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Life is too short to waste time on a bad cup of coffee – microbes can help with that

WRIGHT-PATTERSON AIR FORCE BASE, Ohio (AFRL) – On the latest episode of the Air Force Research Laboratory’s podcast – Lab Life, Dr. Rajesh Naik and Dr. Justin Gallivan from AFRL’s 711th Human Performance Wing discuss the perfect cup of coffee, microbes, DNA sequencing, and AFRL’s Biotechnology Grand Challenges.

According to Gallivan, who is a senior scientist of Systems and Synthetic Biology, life is too short to waste time on a bad cup of coffee.

“I actually used to be a professor of chemistry at Emory University in Atlanta, and not too far from my office was a wonderful independent coffee shop,” said Gallivan.

Gallivan says the baristas there were really terrific and that he got to be good friends with them and learn a lot about the science behind coffee such as where coffee originates, as well as the usual things about brewing it, from what makes good quality coffee, to some of the factors to be aware of if you’re going to prepare a good cup.

“You’d be amazed at how well you can coax certain flavors out of coffee,” Gallivan said. “For instance, I used to feel it was necessary to drink coffee with milk – just because it was so bitter. When I learned how to make coffee correctly, I learned that I didn’t actually need the milk so I actually drink coffee black now, but every once in a while I will go with a cappuccino, or a cortado which is more my speed.”

Earlier in his career, Gallivan was a program manager at the Defense Advanced Research Projects Agency, or DARPA, where he and his team conducted research related to tracking where coffee beans originated based on microbes on the surface of the coffee beans.

“The goal of course, wasn’t specifically coffee, although it provided a really good use case,” Gallivan says. “The problem we were interested in addressing was determining the origin of particular items.”

With that in mind, it turns out that everyone and everything is covered in microbes– mostly bacteria, as well as some viruses, of which many are innocuous – we’re not talking COVID in this discussion, said Gallivan.

“Those microbes imprint on us and differ in various environments, so it turns out that with the advent of high-throughput DNA sequencing, we can essentially gather up the DNA from all the microbes that are on a surface, run it through a DNA sequencer, and we can essentially identify what types of microbes they are,” Gallivan says. “Because the microbial burden is different in different communities, there are differences, and it turns out that those can reflect geography,” Gallivan said.

Now why is this of interest in the coffee industry? “One of the things that is important in a lot of contexts is validating a supply chain. So, if we want to know, ‘Did something come from where a vendor says it did, or is a part original?’ one way to do that would be to sample the microbes in the known factory, or where we think it should have come from and then subsequently sample the product when it comes to us so we can determine whether or not it came from a legitimate source.”

Gallivan relates that supply chain validation is a huge problem, not just within the Department of Defense, but also within business in general.

“For instance, if you buy something you believe is being made in a particular factory, you don’t want to find out that it is being made by slave labor in a different part of the world. This type of technology can provide some insight into that.”

The interesting thing about coffee as a test case is that purchasers will pay a premium for coffee that comes from a particular location, often even just a single farm. “The microbial signatures are really good, so we work with some partners within industry to sort of determine whether or not this technology could be used to determine the providence of objects. It turns out it actually works pretty well. It all comes back to this idea that we and everything around us are covered in microbes,” Gallivan says.

Dr. Rajesh Naik, chief scientist of AFRL’s 711th Human Performance Wing, says the costs of gene sequencing and the associated analytics is becoming more mainstream, automated and affordable.

“It’s not just the highly educated molecular biologists, or data scientists– it’s becoming more multi-disciplinary,” Naik says. “It could be electronic components, because going back to coffee for example, the beans coming from all these different parts of the world, you can figure out the provenance of the material using some of these biological tools for supply chain integrity and security.”

Furthering the discussion, Gallivan explains that microbes are essentially anything that’s small and of biological origin.

“Microbes get a bad rap because when we think about sort of the public vernacular, we think, ‘Oh, I got E. coli poisoning or salmonella,’ or something like that, but the vast majority of microbes have evolved along with us for thousands of years, and they co-exist.”

“On our skin, they’re there even if we wash with soap, they come back. Within our guts, microbes help digest food, so they can break down some of the more complex things that we eat into smaller components that can get absorbed by our body. It turns out that there are lots of interactions with the microbes that live in our gut and our immune system and it turns out that our gut actually has lots and lots of synapses, or connections to your brain. There is something called the gut-brain axis, so when you think about your ‘gut feelings,’ that actually is more than just an expression,” Gallivan says.

Naik shares that there are many fascinating things happening in the biotechnology space today including biosynthesized materials, biofuels for future hypersonic vehicles, or opportunities to enhance the physical and cognitive resilience of warfighters. “Biotechnology is an enabler that allows you to develop novel solutions that can be then introduced into a commercial application or a military application,” said Naik.

In fact, AFRL recently held three Biotechnology Grand Challenges that were awarded to the external community, looking to U.S. industrial partners as well as internationally, to solve some problems and mature some existing technologies to a higher technology readiness level.

“We, within the lab have done some initial technology demonstrations with some of these approaches, but now we need to have robust industrial support to mature that technology so it can make a product that the Air Force can pull into its inventory.”

Those three new biotechnology challenges that AFRL sponsored are doing exactly that. One is precursor materials for high temperature resins and according to Naik, there are unique challenges there that synthetic biology can address.

The second is in the area of biofuels, because if you want high-energy density fuels, there are some challenges with existing processes, Naik says, and there is a way to synthesize some of the precursor molecules using synthetic biology approaches that could be much more cost-effective than using conventional methods.

The third biotechnology challenge is on engineering the gut microbiome to enhance human performance.

“How can we improve physical and cognitive performance in warfighters by engineering microbiomes so maybe sometime in the future, like you can go buy a probiotic from the grocery store, and you drink a designer probiotics before a mission so it provides you with additional physical and cognitive protection in our operational environments.”

Naik says that microbes provide some layer of protection for humans. “They keep the bad actors away. They provide a perfect balance between good health vs. getting infected by bad things.”

“Think about if there is a way to engineer some of those things that can prevent corrosion in our aircraft systems or protect fuels from getting degraded. There are so many things you could think about as applications. One of things we do for the Air Force is in support of our Aeromedical Evacuation mission. Maybe there might be smart bandages that might have some biologically synthesized materials or contain microbes that can release compounds in response to given stimuli to enhance wound healing or do all sorts of neat things,” Naik said.

Naik says as an enterprise, AFRL has a biotechnology portfolio where scientists and engineers are partnering across technology directorates, with academia, U.S. industrial and international partners, and other military services to work on problems that are Air Force specific and have opportunities for us to leverage some of these biotechnological advancements.

“It’s an opportunity to develop some unique Air Force solutions and show how biotechnology can be a game-changing or paradigm shifting capability for the Air Force. The onus is on us to do that and I think we have a very strong and smart workforce in the organization that is capable of delivering on that ask,” Naik said.

For those interested in listening to the full episode, this Lab Life podcast is available on multiple platforms: