“Beneficial” is not quite the word I would use. “Co-dependent” is a bit more accurate. Imagine a tug of war, our immune system on one side and bacteria on the other. Our bodies put just enough energy into our immune systems to ensure that there is an even match - that there is a stable balance between the two sides, what physiologists call “homeostasis”. Most diseases involve a disruption of homeostasis, either as a cause or a consequence.
Because bacteria have always been present in the environment of our ancestors, we’ve evolved to expect a certain amount of pull from the bacteria on the other side of the rope, and our immune systems are programmed to begin tugging right away.
But what happens when one side lets go of the rope? The side that is still pulling collapses in a disorderly heap, and probably gets a few bruises and cuts in the process.
So it is with our immune system. It starts pulling, but if no bacteria are pulling back it starts falling all over itself. The result is a variety of autoimmune disorders: asthma, allergies, inflammatory bowel disease, type 1 diabetes, rheumatoid arthritis etc .
We have not heard so much about “beneficial” viruses because we know even less about the virome than we do about the microbiome. But there is some evidence that gut viruses also modulate immune activity and can help prevent or suppress acute viral and bacterial infections .
Our dependence on bacteria and viruses for health makes sense only in light of evolution through natural selection. There are no functions provided by our microbiome that we could not in principle provide ourselves. It is a crazy Rube Goldberg system that would never be created by any rational designer.
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