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Microbiome: Nature or Nurture?

Nature Research Microbiology Community
The paper in Nature is here: http://go.nature.com/2FIwXvy
Where does our gut microbiome come from? In recent years this has become a much sought after question. While we know that our microbiomes are similar to those of our parents, we don’t know if this is because we share the same genes or because we lived in the same house when growing up. This question may even have practical implications. For example, if our genes exert a strong influence on our microbiome, then microbiome transplants may require finding a genetically-compatible donor, which complicates the deployment of these techniques. Hence, the classic question of nature-versus-nurture has deep clinical implications with respect to our microbiome.
We were therefore very excited by the opportunity to investigate this nature-versus-nurture question hands-on, based on a cohort of ~1000 Israeli individuals with genetic and microbiome profiles that we collected as part of our large-scale personalized nutrition project . Our cohort is especially interesting due to Israel’s unique history: Most of Israel’s population originates from recent immigration from around the world, yet the current population shares very similar diet and lifestyle habits. This setting approximates the ideal lab experiment, which would consist of placing genetically diverse individuals under the same environmental conditions and observing how this influences their microbiome.
With great excitement we began analyzing the data, expecting an initial barrage of promising discoveries, and preparing ourselves to be good scientists and remain skeptical at these initial results until we could validate them.
Certain that we would find strong links between genetics and microbiome, we began the analysis, but to our great surprise (and strong disappointment!) we did not find any significant associations. We were sure that we got it all wrong. At this stage we started questioning the quality of our data and thought perhaps there are mix-ups of samples. After a lengthy analysis process that involved matching microbiome samples to their matching subject by matching human DNA traces in stool samples, we were convinced that there were no such mix-ups. Unbeknownst to us, these investigations would eventually form an important part of our paper. The moment of realization that this is an important finding was when we realized that in our data, we can we successfully predict the ancestral origins of our participants with their DNA but not with their microbiome. In other words, while closely ancestral individuals have more similar DNA, closely ancestral individuals don’t have more similar microbiome.
We were able to establish that ancestry is not…

Microbiome: Nature or Nurture?
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