The Microbiome 101

John Tillotson, CEO of Microbe Detectives, recently got together with Professor Jack Gilbert, one of the world’s leading microbiome experts, to get some of his insights on the big picture of the microbiome movement.


Professor Jack Gilbert, Ph.D.
Director of the Microbiome Center and Professor of Surgery, University of Chicago; Group Leader for Microbial Ecology, Argonne National Laboratory.

Tell me a little bit about your work.

I’m an ecologist but I’m also a professor of surgery. So I’m applying ecology like the same stuff you’d find in trees, and you know, farmers and conservationists looking at how forests work, or how a grasslands and prairies function, right, but I’m applying that research to our bodies. The bacteria that live inside our bodies are also an ecosystem. So I can understand the ecological dynamics of that ecosystem and use it to redefine the health of the person.

What does the term “microbiome” mean?

The microbiome is an ecosystem inside your body. It’s the bacteria, the fungi, viruses – they live in your gut, on your skin, in your mouth. We also find them in our homes. Your home environment, the walls and the floors, also have a microbiome, and so do all the animals and plants, and the oceans, and soils all over the world; they all have a microbiome, a microbial ecosystem full of all of these tiny unimaginably small organisms that are changing the world around us.

Why is it such a hot topic today?

The research that we’re doing is extremely exciting because it changes the paradigm of how we think about health and well-being and the world around us. It’s a hot topic because our research is changing how we practice medicine, or how we change our ecosystems to preserve the functions that are valuable for maintaining human health, or maybe even how we alter the fabrication of materials and products in our world, even how we purify oil for refining purposes to create gasoline. The microbiome can play a role in all of these things. It’s extremely exciting to be able to understand it and use it for our research.

What is the water microbiome?

Rivers, lakes – they are all environments in which we find millions and billions and trillions of microorganisms, bacteria, viruses, archea – they are prolific in all of the waterborne environments on the earth. If we want to say look at the Chicago River, we’re standing in Chicago, if we want to understand how that ecosystem functions and how to maintain it for the health of the ecosystem and the well-being of the people that use that water, we have to be able to explore that environment to understand which bacteria are there, which fungal organisms are there, and how they’re all interacting. And if we disturb it, that changes the dynamic of that system and alters the health of that environment. We are using our understanding of the bacteria, the viruses, the fungi, in water and how it interacts with the animals and humans that use that water, to try and understand the health of those ecosystems.

Why is this field of work important?

We are changing the way the microbiome is being used in academia. For sure, our research is changing. We are employing people that understand microbial ecology into a department of surgery. That’s my main job. I’m a surgeon that studies the microbiome. Right, this is a very bizarre setup compared to what we’re used to, but it’s also changing how we apply that into the technological advances that industries and businesses are using. We try and understand how the microbiome could be useful say for treating disease. How can I develop the next generation of probiotics to stimulate our immune systems? to maybe change the way our brains function? to alter how likely we are to become obese? Right, these are the ways in which we’re using the microbial world to change medicine and practices for the better. This is really simple for us. We’re actually able to change our microbiome quite simply by eating different foods, by using certain types of probiotic, or even by changing the way we exercise. We can alter the bacterial community of our body and we can affect change in our health. That’s changing the way we practice medicine, the way we perform surgery, the way we follow up with treatments of our the subjects, in order so they can recover much better. People are taking the microbiome and embracing it as a new health care regimen as well as trying to understand how we can use it to alter the health and improve the functional capacity of our environments. Imagine food security, medicine, the way in which we restore ecosystems so we can preserve the functionality for eons to come.

When we look at the types of water sources that we have for drinking, for recreation, we usually think we want to avoid consuming some of that water necessarily. Some of it might have dangerous pathogens in it. We want to understand how to prevent those dangerous pathogens from proliferating. It’s extremely difficult to say, for example, how the trillions and trillions of organisms in a body of water you may be canoeing in, how many of those could be damaging to your health. We just don’t know, so we’re trying to understand the ecosystem of that body of water, of that lake of that river, and how when you interact with it, when you go swimming in it, when you take a canoe out in it, or when you go riding in it, or your children are playing on the beach, how that interaction may influence their health. We need to understand how to improve the health of that water, so that children don’t get sick, but we also need to make sure that we can understand health promoting benefits in that water. There may be microorganisms in the river that could actually help your child to live a healthier more productive life.

What is metagenomics?

The way we understand our microbial world around us is by sequencing the genomes and the other molecules that live inside the cells of those organisms. Just the same as we’ve done with the human genome. We’ve sequenced the genome of a human. Now we can track and understand disease susceptibility. We do the same thing with the bacteria you have in your body, forty trillion microorganisms. Every one of them has a genome. We use something called metagenomics which is sequencing all of those genomes together to reconstruct our understanding of what those organisms do. We sequence the DNA of your microbiome, to really crack down on how they function and how they can be useful for treating your disease.

Where are we now in this journey? Where do you think it may take us?

The microbiome is on the cusp of a revolution but like every revolution it’s starting out as a basic science principle. We are laying the foundations of understanding how the microbiome functions, how we can manipulate it to change the health of our environments, and of our patients. But it’s very early days. We are only just starting to understand how to develop the next-generation of probiotic therapeutics for example that can help us to treat patients. We are in very early stages even of investment in this space. We are starting up companies. We are exploring ways to manipulate the microbiome to improve health. Venture capitalists are coming on board to see if this is a viable option. It’s a very exciting time but it’s also a very early phase study. We think that in the next five to ten years we’re going to see a dramatic improvement in our ability to manipulate health and well-being by using the bacterial communities in our body. But we need to do it in a very precise and controlled and ethically responsible way.

What do you hope we accomplish at the Microbiome Water Summit?

What I hope to come out of this exciting leadership conference is an opportunity to have a open and progressive dialogue about how the microbiome can be used to improve the health and well-being of people and environments around us. How we can use our current discussion format in order to change the way in which we’re developing this science and the way in which we’re commercializing it. We need to be informed. We need to be excited and engaged. We also need to take a step back sometimes and really understand how this research and the investment into the research for commercial development is progressing. When we can do that in a an open forum, we have much more capability to change the dialogue and alter the design of the work.

Microbiome Water Summit 2017

  • Learn from leaders in this ground-breaking field
  • Network with a new community of innovators
  • View live streaming on the Internet

Presentations and panel discussions

  • Invisible Influence: The Microbiome in Health
  • Metagenomic Applications in Wastewater
  • Key Findings & Insights:
    • Biological Nutrient Removal (BNR) Study
    • Biogas Anaerobic Digester Study
  • Source Water Characterization
  • The Shedd Aquarium Microbiome Project
microbiome water summit shedd