Sneezes may be the result of bacteria in your gut. The Human Microbiome Project is a bold attempt to understand how all the microorganisms in the human body contribute to health problems such as allergic reactions. (Bonnie Jo Mount/The Washington Post)

When we think of allergies, we typically think of the scratchy eyes and sneezing that are the hallmark of the onset of allergy season. But what if these allergies had more to do with the bacteria and microbes in your gut than anything going on in your head?

That’s one of the findings that appears to be emerging from the work of the Human Microbiome Project, a multi-year, $100+ million project from the National Institutes of Health that is attempting to create a map of all the microbes in and on your body. There are literally tens of trillions bacteria, viruses and microorganisms that inhabit your nasal passages, skin, oral cavities and gastrointestinal tract. The problem is, we really don’t know what all these microorganisms actually do. The growing consensus, however, is that an imbalance in your personal microbiome can lead to some allergies and even certain diseases.

Not surprisingly, the Human Microbiome Project has been likened to a similar type of project – the Human Genome Project – for its ability to tell us about what makes us uniquely human. Just as the Human Genome Project gave us a way of understanding how our genes work, the Human Microbiome Project seeks to understand how the genes of all the microorganisms tagging along for a ride on the human body work. 

And, just as a number of companies – like 23andme – emerged from the research efforts of the Human Genome Project, we’re starting to see a new generation of biotech startups that are focusing specifically on the human microbiome. These companies are looking at ways to restore balance to populations of microorganisms in and on the body that, when they fall out of equilibrium, may lead to disease. Last June, one of these companies – the VC-backed Second Genome – received a major investment from Johnson & Johnson in one of the first big forays by Big Pharma into the microbiome spaceAs suggested by its name, Second Genome is trying to figure out the link between illness and the human body’s “second genome” (i.e. all the genetic material contained within the trillions of microorganisms in your body).

And – for allergy sufferers – here’s the good news: Second Genome has appeared to isolate a link between allergic diseases and the bacteria living in your gut. What it means is that you may one day buy a drug from Johnson & Johnson that injects bacteria into your body to prevent allergies or minimize allergic reactions. Instead of buying an over-the-counter antihistamine drug during the peak of the pollen vortex, you’d buy a bacterial therapy pioneered by a microbiome company. At a time when some of us ingest probiotic yogurts to get a mix of the “good bacteria” in the morning, this is not as far-fetched as it might sound.

Winter is finally behind us, which means it's time for spring allergies. From the millions of missed workdays each year, to the booming allergy drug industry, to the spring allergy capital of America—here are a few things you might not have known about allergy season. (Davin Coburn/The Washington Post)


The building block of the “microorganisms causes allergies” theory is something called the hygiene hypothesis – the idea that we’ve gotten so good in Western society of ridding ourselves of all the nasty bacterial infections of everyday life that we’re inadvertently getting rid of some of the helpful bacteria that appear to help us maintain health. (Just think of how quick so many of us are to reach for the hand sanitizer these days or ask our doctors for antibiotics as examples of how Western society positively abhors bacteria.) As a result of this long-term trend, the immune systems of individuals in Western society are more susceptible to allergic reactions and problems like asthma since they’re losing some of the helpful bacteria along the way. In one study documented in the Journal of Allergy and Clinical Immunology, children with less diverse gut bacteria actually appear to have a higher sensitivity to allergies than children with more diverse gut bacteria.

Admittedly, the idea that bacteria in our guts play a key role in regulating aspects of human health is a tough theory to wrap one’s head around. (Even harder than the “selfish gene” theory proposed by the ever-controversial Richard Dawkins more than 30 years ago, in which he basically proposed that humans were being used by genes to replicate themselves for future generations.) It’s like we went to bed with one extremely beautiful genome, and woke up with a second, much uglier genome that’s an order of magnitude bigger than this first genome and co-evolving along with the first genome in strange ways. The next time your allergies act up, though, you’ll rethink who to blame — it may just be the tens of trillions bacteria we take with us everywhere we go.