How can we fight the threat posed by these diseases without relying on antibiotics or antivirals? What kind of prevention efforts can be made to reduce the problem? Christopher Belnap is CEO and founder of Resilient Biotics, a company focused on exploring the capabilities of microbiome and biotherapeutics within these areas. In this interview with Supertrends, Christopher discusses the work of his company, how it is implementing machine learning in its efforts to tackle respiratory diseases, the outlook on the frequency of respiratory pandemics, the future of the respiratory health market, and more.

Supertrends: Could you introduce yourself and explain what your company does?

Christopher Belnap: My name is Christopher Belnap. I am the CEO and founder of Resilient Biotics, a US-based company in the microbiome industry focused on the development of live biotherapeutics to address respiratory diseases, specifically respiratory infectious diseases. Our main products are intended for animal applications, particularly cattle and swine.

Supertrends: As a company, how do you differentiate yourselves from your competitors?

C.B.: Broadly speaking, within the microbiome space, we are perhaps the first company to develop products based on knowledge and discovery within the respiratory microbiome. We have built our own databases and sample collections from respiratory tract samples to mine that data and then design therapeutics that can be applied back to a host species for health. Our focus on discovery and therapeutic development in the respiratory tract is quite unique within the microbiome industry, and it differentiates us from many other microbiome companies.

Supertrends: We are talking about the microbiome. How would you explain this term to someone who hasn't heard it before?

C.B.: Great question. The microbiome is a collection of microorganisms—commensal microorganisms—that live on host tissues. A host can be a human, an animal, or even an insect. The roles these organisms play are quite diverse. In the case of the gastrointestinal tract, they help digest food by breaking down materials that the host cannot break down, but they also train the immune system, triggering low-level immune responses, among other functions. There is also ecological competition with opportunistic pathogens, which is quite important in the respiratory tract.

Supertrends: How are you implementing AI in your business? What advantages does it provide?

C.B.: We are now implementing machine learning approaches. This technology is heavily used in the microbiome field because the type of data we analyze as biologists is quite complex. When you aggregate all the microbiomes present in that host—such as the gastrointestinal microbiome, the oral microbiome, the respiratory tract microbiome, et cetera—you’ll find thousands and thousands of microbial taxa. Each taxon has functional capacity that we can mine, therefore we can examine the genome of each microorganism which can have thousands of genes. When you start to multiply these numbers for each organism, it becomes really, really large. The way to deal with big numbers is to employ these types of computer software approaches—in particular, machine learning—to tease out patterns that are difficult to observe with traditional statistics.

Supertrends: Is there any other AI tool that you are exploring, besides machine learning?

C.B.: Yes, absolutely. We are integrating text-based AI, which is now widely available. You can think of ChatGPT as one example. One ongoing problem in microbiology worldwide is aligning DNA sequence data to provide information on which type of organism you have. Matching sequence data to naming conventions in larger public databases is not straightforward, so we can use ChatGPT to effectively look at different instances of how an organism is named and provide us with a result or a readout of the most likely match.

Supertrends: What challenges are you facing in the implementation of these AI tools?

C.B.: We have challenges similar to those encountered in other data science fields, where integrating AI into a workflow is not always straightforward. With AI, you need quite extensive databases that the tool can query or connect to in order to answer questions. This means you need some standardization of databases worldwide to set up these types of queries. In biology and the microbiome field, there are difficulties in finding sequenced DNA, metadata information, or taxonomic information that is standardized across different databases and available worldwide.

Supertrends: What areas of improvement do you find in your data management system?

C.B.: I think the main area of improvement would be the integration of newer AI pipelines. This is something we, like many others, are actively working on. We have lots of data formats in our platform, like inventory samples, data generated at the benchtop in the lab, and computational data. Integrating these different data formats and then querying them with AI-based software is a challenge for anyone. It is particularly challenging for small companies trying to be innovative in this space. However, there's clearly a lot of potential to utilize this newer software and its capabilities.

Supertrends: Where have you found your biggest pool of customers? Which countries seem to be more interested? Are you finding more customers on the human or animal health side?

C.B.: We are heavily focused on the development of animal health products, partly guided by support from the agricultural industry. We see our eventual customers in countries with large commercial herds of production animals, such as the US, Canada, South America, and Australia, which have the biggest cattle markets. In Europe, we have a significant dairy segment as well and a substantial swine segment, making these areas targets as we expand globally. In animal health, we have a lot of traction right now and ongoing partnerships for development of products in North America.

