About the world within us

They're everywhere. Too small to be seen by the unaided eye and too numerous to count, they inhabit our insides and outsides, our guts and the surface of our skin.

They are the bacteria, viruses, parasites, and other organisms that make up what scientists call our microbiome. It's a complex environment, and scientists are only just beginning to understand and appreciate its vitally important role in keeping us healthy and signaling when we are sick.

This week, Penn Vet, Penn Medicine, and the Children's Hospital of Philadelphia will host their second annual microbiome symposium. On Wednesday, Jo Handelsman, associate director of science at the White House Office of Science and Technology Policy, will give a public talk on Earth's microbiomes and the research and policy opportunities they present. It will be at 6 p.m. at Penn Vet's Hill Pavilion, 380 S. University Ave. Admission is free, but registration is recommended here.

Immunologist Daniel Beiting, research assistant professor at Penn Vet and a key player in its Center for Host-Microbial Interactions, spoke to us recently about microbiomes.

What, exactly, is our microbiome?

It's the collection of microorganisms that live in and on our bodies. When a lot of people talk about the microbiome, they're often referring to bacteria. But it's more complex. It includes viruses. It includes more complex microorganisms like protozoa and fungi.

These organisms have for a long time evaded our attempts to understand them.

In the last 10 years, this field has exploded. The microbiome is sexy now because we can actually study it. With advances in technology and the era of genomics, scientists can capture a molecular footprint of what's there. We're still in the era where we're just cataloging things. But we're doing it on a much greater scale, and we're using cutting-edge tools.

How many organisms are we talking about?

People are not entirely sure. But numbers you'll hear are that there are about 100 trillion organisms that each person carries around. The majority live in our intestine, and the majority of those live in the colon.

In that 100 trillion bugs, there are a couple hundred, or maybe as many as a thousand, species. Bacteria, like our own cells, have genes in them. In terms of gene content, they outnumber our own genome 100 to 1. It's a massive amount of life and information encoded within this microbiome.

What do these organisms do? Do they benefit us?

These are by and large a good thing. Part of how our bodies evolved is to be in contact with these microbes. When you eat, you're eating for two. You're eating for yourself, and you're also feeding this community. They're helping you break down that food and releasing lots of molecules that are important for intestinal health and brain health. Because we're still at this cataloging stage, scientists are looking at somebody who is healthy and someone who is sick.

What's generally seen is that, during disease, the diversity, that rich ecosystem in the gut or on the skin, seems to crash. Just as with a reef or a rain forest, the richer the ecosystem the better. That starts to raise some questions about, well, maybe using too many antibiotics early in life may be a bad thing. Maybe there could be an effect from the degree to which we live in a sanitary environment.

The big question moving forward in this field: Are the changes coincidental, or are they part of the disease process? Does that mean we should target the microbiome as a way to treat disease? I think there's no question that that's the case for certain diseases, like obesity. It becomes more and more apparent every year that microbes that live in your gut can contribute to obesity.

Can we do things to change our microbiome to enhance health?

Not very intelligently right now. We don't have boutique mixes of microbes, because we don't know what they're doing yet. But that is definitely the horizon. As for overall diet, it seems that eating a diet that would be considered healthy by other measures is a good thing. Having lots of fiber and vegetables is important for maintaining gut health. Outside that, it's hard to make specific recommendations. We're not at that point yet.

It sounds as though this has the potential to revolutionize medicine.

I wholeheartedly believe that. Future physicians and future veterinarians will be faced with a life where the microbiome will be a prognostic and therapeutic target. It will be something that they look at to understand if disease is happening, and something that they actually try to manipulate to treat disease.

As an example: Somebody comes in, they have abdominal pain, and you may be able to sample the stool or some saliva or their skin and tell if a disease process is occurring, and what that disease process might be.