Listen to Victoria’s Conversation with Ray Sambrotto of Allied Microbiota Here:
Can environmental biotech finally crack the code on PFAS, “forever chemicals,” and other persistent pollutants? Ray Sambrotto, CEO of Allied Microbiota, joins Victoria Meyer to share how advances in microbial technology are reshaping the landscape of remediation in the chemical industry. With a foundation in environmental microbiology and years of academic research, Ray explains his journey from oceanography to entrepreneurship, revealing how precise strains of bacteria can tackle tough contaminants—speeding up processes previously measured in years down to mere weeks.
Victoria and Ray discuss the shift from traditional clean-up methods to scalable, biologically driven solutions for soil and wastewater. The conversation covers regulatory hurdles, the integration of AI for microbial discovery, and how collaboration between specialty biotech firms and established engineering players can expedite commercial scale-up. As regulatory standards tighten and the demand for cost-effective cleanup grows, Allied Microbiota’s approach signals a new era where biology is not just an afterthought but a strategic asset in achieving industrial and environmental goals.
Victoria and Ray discuss the following topics in this week’s episode:
- Transforming university research into commercial products
- Utilizing microbiology to break down “forever chemicals” in soil and water faster.
- Building strategic partnerships to enable scale-up
- How AI and machine learning can accelerate development
Killer Quote: “We’ve been able to speed up that decontamination process by order of magnitude, so going from years to weeks in terms of cleaning up the soil.” – Ray Sambrotto
Watch Victoria and Ray’s Conversation on Youtube Here:
How Allied Microbiota Tackles PFAS and Pollution Through Biotech with Ray Sambrotto
Welcome back to The Chemical Show, where leaders talk business. Today I am speaking with Ray Sambrotto who is the CEO of Allied Microbiota. Ray has sought microbes and a better understanding of the roles they play in the environment around the world throughout his career. He has spent much of his career as a research professor in environmental microbiology at Columbia University and he decided to venture into entrepreneurship and taking his insights on environmentalism and microbes and I guess bioremediation and other good things that Ray’s going to share with us, into leading Allied Microbiota to help operationalize biotech for environmental problems.
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So we are going to be having a conversation about the role of biotech in environmental remediation, how it plays into the chemical industry and more. Ray, welcome to The Chemical Show.
Thank you Victoria. Good to be here. Thanks for having me.
Absolutely, I am really glad to have you here. First of all, let’s just start with you. Tell us a little bit about your origin story, what got you interested in this space and then what led you to start Allied Mirobiota?
I’ve always been a big fan of the environment and things that happen environmentally. I was a uplander in upstate New York, but I always sought after the big blue ocean. So I eventually found myself getting an advanced degree in oceanography and particularly microbiology, the bugs that live in the the ocean. I did that for a long time and that was my academic expertise. Everyone has their little cellular area in academia and that was mine and it fit me. It was enjoyable. Academic research is great really and you get to follow the basic research and in my case doubly so because it got me outside and into the environment and on ships all over the global ocean. So that fit me just perfectly.
But toward the last 10 years or so, I became more interested in the application of what we were learning. How to make some of the things that we’ve learned and I’ve come up with over the years into commercial applications, that could help alleviate some of the problems and challenges we have in the environment. That was the genesis of Allied Microbiota.
So tell us a little bit about Allied Microbiota and your products and what you guys are doing.
It’s essentially biotech for the environment. Now most biotech is obviously biopharma and with good reason. It provides drugs and services and things that we need. We can crib a lot of that technology into the environmental space. A lot of the same technology that’s used for biology and pharmaceutical applications can be repurposed for things in the environment. That’s the general approach. In particular, we’re coming out of applications that have been fairly long standing in the environmental space, particularly things like bioremediation where you take strains of bacteria and apply them to the breakdown of contaminants in the environment. This has been a long standing application for the last several decades now.
It started off simply just using the bugs that were already in the soil and things, but now we’ve progressed to the point where we can take very specific strains that are shown to be more efficient at breaking down certain contaminants and then use them in a selective manner. Bringing more capable bugs to bear on the problem, as it were.
Yeah, interesting. Well, as you talk about microbiotics and just how we’ve used that for remediation, I mean that’s the fundamentals of wastewater treatment, right? Using biology and microbes to clean up water. And obviously we’re using it a lot to clean up the soil. I know one of the topics we started talking about earlier, Ray, was around PFAS. We know that we’ve got a PFAS issue and concern. It sounds like you guys have figured out a way to use your microbes from Allied Microbiota to address PFAS contamination.
