Barnwell Bio—a startup whose founders cut their teeth building wastewater bio-surveillance systems during the COVID pandemic—is now turning its attention to the poultry industry, using metagenomic sequencing to help producers spot emerging disease threats earlier.
Armed with $6 million in seed funding in a round led by Twelve Below, the New York-based startup is targeting poultry barns in the Midwest and Southeast.
Partners include Mississippi State University, meat and poultry processor West Liberty Foods, and egg producer Vital Farms.
How it works, and why it matters
Rather than testing animals for a single pathogen, Barnwell Bio collects foot swabs from the barn—which contains fecal matter from the birds—to capture the broader microbial ecosystem spanning bacteria, fungi, parasites, and viruses.
It then creates a “microbiome fingerprint” unique to each facility, enabling detection of pathogens before clinical symptoms appear while also tracking levels of good, bad, and neutral gut bacteria. This helps producers, vets, and feed additive suppliers assess the effectiveness of interventions and spot early warning signs when things drift out of balance.
“In our team’s time scaling the nation’s wastewater monitoring infrastructure [where sewage monitoring provided early outbreak warnings], we saw how powerful of a leading indicator it can be,” said cofounder and COO Casey McGinley.
“By shifting the focus from individual sick birds to the entire environment, we can flag a pathogen spike weeks before it becomes a crisis.”
Proactive flock management vs reactive firefighting
Cofounder and CEO Michael Rhys told AgFunderNews: “We extract the DNA from the samples, put it through the metagenomic sequencing, and translate that into risk scores and visualization so producers can understand what’s happening in their barns.”
But how actionable is this information?
According to Rhys: “If you detect some things early there might be antibiotics you can use, biosecurity measures you can step up, feed additives you can use. It may be adding things to the water to clear out certain bacteria.”
McGinley added: “There are lots of things you can do to prevent things from getting worse and becoming really a problematic outbreak.
“Right now we’re focused on specific pathogens that we know are problematic and how those levels are trending over time. But we’re also looking across the whole microbiome to understand how different interventions are impacting good, bad and neutral bacteria [populations].”
According to Rhys: “One big use case we’re really excited about is looking at the microbiome fingerprint of high-performing versus low-performing barns. By looking at that over time, we can pick up patterns.”
Whole-barn intelligence
The approach is already generating some unexpected insights, said McGinley, citing a customer that wanted to assess the impact of applying a probiotic litter amendment in a barn prior to bird placement. Barnwell’s monitoring detected a spike in the species making up the additive five days after application, but the effect was short-lived: in the next sample, taken a week later, levels of beneficial bacteria had returned to baseline.
However, the data did show that the amendment reduced Staphylococcus levels for about a week—an entirely unexpected result—prompting the customer to change tack and test the additive in pullet houses ahead of high-stress vaccination periods instead.
Rhys added: “We haven’t come across anyone doing what we’re doing. And as we continue to build out our data set, we’ll be able to generate even more compelling insights just from benchmarking and from some of the predictive work we’re able to do. We can also look at antibiotic resistance genes and other functional gene markers like virulence.
“But when we start with folks, we always say give us your biggest problem, and let’s see how we can help you solve that more quickly.”
Avian flu: From pathogen presence to variant-level surveillance
For avian flu, one of the biggest threats to the egg industry, Barnwell has a grant from the Foundation for Food & Agriculture Research (FFAR) to build out an RNA platform for early detection, says Rhys. “One thing that’s really exciting that we’re developing is understanding the different variants circulating in a given premises, as we did with COVID.
“This will have implications for things like vaccine efficacy if we ever get to a place where birds are able to get vaccines. But even beyond that, there are going to be some benefits of doing more surveillance for bird flu. Another big one we’re looking at is avian metapneumovirus.”
As for the business case for early detection for avian flu, he said, early information helps firms prioritize resources. “In an ideal world, biosecurity would be really tight all the time. But in reality, it’s really hard to do that and it’s really expensive.”
Why investors are backing microbiome intelligence for poultry
Raising money is never easy, said Rhys. But investors could quickly see the value proposition. “This is an industry which is under-invested from a venture capital side, but we’re generating a unique data asset. And if you start to think about what’s going on with AI and machine learning, the data set we’re building becomes more and more valuable.”
He added: “The other thing [that appealed to investors] was that we started with poultry, but there is absolutely an opportunity to apply this platform to other livestock species.”
Other investors in the seed round include Max Ventures, Dorm Room Fund, Banter Capital, Planeteer Capital, AgVentures Alliance, Daybreak Ventures, and Alumni Ventures.
Barnwell Bio was founded in 2024 by Jake Byrnes (CSO), Casey McGinley (COO), and Michael Rhys (CEO), who previously worked together at wastewater intelligence firm Biobot Analytics. Barnwell focuses on the poultry sector, where it combines environmental sampling with metagenomic sequencing to help producers detect disease early and get a better understanding of the drivers of flock health.
👉 Layers: Early detection of E. coli, Eimeria species, Avibacterium paragallinarum (Coryza), and Egg Drop Syndrome virus, helping firms reduce mortality and maintain steady lay rates.
👉 Broilers: Early detection of threats such as Enterococcus species, Eimeria species, Clostridium perfringens, and Salmonella enterica before they impact growth.
👉 Breeders: Early detection of pathogens such as Staphylococcus, Enterococcus, and Mycoplasma species.
👉 Feed/pharma companies: Microbiome data can help firms evaluate the efficacy, mechanism of action, and overall impact of their products on bird health.
