On Your Skin, In Your Gut, and All Around: A Microbiome Q&A

Microbes are on us and in us, and researchers are increasingly becoming aware that they are a vital part of us. Across The Children’s Hospital of Philadelphia and University of Pennsylvania a variety of research efforts are underway to understand these populations of bacteria, viruses, and other tiny life forms, known as the microbiome, and their impact on health. The Penn-CHOP Microbiome Program and the CHOP Microbiome Center, launched last year, have helped to coalesce these efforts locally. Nationally, studies of the microbiome are all the rage. This spring, the White House announced a National Microbiome Initiative to advance understanding of microbiomes to aid in the development of useful applications in multiple areas.

To put these trends into context and introduce some key microbiome research themes in pediatrics, Cornerstone recently chatted with Lindsey Albenberg, DO, a pediatric gastroenterologist at CHOP and assistant professor of Pediatrics at the Perelman School of Medicine at the University of Pennsylvania. Dr. Albenberg has incorporated microbiome research into her work on pediatric inflammatory bowel disease (IBD) for years, since before the microbiome became one of the hottest topics in medicine. The edited conversation follows below.

What does the White House initiative putting a national spotlight on the microbiome signal to you?

We’re really only 10 percent human based on the number of microbial genes that are within us. These microbes do many important things for us and have many important functions. They’re not just living within us because we’re providing them a nice place to live. The relationship is extremely important, and people are catching on to the importance of that at a larger scale.

I think the government is recognizing the importance of studying this area because the environment and specifically the microbiome could really have an impact on diseases that are becoming increasingly prevalent in our modern society.

It is one more indicator that interest in the microbiome has caught on, not just from the medical and scientific community, much more broadly, on a national, international, and local scale.

Tell us about your specialty and how your research relates to the microbiome of the human gut.

The work that I do is centered around pediatric IBD — Crohn’s disease and ulcerative colitis. These diseases affect 1.5 million Americans, and at least 25 percent of those newly diagnosed are in the pediatric age group. And it’s rapidly increasing, particularly in the pediatric population, and even in very young populations. We’re seeing kids more frequently, and we’re seeing younger children as well — even infants and children under the age of 5 who have IBD.

There are genetic factors that lead to the development of disease, but environmental factors seem to be potentially even more relevant or important in many people. Within the gut, the main environmental exposures are diet and gut bacteria. Some of the work that I do is more microbiome related, some is diet and microbiome, and I’m also interested in the roles of antibiotics and probiotics to treat IBD by altering the microbiome. A major goal is to better understand the mechanism of the development of the disease for prevention and new treatment strategies.

What do you think about the explosion of interest in the microbiome in the last few years, and how have you seen the field changing?

I think it’s amazing. Initially microbiome research was very focused on the gut microbiome. And, initially, when we said gut microbiome it meant bacteria. The definition of the microbiome and studies of it have expanded into other types of organisms, including fungi and viruses. And then interest in the microbiome has expanded into other body sites. It has been really just fascinating to watch.

We know that there are distinct microbiomes at each body site. Your gut has a microbiome; your skin has a microbiome; your respiratory tract has a microbiome. There has been an explosion of studies and of data and literature that try to link the microbiomes of the various body sites to different disease processes. I think every discipline in medicine has some focus now on the microbiome and the impact that it may have on health, which I think is really amazing.

The other thing, as a pediatrician, that I think has been fascinating, is all the interest in the gut microbiome development and how that leads to health. Development of the microbiome is a huge area of study looking at questions of how we colonize our microbiomes, from birth through the early toddler years when the microbiome becomes more stable and starts to look like the adult microbiome. Things that may have an impact include mode of delivery (vaginal delivery vs. caesarian section), infant feeding (breastfeeding vs. formula feeding), as well as antibiotics that we use early on in life. There’s some data suggesting that antibiotic use early in life may be related to the development of IBD and may be related to the development of other diseases and obesity.

Generally, there has been a lot of interest in the microbiome as it relates to many pediatric diseases, or many diseases that are relevant to pediatrics. Judith Kelsen and I are writing a review paper now about the microbiome in general in pediatrics, and there is a lot of interest in the allergy and immunology world about questions like how the lung and respiratory microbiome relates to asthma and cystic fibrosis, and how the skin microbiome relates to eczema and atopic disease. This has been a huge area of study which many people at CHOP have been a part of.

There’s also a growing focus on gut ecology, going beyond just seeing what microbes are present to ask why and what are they doing. It’s definitely becoming more sophisticated and more detailed, and I think we’re going to learn a lot more about what these bugs are doing for us, what metabolites they’re producing, and what impact those metabolites have on your body. That’s the direction the field is moving in.