Yes. So bioremediation has dealt with all of the standard contaminants in the past, things like petroleum, which is pretty much everywhere. And then the more difficult or recalcitrant contaminants, the halogenated things chlorinated by phenyls and things like that. We’ve made our mark with developing strains that could handle the really recalcitrant things like polychlorinated biphenyls, PCBs and things like that. You would think that at this point it would just be a historical problem about cleaning up some of the residues from the prior century. But unfortunately there’s a category called the emerging contaminants which continue to evolve or continue to emerge in the industrial space that are of some concern. The chief one that you just mentioned is PFAS (per- and polyfluoroalkyl substances). So these fluorocarbons that have proven very useful in a variety of things, everything from nonstick cookware to firefighting foams, but have been extraordinarily difficult to break down.
So people are very interested in more solutions than that.
How does this really work? So I think about microbiology and I think about the bugs, we’re using a lot of microbes and other things around the industry and really around all of us just to do different things. How does this actually work, and what’s unique maybe about the technology that you guys are bringing to the market?
Well, we call it Bioremediation 2.0. So really using the tools that we’ve got over the last quarter century, the newer bio tools, to bring to bear on these environmental problems, I mean, it was only about 20 years ago we learned how to actually identify most of the organisms in the environment. We graduated from just culture dependent techniques to the genetic techniques that we use now. So we can get a pretty good idea of what’s there and then that helps us to select taxons that really would be most useful to us. So we have the literature now growing year by year in terms of people reporting on various applications of the different bacteria. And we have the toolset building up that we can use.
Yeah. I’m trying to wrap my head a little bit around this. I know you guys are in the midst of commercializing this. What does that look like? How do you produce these microbes? How do you tailor it to the right solutions? Are these big batches or small quantities? I mean, I’m assuming you guys have gone beyond the lab, but how do you go from lab to environment?
That’s the critical thing, the scale up, which is the big kahuna in many of these technologies. And that’s certainly the case in ours as well. Certainly no problem at the benchtop. We have very good methods for growing bacteria and characterizing their various capabilities with relation to different contaminants. So that comes out of the benchtop and we can do that quite well. But as you say, the challenge comes when you have to go to the environmental scale. It’s not benchtop that matters anymore. It’s tens of thousands of gallons of wastewater that are being produced every day by a certain industry.
It’s hundreds or perhaps thousands of tons of soil that’s been contaminated by a certain chemical. So that’s the challenge. We’ve been doing pilot work with a variety of cooperative industries, one of which has been a soil remediation company and they brought in soil. We worked at their facility outside of Newark, Delaware and they would bring in the soil and we would mix it with our strains of bacteria. It was mostly petroleum contaminated soil, so we cut our teeth on these kinds of case studies where we were able to work with large volumes of soil and do a time series of the effect of treating them with our bacteria. Now we have some good documentation of how fast things like that are and how much better it is than other methods.
The selling point for the biology has been its low cost, but a big drawback has been the time. The biological breakdown rates are usually very slow and people want to get the soil out and get something built and they don’t have time to wait for a long time. So with the newer applications that we’re developing, we’ve been able to speed up that decontamination process by order of magnitude, so going from years to weeks in terms of cleaning up the soil.
Yeah, so that’s huge. In fact, that’s probably maybe one of the winning value propositions is just being able to speed that up. Because we know, as you say, nobody actually likes to wait to get results. We want our results instantly. Time to execute and time to delivery becomes really critical.
And the incumbent technology there that’s always won that battle has been landfills. You know, cut it and drag it to a landfill. We’ve been able to equalize the rates there because the tipping fees and landfills, particularly for the highly contaminated soils and materials, has gone up dramatically and will probably continue to do so as.
What does that mean? What are tipping fees?
When you bring a truck to a landfill and they say, okay, you have 10 tons of material that’s going to cost you this much to dump it. That tipping fee is dependent on the class of materials. So for class C landfills, which are very restrictive, highly hazardous material, the tipping fees have gone up drastically.
Yeah, that makes sense. What about the whole regulatory aspect of this? I’ve worked with and talked to a lot of leaders that are in startups that are bringing new products to market. And one of the biggest challenges, of course, is getting regulatory approvals. How are you guys tackling and approaching that.
