Se Jin Song1, Christian Lauber2, Elizabeth K Costello3, Catherine A Lozupone4†b, Gregory Humphrey2, Donna Berg-Lyons2, J Gregory Caporaso5,6, Dan Knights7,8, Jose C Clemente4†a, Sara Nakielny9, Jeffrey I Gordon10, Noah Fierer1,2, Rob Knight11,12*
1Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, United States; 2Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Boulder, United States; 3Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States; 4Department of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, United States; 5Department of Computer Science, Northern Arizona University, Flagstaff, United States; 6Argonne National Laboratory, Institute for Genomics and Systems Biology, Argonne, United States; 7Department of Computer Science and Engineering, University of Minnesota, Minneapolis, United States; 8BioTechnology Institute, University of Minnesota, Saint Paul, United States; 9Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States; 10Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, United States; 11Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Boulder, United States; 12Biofrontiers Institute, University of Colorado, Boulder, Boulder, United States
*For correspondence: Rob Knight
†Present address: aMount Sinai School of Medicine, New York, United States; bDivision of Biomedical Informatics and Personalized Medicine, Department of Medicine, Anschutz Medical Campus, University of Colorado, Denver, United States
Competing interests: The authors declare that no competing interests exist.
Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape our microbial communities. To quantify this microbial exchange, we surveyed fecal, oral, and skin microbiota from 60 families (spousal units with children, dogs, both, or neither). Household members, particularly couples, shared more of their microbiota than individuals from different households, with stronger effects of co-habitation on skin than oral or fecal microbiota. Dog ownership significantly increased the shared skin microbiota in cohabiting adults, and dog-owning adults shared more ‘skin’ microbiota with their own dogs than with other dogs. Although the degree to which these shared microbes have a true niche on the human body, vs transient detection after direct contact, is unknown, these results suggest that direct and frequent contact with our cohabitants may significantly shape the composition of our microbial communities.
KEYWORDS: Human, companion animals, environmental microbial reservoirs, family structure, metagenomics, microbial community transmission