Meet the Scientist — Dr. Jack Gilbert

Innate Immunity
Dr. Gilbert talks about commercializing microbiome research
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Dr. Jack Gilbert earned his Ph.D. from Nottingham University, UK in 2002, and received his postdoctoral training in Canada at Queens University. From 2005, he worked for Plymouth Marine Laboratory as a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr. Gilbert is an Environmental Microbiologist at Argonne National Laboratory, Professor in the Department of Ecology and Evolution at University of Chicago, and senior fellow of the Institute of Genomic and Systems Biology.

Dr. Gilbert is currently applying next-generation sequencing technologies to microbial metagenomics and metatranscriptomics to test fundamental hypotheses in microbial ecology. He has authored over 90 publications and book chapters on metagenomics and approaches to ecosystem ecology. He has focused on analyzing microbial function and diversity, with a specific focus on nitrogen and phosphorus cycling, with the aim of predicting the metabolic output from a microbial community. He is currently working on generating observational and mechanistic models of microbial communities associated with aquatic and terrestrial ecosystems. He is on the board of the Genomic Standards Consortium, is an academic editor for PLoS ONE and senior editor for the ISME Journal, and is PI for the Earth Microbiome Project, Home Microbiome Project, and Hospital Microbiome Project.

We recently sat down with Dr. Gilbert to get his perspective on microbiome research and find out what the future might hold for the commercialization of this research into real products.
In your opinion how far has the microbiome market already been developed?
The commercialization of microbiome research is currently still in its infancy. What we are really trying to do at the moment is understand how microbes interact with their environment, and specifically with their hosts. That could lead to a number of key paradigm shifting conceptualizations that could be commercially exploited. One of those that we’re all very familiar with is the idea of a probiotic, this so-called drink that contains microorganisms which can benefit your digestion, or you know, make you healthy.

You can very readily take that out of the human context and put it into an environmental context. One such example is agricultural farms. If you grow crops in different areas of your farm, as a farmer you'll very quickly notice that certain parts of your farm have better productivity of the same crop compared to another part of your farm. Or, certain parts of the farm have better disease resistance compared to another part of the farm, and this could be very readily applied. A lot of the disease resistance (the natural resistance of the plant to disease) and the productivity of that plant (in amount of biomass or fruits, or seeds, or whatever it generates) can be very readily conceived of as coming from the microbiome that is associated with the plant or the soil in which the plant is growing.

So if we take that to its natural conclusion, if you could take the good microbiome, with its high productivity and its high disease resistance, and spread it more evenly across your farm area, then theoretically all of your crops would be highly productive and highly disease resistant. We know a lot of these kinds of ideas are being exploited in different niches.

A good secondary example is the idea of fecal transplants in humans to overcome serious gastrointestinal diseases causing persistent diarrheal infections. We exchange the gut contents of a healthy human being and put them into a disease carrier and you get an actual reduction in the disease state of the affected individual, leading to an improved health situation. So they are more able to resist persistent diarrheal infections. That is an interesting paradigm when you think about it.

That is very interesting, but isn't this still very far away from being a product on the market?
I don't think it is very far away. I like to think in terms of a 3–5 year market range. We're looking at the current situation, and we have a lot of evidence to suggest that it is viable. We just now need to do the hard work in terms of defining how viable it is and what the other impacts of doing this might be. For example, if you can imagine I develop a probiotic for fish disease in northern Canada, and somebody markets that and starts applying it to fish in the tropics, or fish in Patagonia, or fish in Australia, and starts spreading around bacteria that may not normally be spread in that way — what environmental consequences will that have?

Now, we came across that question when we were doing the original genetic modification, and GM (genetically modified) crops and GM products were very concerning — was this mutation going to be spread to the environment? So there are ethical and philosophical considerations for all of this research. However, if we handle it properly, and more importantly, if we define the environmental and biogeographic constraints of microbial communities, we can start making regional solutions to regional problems, and that will have a very significant impact for the market. Market regionalization is highly commercial, and if we can take that product and create something more bespoke, more defined, more designed for your problem, then we will have a much better opportunity to provide a fair service to people.

What are some your next research projects?
I have a lot of ongoing projects and a lot of new ideas — constantly reforming new ideas. We like to stay on the cutting edge, so we are trying to do things which would normally be considered too broad or large to cope with by single laboratories, through involving significant collaborations with other research institutes. Or for what we consider potentially a little bit too much on the edge for most funding agencies, we exploit our extensive, collaborative network with private foundations to try and drive forward the cutting edge of that research — where it may be a little bit risky but obviously has potential for high reward.

So we are particularly interested in the successional development of microbial communities and how different bacterial organisms respond metabolically to their colonization of a particular environment. We are interested in this especially in plants, but also in human situations and in buildings. And we're trying to define when organism A lands on a site, how does it maintain or influence that site so when organism B lands, it metabolically interacts, competes, or is outcompeted by the first organism.

It's basic ecological theory, but there are new paradigms that we can test and explore to make use of that understanding to develop so-called commercialization products that we just talked about before.

In which area do you think we are closest to seeing the first products — for human diseases, or agriculture, or others?
At the moment the most significant area of this research is being done in humans.
There is a collaborator we have at the University of Minnesota, Mike Sadowsky, and he has been doing some incredible work with the fecal transplant — the probiotic of the human colon — and getting rid of those diarrhetic diseases.

I think that is the key area that we’ve found focus in, in terms of developing near-term products. However, we are not so far off doing this in soils. The most complex environments we’re doing it in are actually marine systems, where you have this dilution effect, and also a significant problem with currents and the movement of the water. It is very hard to see an ocean with a microbial population, because it very quickly dispersed. Overcoming those kinds of technical barriers is an engineering problem, and is the reason we really should be collaborating, discussing, and interacting more with engineers. These are the people who can come with clever solutions to our significant problems.