Environmental engineering is a highly regulated area and we got around it in the soil remediation work we did because we were working at an existing facility. So they had all of the permits. The permitting is an important part of this, particularly when working in the environment. All of these activities have to be permitted. And so we’ve been working with companies that have handled the permitting for us. We do not intend to be a contractor ourselves. We are a specialty company that is developing specific tools for these larger environmental engineering companies.
Got it. So you’ll be partnering with them to bring your product to market and the solutions to market?
Yes.
That’s great. You know, we talk about just kind of how Allied Microbiota fits into the broader chemical space and just environmental space. How do you see this transforming? Where does it fit in? As we look at the products that you’re bringing to market, the technologies you’re bringing to market and looking forward over the next five to ten years, where do you see this fit and how do we bring you guys in to the mix?
Well, lowering the costs for existing procedures like decontaminating soils and sediments, I think we can provide a more cost effective alternative to what’s going on right now. So based on the case studies we’ve already developed and then in the new and emerging problems such as the PFAS we mentioned earlier, we found that they really are not the forever chemicals that they were claimed to be. A lot of that’s been repeated quite often in the press. But they’re actually amenable to breakdown almost certainly at different, much lower rates than other things because the fluorocarbon bonds are so difficult to break. The fluorocarbon bonds have been something that have been almost excluded from biochemistry. So there are very few biochemical pathways that can be used to break them down. But we found that we can get breakdown of some of the common PFAS, particularly some of the regulated PFAS, PFOS and PFOA.
We can either change them chemically into less toxic forms or at least break down the carbon bond to break them into smaller compounds which are less toxic.
So that starts to address one of my questions, which is what does this stuff turn into? You’re remediating it in the soil and going, let’s use PFAS as the example, from PFAS to what? How does that work?
Well, we’ve been doing our homework there with a lot of LC-MS spec work to actually look at what happens when you do that. Not only how much of the product disappears, but what are the breakdown products because you have to worry about forming something that’s also toxic in the breakdown pool. So we’ve been looking at that and it’s heavy sledding. It’s a lot of analytical work, but we’ve identified and been able to mass balance a lot of the work we’ve done in terms of how much goes into the various breakdown pools.
What role does AI play in any of this, Ray? I’ve talked with a lot of different companies especially ones that are bringing AI solutions to do, let’s just say product formulations or figuring out some of this deep scientific work to get from concept to reality. How are you guys using digital and AI in the development of your products?
We’ve been using machine learning approaches mainly for prospecting capabilities in the bacteria. Obviously there’s millions and millions of different bacteria, so where would you go looking? We call it bioprospecting for new things and we’ve been using machine learning to help us with that, mostly from the genetics and bioinformatics end of things.
Yeah, that makes sense. That’s probably the right place to start, letting it shortcut some of that work that you would otherwise have to do.
I think we’re certainly just at the tip of the iceberg with that. There’ll be a lot more we can do.
Yeah, we’ve talked a bit about your products, we’ve talked about what the solution is, where do you guys fit in the industrial value chain? There’s always this concept and on The Chemical Show we talk with leaders across the value chain. Where are you fitting into the value chain?
Yeah, so the idea is to go beyond the bioremediation. Bioremediation has been an afterthought, we’ve made a mess and now we have to go clean it up. Well, okay, so hopefully we’ll clean it all up. At that point we can focus where we should be focused, which is internalizing the remediation process within the walls of the industry so that you’re really having no impact now. So there won’t be any future messes to clean up because we’ll handle it inside the process itself. And so we’re getting into that. I’d say the wastewater industrial pretreatment is already a fairly mature engineering area and where people are recognizing that they’re going to build these solutions directly into their process, it’s not going to be an afterthought. They’re going to treat the material inside the building.
Yeah, so that’s interesting. I mean, that’s absolutely true in the production process of chemicals, right?
Yes.
When I think about the PFAS issue it’s not a production issue, it’s a usage issue because obviously it’s been used in firefighting foams for instance, where it was the wonder chemical for a while. Inside the four walls of the manufacturing plant, presumably some of that was done, but it’s getting out into the broader world. So I guess it’s kind of a combination that you treated on the front end during the manufacturing process and that you’re ready to treat it on the back end in the after use process.
