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A Surprising Comparison of Male vs. Female Microbiomes

I must admit, I was curious. So I went over to the desk of our brilliant Lead Data Scientist, Dr. Siavosh Rezvan-Behbahani, to find out.

Could you look at all of uBiome’s gut samples, I asked, and see what the difference in microbiome composition is between men and women? And the corollary, is it possible to predict from microbiomial data whether the person giving the sample was male or female?

With human DNA, of course you can determine gender based on the chromosome signature XX vs. XY. But does the microbiome have a gender signature too?

Siavosh dove in. He spent many hours analyzing, plotting numbers, running different machine learning classifier algorithms. He looked at healthy male and female samples in part of our dataset, all the way down to genus level.

And here’s what he found, which blew my mind.

male female ubiome

It turns out that in our dataset, there is no statistically significant difference between male microbiomes and female microbiomes. And, given a random sample, we would not be able to determine if it came from a man or a woman.

This result is fascinating to me, because it suggests that maybe men and women aren’t that different in some ways. We all have two eyes, and belly buttons, and similar proportions of bacteria swimming around inside our intestines.

(Of course there’s the standard disclaimer that this is just what we observe in our gut dataset, and may not be representative of the entire human population. It’s also possible that there is a difference but it’s much more subtle than we expect. In any case, this result is encouraging me to think up other questions to ask!)

If you’re curious about something too, please tell me in the comments what kinds of data discoveries you’d like to hear about next.

38 Thoughts on “A Surprising Comparison of Male vs. Female Microbiomes”

  • Rob Boulton says:

    I submit that it might – or might *have* been, once – possible to determine the region, or at any rate the extent to which the contributors of samples have maintained traditional diets or have succumbed to the SAD diet structure of junk “foods” and carbonated drinks. This theory is based mostly on an excerpt from Michael Pollan’s book, “In Defense of Food”, which details the case of ten Australian aborigines living on a Western style diet in a small town and the range of diseases they had. A nutrition researcher persuaded them to go back to the bush style of living – eating the diet their ancestors had eaten for centuries. The story is available at

    I think it’s almost certain that the microbiome from samples at the time they were living in town and suffering from a range of diseases would be markedly different from the microbiome obtained had they given samples at the end of the seven weeks of the experiment.

  • Ken Lassesen says:

    What about this study?

    Science. 2013 Mar 1;339(6123):1084-8. doi: 10.1126/science.1233521. Epub 2013 Jan 17.
    Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity.
    Gender bias in autoimmunity is influenced by microbiota

  • OonaBelle says:

    What about a comparison of the microbiomes of folks with different IQ’s? Old versus young? Does the microbiome “age” Also those of different socioecomoic status? This is a touchy subject for some folks, for obvious reasons, but still, it would be fascinating to explore!

  • Laura Henze Russell says:

    Could you look at the microbiomes of those with mercury toxicity?

    Of those with methylation genomic variants that make it harder to excrete mercury?

    Of those with and without dental amalgam (50% mercury) fillings?

    Of those with higher vs. lower levels of high-mercury fish consumption?

  • Sima says:

    Very interesting, but ….How many people was the analysis based on? How many males? How many females? All adults? Or children also? And if children also, what percentage?

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