The Microbiome Family

We have a special treat for you today. Guest blogger Dr. Jonathan Hausmann, pediatric and adult rheumatologist at Boston Children’s Hospital and Beth Israel Deaconess Medical Center, has launched his own citizen scientist experiment – the microbiome family.

Join us on the exploration of his family’s changing microbiome with this yearlong blog series.

They say having a baby changes everything about you—your priorities, quality of sleep, happiness, relationships with your spouse, friends, and family—and, of course, your bank account balance. I want to find out if this also held true for my microbiome.

My wife and I are about to have our first baby. How will the baby change our microbiomes, and how will we shape hers?

I have been interested in the role microbes play in health and disease since college, when I studied evolutionary biology, the field that explains how our current traits evolved over hundreds of thousands of years as a result of our exposure to microbes and the environment.

Now, as a pediatric and adult rheumatologist, I really believe that better understanding our evolutionary past will help us treat or prevent some of the diseases that plague us today, a fact that is sometimes overlooked in modern medicine.

Most of the diseases I care for—including rheumatoid arthritis and lupus—have puzzled researchers for years, because no clear causes have been found. The study of bacteria and the microbiome may help unlock some of the mysteries of rheumatology, as it has done in the past with other mysterious rheumatic illnesses. For example, a bizarre epidemic of arthritis in Connecticut in the 1970s was eventually found to be due to a species of bacteria, now called Borrelia burgdorferi. We’ve found that viruses are involved in many cases of polyarteritis nodosa and cryoglobulinemic vasculitis. Also, recent research suggests that the oral bacteria P. gingivalis may contribute to rheumatoid arthritis, and that varicella zoster may be involved in giant cell arteritis.

But microbes do not always harm our health. In fact, our well-being could depend on them. An infant’s immune system needs to be exposed to microbes for normal immune function. Our modern aseptic environment—with baby bottle sterilizers and broad use of antibiotics in toothpaste, food, and even in toys—may have inadvertently led to the increase in autoimmune and allergic diseases, a theory known as the Hygiene Hypothesis.

Surprisingly, infants may well encounter microbes much earlier than we thought. We used to believe that fetuses grow in a sterile environment while in the womb, and that they first encounter bacteria as they pass through their mother’s birth canal. However, recent research suggests that mothers may transmit bacteria to their offspring while they are still in the womb, meaning that the newborn gut microbiome is not sterile.

To investigate what this microbiome looks like, I will collect a sample of our baby’s very first poop—which is known as meconium—then send it to uBiome for microbiome analysis. I also want to explore how our infant’s microbiome will change as she grows. Many factors are known to affect the infant microbiome, including method of delivery (vaginal birth vs. cesarean section), food (breast milk vs. formula), exposure to antibiotics, and the environment in which she is raised. I predict that my wife and I will also play a role in shaping the microbiome of our future daughter, and that she, too, will affect ours.

So for the next year, we will analyze our family’s microbiomes every month to see how they change. Will our baby’s microbiome begin to look like ours? Will our microbiomes begin to look like hers? How will our microbiomes compare to that of other uBiome users? Stay tuned to discover what happens!

Dr. Jonathan Hausmann is a pediatric and adult rheumatologist at Boston Children’s Hospital and Beth Israel Deaconess Medical Center. In addition to studying the microbiome in rheumatic illnesses, Dr. Hausmann recently launched Feverprints, a crowdsourced research study that leverages the iPhone and Apple’s ResearchKit to explore body temperatures in health and disease. Read Dr. Hausmann’s blog at