Home » Microbiome Mining: How It Can Help Us Save the Planet

Microbiome Mining: How It Can Help Us Save the Planet

by Editor CTS

Starting 2023 on a high note, we add a new section to our website, called Company Profiles. Here we will review companies working in science space that are doing groundbreaking work that will one day change the way we live. 

Drug discovery rate has stalled
Drug discovery rate has stalled in recent years
Photo credit: Pexels

To kick off this series, we spoke to the Dublin, Ohio-based Biosortia Microbiomics. We are thankful to company CEO, Ross Youngs, who spent his valuable time walking us through the concept of microbiome mining and how it could help us save the planet. 

Ross Youngs Biosortia Microbiomics
Ross Youngs

The interview has been lightly edited for clarity. 

Coffee Table Science (CTS): What is your background? How did you get involved in this? 

Ross Youngs (RY): My background is pretty diverse. I studied environmental science and industrial engineering in college, got into the medical imaging business, and then the optical and video disc business where I was for eight years. It was a field that required new technologies to create products and a terrific learning opportunity.

In 1988, I started my own company which was in the Inc 500 for five years in a row. We picked some plastic products that we’re going to sell in the marketplace and did really well. Along that pathway, I started to look at bioplastics which then pivoted me toward drug discovery.

CTS: How did Biosortia Microbiomics start?

RY: While we were working on bioplastics in the mid-2000s, we started to realize that we were going to pivot to algal recovery as a source of bioplastics. We started to investigate that technology and invented a way to remove microbes from the water that nobody had ever conceived. We ended up getting funding from the Department of Energy to advance that technology.

We changed the name of the company at that time to Algae Venture Systems, as we were going to focus on the systems that were required for algal biofuels and algal products. A couple years into that we recognized that what we really had access to was essentially the hidden chemistry of life, the kind of chemistry microbes make, which is the most drug-like chemistry on the planet which dominates even the human body.

People do not know that the human microbiome makes 10s of 1000s of small molecules, turning things on or off, up, or down. Science today doesn’t even know about even a small fraction of what those molecules are. And we had this opportunity to obtain those molecules from nature and changed the name to Biosortia Microbiomics.

Now the company is moving this breakthrough technology forward that we think is going to have an amazing impact on drug discovery, agri-chemical sustainability, and beyond. It works with all the existing technologies, whether it’s machine learning AI, or whether it’s synthetic biology, we actually close the gaps and make their jobs easier.

CTS: What is small molecule research?

RY: Small molecules are molecules that can pass the blood-brain barrier, can penetrate cells, and hit targets in biology, so we consider them the switches of turning things on or off. They essentially go on to become drugs. There are 19,000 approved drugs on the market today. 90% of those are small molecules.

Drug development
Photo credit: Pixabay

For example, penicillin, an antibiotic is a small molecule, and aspirin which relieves pain is a small molecule. I could go on and on with examples of small molecules because they are the easiest to approve, and have the shortest life in humans so if something isn’t going right, one can discontinue that medicine quickly.

CTS: Why can’t we use bioreactors to get these small molecules in large numbers?

RY: One of the biggest issues in the last 60 years is that drug discovery has been relatively flat. We’ve not brought a lot of new drugs to the market or new opportunities to cure disease. There are over 14,000 diseases that have no treatments or cures.

In the last 10 years, the cost of bringing a drug to the market has increased by 300%. Now, the amount of money that society is spending has gone up dramatically, and it’s not delivering results. One of the biggest reasons it’s not delivering results is all these new technologies have not been able to uncover the biosynthetic potential of microbes.

What we are doing has changed the game dramatically. We don’t have to guess what’s going on in biology, or indirectly try to figure it out, we can go right to the sources of microbiomes and collect them at a scale and quantity, where we can directly understand the chemistry, those small molecules that are so vital to next generation products and life sciences.

CTS: What is industrial-scale microbiome mining? 

Historically, it’s been very difficult to collect microbes at a scale out of a habitat or an environment. What Biosortia’s breakthrough does is it allows us to capture a microbiome and an aquatic habitat, which overlaps the human microbiome at a minimum of 73%. Our technology isn’t capturing what’s typical in a lab, which might be a 100-milliliter sample. We capture 200 million times that quantity.

Microbiome Mining
Microbiome Mining

So when we’re looking at molecules that are in the parts per billions, the parts per trillions, we can actually concentrate and amplify those molecules. So they’re in researchable quantities. And we do that with a complex set of technologies that we’ve invented that are non-chemical, and completely environmentally friendly.

