Two of a kind: How we share our microbiome with our partner

Tuesday, August 1, 2017

Couple holding hands sitting on a bed.Biologists at the University of Waterloo find the unique microbial communities living on our feet can be used to predict who we live with.

The study, published this month in mSystems, combined high-throughput sequencing and artificial intelligence to see what the microbome living on the skin of cohabiting couples can tell us about the microbial “fingerprints” that we leave on our loved ones.

“Your feet not only look like yourself, they look a lot like your partner as well,” says first author and study lead Ashley Ross, a master’s student with Biology Professor Josh Neufeld.

The researchers analyzed the microbiome from 330 skin swabs from 17 sites on participants’ skin - including the upper eyelids, outer nostrils, inner nostrils, armpits, torso, back, navel, and palms of hands – and compared the results to those from the corresponding partners. The commonalities were strong enough that a machine learning algorithm could usually match couples from their microbiome results alone.

Ross says previous research has shown that skin microbial communities vary within an individual from region to region, but she wanted to know what other factors – like cohabitation – help shape the microbiome.

The researchers found differences depending on where the sample was taken. For example, the bottom of the feet showed the highest agreement between couples but samples from the inner thigh correlated almost exclusively with a participant’s biological sex.

“In hindsight, it makes sense,” says Neufeld, a member of the Water Institute. “You shower and walk on the same floor barefoot, and this process likely serves as an effective form of microbial exchange with your partner, and also with your home itself.”

This type of microbiome profiling can get complex quickly, depending on how many sites you are comparing, which is why the researchers turned to machine learning to compare profiles. Once it was trained to look for cohabitating couples, the program yielded an accurate matching 86 per cent of the time, which was always more accurate than incorrectly matched partners.

“Ultimately what we're trying to learn is whether these skin microorganisms have co-evolved with their hosts over time,” Neufeld says.

Neufeld says the study is part of a larger research focus aimed at understanding how skin microbiomes adapt and change with their host – not only people, but other mammals as well. In previous work, Ross and Neufeld analyzed and compared the microbial communities on door handles at the University of Waterloo.

The paper’s authors also include Andrew Doxey, a professor of biology with a cross-appointment to computer science. Funding for the project was provided through a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada. Ashley Ross was supported by a Canada Graduate Scholarship from the Canadian Institutes for Health Research (CIHR).

Science in the Media

This story was featured by the following outlets:

  • Lovers Share Colonies of Skin Microbes, Study Finds. July 31, 2017. The New York Times.
  • Living together means sharing more than the bathroom: Researchers find couples end up sharing MICROBES. July 19, 2017. UK Daily Mail
  • The couple that lives together shares skin bacteria together. July 26, 2017. Medicine Net. USNews.
  • Your stinky feet can reveal who you are living with. July 21, 2017. Popular Science.
  • Your body actually changes when you move in with someone. July 26, 2017. Bustle.
  • Couples share not just love, but bacteria too. July 28, 2017. Deccan Chronicle.