Why you shouldn’t believe anything you read about the microbiome


New scientific discoveries are incredibly exciting, but often poorly understood and misused in dangerous ways.

Consider the discovery of radioactivity. It profoundly changed everything from medical imaging to nuclear power to atomic warfare. But before it was completely understood (no one knew it could lead to genetic mutations that result in cancer) it was misused in a variety of ways that range from humorous to horrifying.

As the website Mental Floss explained in a its post 11 Ways We Used Radiation in Everyday Life:

…Once upon a time, radiation in different forms was new and wondrous and had a million uses -medications, cosmetics, industrial applications, and even entertainment. It was only later that the danger became evident.

These uses ranged from radioactive toothpaste, advertised as providing a bright smile and freshening your breath by killing bacteria in the mouth, to radioactive cosmetics to make your complexion “glow” and prevent aging, to patent medicines, to radioactive suppositories designed to deliver healthful radiation directly to internal organs. There is no way to know how many cases of cancer and how many deaths might have been caused by the enthusiastic adoption of radiation as a “cure.”

We appear to have learned nothing from that debacle even though the message could not be clearer: Do not implement new medical discoveries until they are thoroughly tested and understood. Indeed, we are eagerly rushing to repeat our mistake, only this time the scientific discovery is the microbiome.

The microbiome will likely turn out to be an exceedingly important factor in human health and disease, just as radiation turned out to be exceedingly important in health and disease (think radiology and treating cancer with radiation). But we are only on the cusp of understanding the microbiome, and therefore, capable of doing terrible harm by turning our speculations into action. That’s the theoretical reason why you shouldn’t believe what you read about the microbiome in the mainstream media, but there are practical reasons as well.

Consider that the micriobiome has its own microbiome, the virome, and it is the interaction between the bacteria and the viruses that prey on them and on human beings, that determines health and disease. There is a small, but growing body of evidence that the human body can harness or at least influence the composition of the virome in order to regulated the microbiome. A paper published last year in PNAS, Bacteriophage adhering to mucus provide a non–host-derived immunity, offers a tantalizing glimpse of the possibilities:

Mucosal surfaces are a main entry point for pathogens and the principal sites of defense against infection. Both bacteria and phage are associated with this mucus. Here we show that phage-to-bacteria ratios were increased, relative to the adjacent environment, on all mucosal surfaces sampled, ranging from cnidarians to humans. In vitro studies of tissue culture cells with and without surface mucus demonstrated that this increase in phage abundance is mucus dependent and protects the underlying epithelium from bacterial infection… Based on these observations, we present the bacteriophage adherence to mucus model that provides a ubiquitous, but non–host-derived, immunity applicable to mucosal surfaces. The model suggests that metazoan mucosal surfaces and phage coevolve to maintain phage adherence. This benefits the metazoan host by limiting mucosal bacteria, and benefits the phage through more frequent interactions with bacterial hosts. The relationships shown here suggest a symbiotic relationship between phage and metazoan hosts that provides a previously unrecognized antimicrobial defense that actively protects mucosal surfaces.

In other words, certain viruses help the body to fight off bacterial infections by killing the bacteria. Even more remarkable, it appears that the animal will change the composition of its mucous to recruit more of the helpful viruses and thereby make it easier to ward off infection by harmful bacteria. Moreover, research suggests that the virome differs far more from person to person than microbiome, suggesting that it may play a greater role in health and disease than the microbiome.

The bottom line is that the microbiome is extremely complex and interacts with the body and with both helpful and pathogenic bacteria in ways that we do not yet comprehend. That’s why any contemporary claims about the microbiome, including claims about possible differences in the microbiome of babies born by C-section vs. babies born by vaginal delivery are the intellectual equivalent of radioactive suppositories. We are dealing with something powerful, but we don’t know enough about it yet to make ANY recommendations since we have no idea of what the optimal microbiome looks like, of how the virome and the microbiome interact, of how the body uses the virome to manage the microbiome, whether individual differencess in the microbiome are clinically meaningful, and the long term effects of attempting to manipulate the microbiome.

The microbiome may well turn out to be as important as radioactivity. Only time, and much more study, will tell. Until then, we should be very careful about making any claims and promising any health benefits. As the example of radioactivity demonstrates, it is all too easy to do more harm then good by manipulating a system that is, as yet, poorly understood.