Cohabiting family members share microbiota with one another and with their dogs

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Cohabiting family members share microbiota with one another and with their dogs

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DOI: April 16, 2013 Cite as eLife 2013;2:e00458


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.


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We thank S Whitehead for help with participant recruitment and sampling. This work was supported in part by the Crohns and Colitis Foundation of America, the National Institutes of Health, and the Howard Hughes Medical Institute.

Decision letter

Detlef Weigel, Reviewing editor, Max Planck Institute for Developmental Biology, Germany

eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see review process). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.

Thank you for choosing to send your work entitled “Cohabiting family members share microbiota with one another and with their dogs” for consideration at eLife. Your article has been evaluated by a Senior editor, Detlef Weigel, who also acted as Reviewing editor, and two outside reviewers.

The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.

Song and colleagues present a fascinating, albeit descriptive, 16S rDNA-based survey of human co-habitation, spanning 60 families with children, dogs, both, or neither. As expected, they appear to find that individuals living together have increased similarity in their associated microbial communities, with a markedly stronger effect on skin microbiota, compared to oral or gut microbiotae. An important advance over earlier work is that dog owners may “swap” microbes with their pets, again most clearly shown for skin microbiota. There are, however, three major concerns:

1. The first one relates to the statistical methods used. Rather than pairwise comparisons, the authors need to apply a general linear mixed model that includes as many covariates as possible, such as collection dates, family size, geographic origin, urban/rural sites, presence of other pets, sequencing runs, and so on.

2. The second major concern is that although the authors suggest potential reasons for the apparent sharing of microbiota between dogs and their owners (see “Mechanistic considerations”), they do not explicitly test the hypothesis that the transfer of rare taxa drives these trends. For example, the authors might filter out taxa that are more commonly found in the dog microbiota, or found at much lower abundance in humans, and then test if that significantly changes the observed trends. Another approach might be to use weighted metrics instead (e.g., Figure 1), as unweighted data can be greatly influenced by rare but novel taxa.

3. Third, based on the hypothesis that “more microbes are shared between individuals who share a greater number of potential microbial sources”, one expects to see an analysis based on the number of human individuals in the household, since other humans are sources, too. This has been relevant for the hygiene hypothesis (more children in a family corresponds with lower incidence of hay fever in later children). Thus, did the number of people in the household explain any of the variance in these analyses? And do later-birth order children host more diverse microbiotae? Also, what can you say about children with dogs versus children without dogs (i.e., not just adults or household members) – are there positive effects of dog ownership?

Some extra analysis is also required for the following points:

A. It is stated that skin microbiota does not change with age as much as stool microbiota, based on a comparison of individuals of different ages. Later on it is stated that skin microbiota tends to reflect environmental microbiota, in agreement with the hypothesis that humans pick up microbes from their dogs. So one interpretation of the absence of a strong age effect is that the skin is more dominated by the environment than the stool microbiota.

B. Are the taxa shared by dog owning adults actually found on dogs? Are the exact same taxa picked up (at the OTU level)? Also, were there effects of the other pets or were the sample sizes simply too small?

C. Finally, Bruce Levin and colleagues asked similar questions based on E. coli strains isolated from household members and their pets in the 1980s – it would be a shame to omit a comparison to these earlier findings. Please take a look at PMID:6376625, for instance.


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