the indoor environment

Simon Lax; Daniel P Smith; Jarrad Hampton-Marcell; Sarah M Owens; Kim M Handley; Nicole M Scott; Sean M Gibbons; Peter Larsen; Benjamin D Shogan; Sophie Weiss; Jessica L Metcalf; Luke K Ursell; Yoshiki Vázquez-Baeza; Will Van Treuren; Nur A Hasan; Molly K Gibson; Rita Colwell; Gautam Dantas; Rob Knight; Jack A Gilbert

doi:10.1126/science.1254529

Longitudinal analysis of microbial interaction between humans and the indoor environment

Science. 2014 Aug 29;345(6200):1048-52. doi: 10.1126/science.1254529.

Authors

Simon Lax¹, Daniel P Smith², Jarrad Hampton-Marcell¹, Sarah M Owens³, Kim M Handley¹, Nicole M Scott¹, Sean M Gibbons⁴, Peter Larsen⁵, Benjamin D Shogan⁶, Sophie Weiss⁷, Jessica L Metcalf⁸, Luke K Ursell⁹, Yoshiki Vázquez-Baeza¹⁰, Will Van Treuren⁸, Nur A Hasan¹¹, Molly K Gibson¹², Rita Colwell¹¹, Gautam Dantas¹², Rob Knight¹³, Jack A Gilbert¹⁴

Affiliations

¹ Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA.
² Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
³ Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Computation Institute, University of Chicago, Chicago, IL 60637, USA.
⁴ Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA.
⁵ Department of Bioscience, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA.
⁶ Department of Surgery, University of Chicago Medicine, 5841 South Maryland Avenue, Chicago, IL 60637, USA.
⁷ Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80304, USA.
⁸ Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA.
⁹ Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80304, USA.
¹⁰ Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80304, USA. Department of Computer Science, University of Colorado at Boulder, Boulder, CO 80304, USA.
¹¹ CosmosID, 387 Technology Drive, Suite 3119, College Park, MD 20742, USA. Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies, University of Maryland College Park, College Park, MD 20742, USA.
¹² Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA.
¹³ Biofrontiers Institute, University of Colorado, 3415 Colorado Avenue, Boulder, CO 80304, USA. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80304, USA. Howard Hughes Medical Institute, Boulder, CO 80309, USA.
¹⁴ Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL 60637, USA. Institute for Genomic and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA. gilbertjack@anl.gov.

Abstract

The bacteria that colonize humans and our built environments have the potential to influence our health. Microbial communities associated with seven families and their homes over 6 weeks were assessed, including three families that moved their home. Microbial communities differed substantially among homes, and the home microbiome was largely sourced from humans. The microbiota in each home were identifiable by family. Network analysis identified humans as the primary bacterial vector, and a Bayesian method significantly matched individuals to their dwellings. Draft genomes of potential human pathogens observed on a kitchen counter could be matched to the hands of occupants. After a house move, the microbial community in the new house rapidly converged on the microbial community of the occupants' former house, suggesting rapid colonization by the family's microbiota.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Bacteria / classification*
Bacteria / genetics
Bacteria / pathogenicity
Beds / microbiology
Family*
Floors and Floorcoverings
Foot / microbiology
Hand / microbiology
Host-Pathogen Interactions*
Household Articles*
Humans
Metagenome
Microbiota / genetics
Microbiota / physiology*
Nose / microbiology
Pets / microbiology
Surface Properties

Abstract

Publication types

MeSH terms

Grants and funding