Yes, the fulfilling of the regulatory responsibilities is one thing. Particularly as the regulatory limits become lower and lower, then it becomes a bigger and bigger marketplace. So trying to keep the costs low and trying to do it as cost effectively as we can. That brings us to another area which is not just removing the contaminant, but turning the contaminant into another commercially valuable product. Now that’s been done in a lot of areas. Biogas has been made from agricultural feedlots for quite some time.
So we’re certainly not the first ones to think of turning waste products into a commodity. But you can help more with some of these industrial processes. If we can get a cost effective way to treat the waste and then defer some of the cost by producing a product, then you’ve made it more cost effective still.
Yeah, across the industry this is what happens. We keep repurposing waste streams and figuring out how to create something good with it that people want, and companies, and businesses want and need to use. I guess it’s part of the continual life cycle of the value chain.
Yeah, I mean that’s how biology works, that’s how ecology works, that’s how the world works that I spent many years in. We need to apply some of this perhaps in something called industrial ecology of finding closed loops for some of these substances.
Yeah. I think that’s interesting. So obviously you’ve been at this for a while. When did you guys really get started on Allied Microbiota? And then where are you guys going next?
Well, I’ve been doing this for quite some time now. Probably about 15 years if you count the years in university, but then stepped out of the university with some IP from the university and in earnest, doing it probably since about 2020.
Okay, so five years in, and I know from talking to a lot of founders, there is no such thing as overnight success, right? It’s a journey. What are you looking to do? You know, what’s your goals and what should we be looking for from Allied Microbiota over the next 18 to 24 months?
We’re starting to get some traction in a couple of areas. So soil is a big one and it’s a huge market and so even a small percentage of that is a big cash flow. And then the wastewater treatment, both on the industrial side and the municipal side too. We have solutions not just in the contaminant world, but also in the domestic sewage world doing some of the nitrogen and nutrient removal a little bit more effectively then it’s been done.
Makes sense. And you guys are working on partners to continue developing your technology and take it to market.
Yes, in parallel, because again, we’re not the main contractor. We’re going to be working with larger companies and established engineering companies to help them provide more bang for their client’s buck on the various things that they are charged with.
So Ray, I always like to talk leadership with my guests because it’s a journey. So this has been a big journey for you. What’s maybe been the biggest surprise as you’ve moved out of academia, taking the work that you’ve done with the environment, with companies, and I know that you’ve probably done a lot of research partnerships with people, and then actually taking it into an enterprise to scale up and commercialize it. What’s been the biggest surprises for you?
Wow, I don’t know where to start with that. I guess I wouldn’t call it a surprise so much as I knew there’d be issues, but how really challenging it is. In the academic world, you have ideas, people get excited about them. You can start to do a seminar series and put together a publication and there you go, that’s the product. In the industrial world, a good idea is great, but you still have to get people to buy that.
And there’s good reasons not to change the way you’re doing something if it’s working. There’s the “if it ain’t broke, don’t fix it” attitude towards new technology. And in the world of remediation, since it’s not typically the key part of the industrial process for most companies, it’s kind of an afterthought. So convincing people that these kinds of approaches are not just cost effective but are going to lead to a better simplified process for them, it’s a process. It’s a road and it’s not a simple one.
Absolutely. So what else do you want people to know about what you’re doing and what Allied is doing?
We’re getting better. As the tools get better and as the regulations continue to increase the market. We’re here and I think you’ll see a lot more of these kinds of solutions, biologically based solutions. There’s chemistry and physics and other things that happen, but biology is certainly ready and it’s been underutilized in the past and I think you’ll see it come on quite strong in the next 5 or 10 years.
Awesome. I think so as well. Well, Ray, thank you so much for joining me today and sharing your story and the story of Allied Microbiota.
Thank you. Victoria, good speaking with you.
Yeah. And thank you everyone for joining us today. Keep listening, keep following, keep sharing and we will talk with you again soon.
About Ray Sambrotto:
Ray Sambrotto
Ray Sambrotto has sought microbes and a better understanding of the roles they play in the environment around the world. The sea, his wife and two children have been a challenging, but enjoyable family. Much of his career was spent as a Research Professor in environmental microbiology at Columbia University before stepping out to help operationalize biotech for environmental problems. Allied Microbiota’s goal is to develop new environmental applications for microbes and expand the roles they already play in industrial processes. We seek to accelerate the diffusion of biotech advances into bioremediation and waste upcycling.