Jun Axup
Jun Axup
Jun 21 · 5 min read
Dylan Nichols and Kevin Honaker (CEO, co-founder) of BiomeSense

The microbiome is extremely exciting, but today it is still a black box of mystery. In order to really harness the therapeutic potential of the microbiome, we need to have more data, and preferably longitudinal data every single day. This is because the critical data is in the way the microbiome changes. BiomeSense is making a system to collect this valuable data with a combination of hardware and low-cost assays, allowing them to capture the most comprehensive data for the microbiome industry.

I sat down with Kevin Honaker, CEO of BiomeSense.

How did you become interested in the microbiome?

I’ve been interested in the concept of precision medicine for a long time. The idea of using individualized data for health has always appealed to me because it’s so simple and obvious, yet can have such a huge impact, which I saw firsthand in my last job at a pharmacogenomics start-up. So, when I first started to learn about the microbiome, I saw its great potential as the next wave of precision medicine, and that’s how my interest grew and I decided it was a space I wanted to pursue.

How did your team come together to start this company?

The initial co-founders of the company were myself and the scientific microbiome lead, Dr. Jack Gilbert, who at the time was a Professor at the University of Chicago. Jack is a world expert in microbiome research, he’s published hundreds of papers and founded American Gut and the Earth Microbiome Project. Through all this work, he realized that the microbiome changes very rapidly, and if we’re not capturing that data, it’s virtually impossible to really understand what’s going on. Over the years he’s tried many different ways to get more data, but none of them really worked — too expensive and hard to get the patients to use them. So, for years he’s been sitting on this and trying to build a tool to enable this time longitudinal data.

I got connected to him in late 2017 while working with the University of Chicago’s technology commercialization team. At the same time we recruited Dr. Savas Tay, a microfluidics expert at the University of Chicago because we needed to build a “lab-on-chip” to make this possible. So, we had the microbiome and engineering expertise from them, then I provided the commercial input, and with that team we started the business in 2018.

How does your technology work? What are the key insights?

Today, the vast majority of microbiome data is acquired via collecting and processing stool samples in a lab. The problem is this is very expensive on a per-sample basis, and more importantly, patients hate doing it — we’ve seen <40% adherence to a single stool sample request! To get more frequent data, you need to address both of those issues.

So, we’ve built a proprietary biosensor that is essentially an automated wetlab that you install in your bathroom. A part of the device is embedded into any toilet and passively collects a small stool sample every time the patient uses the bathroom, so they don’t even have to interact with it at all. This sample is passed to an advanced microfluidic system that processes it to isolate the microbial DNA. Some of that DNA is stored for downstream sequencing and the rest passed to our screening assay which provides a low-cost microbiome readout automatically.

This required some pretty advanced engineering, but luckily we have an extremely prestigious team of scientists and engineers that helped us put it all together!

What has been some of your biggest learnings while at IndieBio?

One of the first things you hear here is the idea of sales, sales, sales and how that solves all problems. I initially thought to myself, “We can’t sell this — we’re still a year away from having a finished product!” Still, I figured it couldn’t hurt to try. So we did, and the customer response was so overwhelming that within weeks we filled up our launch pilot program, and even had to turn down another five studies. We’re going to be working with Mayo Clinic, Harvard’s Dana-Farber, University of Chicago, UCSF, to name a few. The response we got helped validate the need for our solution. The idea of being able to do that earlier than you might think was my key learning.

How do you think the success of your company will change the microbiome industry?

I believe we’ll completely re-shape how the microbiome is used and understood. Today, we barely understand the microbiome — every other day you read article linking the microbiome to all kinds of health conditions, but when you ask how it does that and why it does that, no one can answer. The one microbiome treatment we have is fecal microbiota transplant to cure C. difficile, and yet people have absolutely no idea how or why it works.

Evidence is mounting that the problem is we’ve dramatically underestimated how clinically important short-term changes in the microbiome are. Today, we essentially can’t see them because we can’t sample frequently enough, so they’ve been ignored — out of sight, out of mind. But new studies are coming out showing that when you sample far more frequently, you can discover more trends and patterns and start to figure out how the microbiome works, not just that it does.

This means we’ve really barely scratched the surface of the discovery potential of the microbiome — these changes are incredibly important for understanding how the body and microbiome interact to alter health, yet we’ve never explored them. By changing that, we’ll dramatically reshape the landscape of microbiome research and in the near future collecting daily data will become the “norm” in research.

What milestones are in your near future?

In the past 4 months, we’ve got a bunch of pilot customers, built a functioning MVP, and expanded the team. So, our next milestone is simple — use our biosensor in clinical trials and start generating data. We’re starting to finalize designs for manufacturing and should be in our pilot’s hands within 12 months. Once that’s done, we’ll start scaling up our analytics and data pipeline, to start building the world’s largest and most valuable microbiome database — and the only one with time-series data. Long-term, this data will enable scientists to observe, understand, and eventually treat microbiome conditions to improve the health of patients.


Watch BiomeSense pitch on IndieBio Demo Day, Tuesday June 25th in San Francisco or via LiveStream. Register here!

Indie Bio

Stories of Accelerating Biology

Jun Axup

Written by

Jun Axup

IndieBio | Scientific Director & Partner

Indie Bio

Indie Bio

Stories of Accelerating Biology

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