CTS: How is it done? 

RY: When we go process a microbiome, we pick a fairly large body of water, which could be a lake, a river that could be a bay, or even an ocean. We process about eight Olympic-sized swimming pools of water to capture just the microbiome, where we also capture viruses. In doing so, we do no environmental harm to the site at all, because these microbes replenish in a matter of hours. What we get are the secrets of what’s going on since we also capture the chemistry our partners, pharma companies, agrochemical companies, and even cosmetic companies have a great deal of interest in.

Concentrate from a batch
Concentrate from a batch

To choose where we’re going to do our microbiome harvesting, we use genomics to understand what metabolic pathways are there, and we use chemistry to understand some of the early chemistry opportunities. As we harvest it, we remove it from the water and start preservation within two minutes and 14 seconds, so we aren’t looking at sludge, we’re looking at an actual living microbiome.

With that, we go through industrial-scale processes of removing the proteins and removing lipids and it leaves just the polarity of small molecules, these drug-like small molecules available for us to do additional work on. In the manufacturing stage, we will fractionate those materials so that we can get at each of the individual small molecules that we have prioritized through analytical understanding. This gives us a library of molecules to share with the companies we work with in order to find new products.

CTS: How do customers approach you? How does Biosortia make money?

RY: Our customers, our collaborators, typically know what they want to find. They’re looking for immunomodulation, they’re looking for immuno-oncology, or looking for anti-infectives like antibiotics against antibiotic-resistant bacteria, potential fungicides, and then in the agri chemical business, targeted herbicides or pesticides.

We are not a biotechnology company in the pure sense. We’re a platform technology and will be working with 400 partners, and customers collaborators simultaneously. The goal is through the relationships we build, we can drive revenue from their successes, as well as some early revenue from working in grants. That’s one of the opportunities we have with a platform that nobody has ever been taught in academia to do and nobody has ever practiced in industry. This is opening up an entirely new, highly sought-after segment getting at these natural, pre-optimized small molecules and microbes. And it really is bringing interest our way.

We build somewhat of an intellectual property (IP) wall around a molecule before it ever gets to a customer. You can’t patent a natural molecule but if you can uncover what it does, that is possibly patentable. So you end up building IP, computationally with machine learning AI, and with chemical derivative work that we do in inside labs. Ultimately, if we do a deal with somebody that is looking, let’s say, for cytokine modulation, or cytokine inhibition, they’ll want multiple products over multiple years.

And we’ll keep providing them opportunities to accept one of these. And as they accept one and move it forward, we’ll keep finding other molecules that hit their targets. So it’s those collaborators and customers that will do the screening and determine which molecules hit their targets, and then those would be selected for moving forward.

CTS: Are there any products that are in the market now?

Yeah, that’s a great question. We do consider ourselves an early revenue company. But this is a technology that is brand new. When genomics hit the scene on day one, there weren’t genomics products in the marketplace.

What I will say about the products that will come from industrial-scale microbiome mining, is you will see more new products come from that technology within 10 years. Compared to all other technologies combined, it is that prolific producer of drug-like molecules that can ultimately go into pipelines of companies across the entire life science segment.

CTS: How can this help save the planet?

Right, and I’m really glad you asked that question because that’s really close to my heart. And what I mean by that is, when you look at harmful algae blooms when you look at the red tides when you look at how we’re somewhat out of whack environmentally, the microbiomes that surround these communities are potentially a way to do impact.

Algal Bloom Photo Credit: Pexels

To give you an example, if you were to look for something that may mitigate or may disadvantage the species around a red tide, the best place to look is with our technology. In a red tide, the opportunity to find a molecule that may inhibit the growth of that species is likely to be present in and where that species grows. So that’s one example, the opportunity to find molecules or enzymes that could be advantageous.

Biofuels is a reality, because life has made a lot of this chemistry, science has only been able to look at a small fraction, the same thing could occur with carbon capture or remediation of hazardous waste sites. So microbiome mining at an industrial scale will bring out numerous new opportunities and solutions. It takes time to work through it and test it. But when you have a new tool in the toolbox that can bring these out these solutions.

CTS: If someone was interested in working in this field, what skills would they need? 

Mostly at the earliest stage of what we do, it’s engineering and processing skills. As we advance forward, it’s certainly going to be database management, machine learning, and AI. It’s going to be laboratory analytical work. Can you run an LCMS, Mass spectrometry, can you run HPLC can you run extraction equipment. So, we have the need for analytical expertise. And then we have the need for engineering and process expertise.

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