On the human side, there are many opportunities worldwide. Europe, in particular, shows more awareness of products that can aid respiratory health. There are large players in the probiotic space based in Europe, which could be a promising market segment for new microbiome products. Asia, with its densely populated countries, is another crucial market. Respiratory diseases thrive in densely populated areas.. As we advance our human health technologies, we will evaluate all global markets for future opportunities.

Supertrends: As a company, you claim that one of your missions is to reduce the reliance on antibiotics. Why should we, as a society, be worried about the overuse of antibiotics?

C.B.: Great question. Antibiotics are one of the greatest advances in medical history. However, when you use an antibiotic to control a bacterial infection, resistant bacteria almost immediately begin to dominate the population within that single host or group of humans or animals. Although antibiotics effectively control infectious diseases, their usage results in resistant organisms within the host species. Over time, the original pathogen, once susceptible to the antibiotic, is replaced by the resistant pathogen, which is happening and has happened in recent history.

When resistant organisms develop, we have few options to address them. They are present in hospitals and other environments, and lacking solutions to stop them is potentially more dangerous than any other type of infectious disease. The World Health Organization has referred to antibiotic-resistant microorganisms as a slow-moving pandemic for which we have no solution. Our company and others in the microbiome field believe that utilizing healthy commensal strains to help exclude pathogens can reduce the need for antibiotics. There are now therapeutic microbiome products that have demonstrated this in practice.

This is particularly relevant in animal health, where fewer treatment options exist compared to humans, and antibiotics remain the main strategy to control farm diseases. Even if farm owners and producers want to reduce antibiotic use, they often lack alternative options. Our company aims to craft new microbiome-based therapeutics and feed additives that reduce pathogens within animal systems. Using our products could lead to less reliance on antibiotics and provide producers with alternative options to control diseases. The industry finds this proposition attractive, as they have acknowledged the problem and want more options.

Supertrends: Is the spread of respiratory diseases expected to increase in the following decades? If so, does climate change have something to do with it?

C.B.: Yes. Increasing population density, globalization, faster travel of people and goods, and climate change all contribute. Climate change allows certain species to change their endemic zones, so species harboring respiratory pathogens can expand their territories and put new human populations at risk.

These factors mean respiratory pandemics, like COVID-19, are predicted to become more frequent. During the COVID-19 pandemic, we saw how quickly the virus spread globally from detection in January 2020 to a pandemic by June 2020—within six months. Influenza is another virus that remains important. While seasonal flu strains infect many people annually with minor impact, more virulent strains originating in animals such as swine flu or avian flu can infect humans and be extremely virulent, potentially causing pandemics. This year, an avian influenza strain began infecting cattle in North America and has infected a few humans, although not severely. This potential for pandemics necessitates additional solutions to prevent widespread infections.

Broader dosing of populations with preventative therapies upon first detection can help reduce pandemic risks. Designing new preventative therapies, like those in the microbiome field or new vaccine therapies, is essential now and will continue to be in the future.

Supertrends: How do you picture this market in 20 years from now?

C.B.: Overall, respiratory health is a growing market, and the need for new therapies is not going away. Both direct treatments, like antivirals, and preventative therapies, like vaccines and microbiome therapies, will be crucial for respiratory health. The microbiome field has significant potential, and last year saw regulatory approval for gut health microbiome therapies which are now available to patients.

Given the complexity within the microbiome, further development is necessary, but numerous diseases could be addressed by these therapies. Continued testing of new microbiome therapies against various diseases and conditions is expected, and more microbiome-based therapeutics will likely emerge in the market over time.

Supertrends: As a company, where would you like to be in 20 years?

C.B.: We aim to be a leader in developing microbiome therapies to address respiratory diseases. Applying our products to human markets could impact conditions like pneumonia, influenza, and chronic obstructive pulmonary disease. Millions of people are affected by these diseases, and antibiotics are often used as the main treatment, which poses a problem as previously discussed.

We want to lead in this field and have multiple products available to help control respiratory diseases. Additionally, we aim to see our products that are currently in development continue to commercialization and help reduce antibiotic use in animals. Addressing diseases and increasing sustainability in one sector, like animal health, can benefit many sectors, including human health.

This text is a transcript of an interview conducted in July 2024. The interview was conducted as part of Supertrends “Interviews with Experts” series.  Please note that the transcript may have been lightly edited for editorial reasons.

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