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Are there differences between male and female gut microbiomes? (NOTE: gut microbiome is the community of microbes living in the gut.) I always thought YES, based on that there seem to be so many biological differences between males and females. But according to this blog entry from uBiome (a microbiome sequencing service which has analyzed thousands of gut microbiomes - the microbes living in the gut ) there aren't. They only looked at gut microbiomes (by analyzing fecal samples), and not at other body sites in this comparison. Other past studies have found  that other body sites have bacteria differences. Even the comments after the post were interesting. From the uBiome Blog:

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.

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!)

Take note: research has linked a lack of microbial diversity in human guts to various diseases. A solution: Eat more plants! From Science Daily:

Compared with apes, people's gut bacteria lack diversity, study finds

The microbes living in people's guts are much less diverse than those in humans' closest relatives, the African apes, an apparently long evolutionary trend that appears to be speeding up in more modern societies, with possible implications for human health, according to a new study.

Based on an analysis of how humans and three lineages of ape diverged from common ancestors, researchers determined that within the lineage that gave rise to modern humans, microbial diversity changed slowly and steadily for millions of years, but that rate of change has accelerated lately in humans from some parts of the world.

People in nonindustrialized societies have gut microbiomes that are 60 percent different from those of chimpanzees. Meanwhile, those living in the U.S. have gut microbiomes that are 70 percent different from those of chimps.

 "On the other hand, in apparently only hundreds of years -- and possibly a lot fewer -- people in the United States lost a great deal of diversity in the bacteria living in their gut."

That rapid change might translate into negative health effects for Americans. Previous research has shown that compared with several populations, people living in the U.S. have the lowest diversity of gut microbes. Still other research has linked a lack of microbial diversity in human guts to various diseases such as asthma, colon cancer and autoimmune diseases.

One possible explanation for humans evolving to have less diversity in their gut microbiomes is that they shifted to a diet with more meat and fewer plants. Plants require complex communities of microbes to break them down, which is not as true for meat.

As for why Americans have experienced much more rapid changes in microbial diversity compared with people in less industrialized societies, some experts have suggested more time spent indoors, increased use of antibacterial soaps and cleaners, widespread use of antibiotics and high numbers of births by Cesarean section all may play a role. Antibiotics and antimicrobial cleaners can kill good bacteria along with the bad, and C-section deliveries prevent babies from receiving certain bacteria from the mother typically conferred during vaginal births.