Founded by research scientists from Northeastern University, the Boston-based biotechnology’s founding mission is to build the world’s largest cultured collection of human gut bacteria and develop the data infrastructure to make sense of it.
This has included creating a Microbiome Vault of data from over 100,000 individuals, a reference genome library of more than three million genes and “food maps” connecting food ingredients to specific microbes.
Jonathan Krive, director of business development at Holobiome, discusses how Holobiome is cultivating the bacterial diversity of the human gut microbiome to deliver on the promise of the microbiome.
NI: What has gone into scaling the business?
JK: Patience and a willingness to do unglamorous work. The strain bank took years of work to build (and lots of poop… samples). The data platform took significant computational investment. The team has grown deliberately from a founding trio to a rockstar set of leaders in AI/ML, microbiology, food science, drug development and regulatory. The focus has been on building in-house capabilities around areas hard to outsource—culturing difficult anaerobes, building reference databases at population scale and navigating regulatory pathways for live biotherapeutics and consumer products.
On the science side, Holobiome has built the world’s most diverse cultured collection of human gut bacteria (at least to our knowledge), a proprietary genome database spanning over three million genomes and cohort of more than 100,000 metagenomes processed through proprietary pipelines. That foundation underwrites every downstream program. This year we are launching interventional trials of over 6,000 people.
On funding, the company has layered venture investment with non-dilutive support from a wide range of sources, including the NIH, ARPA-H and TRISH (the Translational Research Institute for Space Health). We have also had strong success in working with a range of corporate partners on R&D.
NI: How has Holobiome gone about mapping the human microbiome? How far along is the company in isolating a representative of every known bacterial species in the human gut?
JK: Three layers: First, cultivation—physically growing every bacterial species within biological samples from real human donors, with priority on health- and disease-associated bugs. Second, deep sequencing—complete genomes of our strain bank, ultra-deep long-read sequencing of our human fecal samples. Third, modeling —using all of the above to build predictive models that connect microbes to host biology.
Holobiome’s culture collection is one of the top in the world and arguably captures the most diversity. We estimate (using our genome database of over 3,000,000 genomes) that there are around 10,000 known species of gut bacteria. Public type-strain collections capture a few hundred gut species at best. Smaller still is the number of bacteria you can buy as a probiotic today—about 50 species (and mostly members of the Lactobacillus/Bifidobacterium genus).
Holobiome is working to “catch them all”. Today our human gut bacteria strain bank is more diverse than every public collection and published paper combined, but there is still a lot of work to do (especially as you move from species to strain clades).
NI: What are some of the greatest challenges and successes in the first years of the business?
JK: Our biggest challenge is likely shared amongst many microbiome companies: The field has promised a lot but has largely not delivered. We think this is a problem born from a mixture of poor education, marketing and how complicated it is to do science well. On the education side, the field is still relatively young, and we have major hurdles to overcome (like growing bacteria and building high quality human datasets). On the marketing side, we’ve seen many groups try to force the function of the promise of the microbiome with existing products—which creates unhealthy incentives. For example, we’ve been approached many times by groups asking for us to “prove their product is good for the microbiome”, but that’s not quite how this works! It’s also difficult to talk about the promise of the microbiome from a food/consumer perspective, due to regulatory challenges (which we’re working to change). On the complicated science front, we’d argue the microbiome is about as complicated as it gets. It requires an insane combination of microbiology, computational biology, drug discovery, food science and ultimately large-scale human trials with multi-modal data (and of course AI/ML). There are a surprising number of microbiome companies without microbiologists.
Our greatest successes have largely come from building the company from first-principles. We started with the strain bank and cultured things never cultured before. We then created a pipeline to identify which of those microbes had promise for improving human health. As this platform matured, we could “unlock” other datasets, like how food and the microbiome interfaces, which gets us closer and closer to understanding the madness of the microbiome. These capabilities drew us to some of the best in the world to join Holobiome, building out our merry band. The next year will bring it all together with large-scale human trials.
NI: As one of the 2026 Probiota Pioneers, how does Holobiome approach treading a path no other firm has gone before, and how does it weigh the risks and benefits?
JK: The ethos is: Do the unsexy infrastructure work first, and let the products earn their place on top of it. A lot of microbiome companies started with a product hypothesis and worked backwards to the science. Holobiome started with the assets—strains, genomes, models—and let the programs emerge from what the data was telling them.
On risk, the biggest concern in this space isn’t being wrong about a single program. Programs fail; that’s biology. The bigger risk is building a thin company where one failed trial sinks the whole thesis. Holobiome is engineered so that the platform underwrites multiple shots on goal—a depression program, a pain program, a program in stress—all drawing from the same core platform. If any one program disappoints, the platform persists, and the next program benefits from the learning.
The company is rigorous about not over-claiming. Holobiome doesn’t put numbers in front of investors or partners that it can’t defend and won’t sell anything until it has human data. That conservatism is sometimes frustrating in the short term, but it’s why Holobiome is still standing while a lot of its peers from the same vintage are not.
NI: How has Holobiome partnered with industry to date, and what’s next?
JK: Holobiome is highly collaborative, having built one of the most robust partnership portfolios in the microbiome industry. Publicly, we have announced engagements with major players such as Kenvue, Unilever, Ingredion and AstraZeneca. These collaborations focus on the unique strengths of our platform: identifying the specific bacterial strains and substrates—be they prebiotics or food ingredients—that modulate biology in measurable ways. This capability allows us to pinpoint potential probiotics, prebiotics, postbiotics or live biotherapeutics with precision. We then validate these candidates through rigorous human studies, working alongside our partners to bring them to market. Holobiome does not operate as a CRO, nor do we play in the direct-to-consumer space; instead, we act as a force multiplier for microbiome innovation within large corporations, engaging in long-term joint development and licensing agreements. We remain open-minded regarding whether assets eventually launch as consumer products or pharmaceuticals—both have a vital role in our ecosystem and the potential to improve lives at scale.
We’re working on something big from a scale perspective, but more to come here in the next year.
NI: In the probiotic, prebiotic and microbiome space, what’s the next research area the industry needs to keep its eye on?
JK: Two things stand out.
First, mechanism over correlation. The field has been awash in studies showing that a bug is “associated with” some disease, but very few have moved to causal understanding—this strain, producing this metabolite, modulating this host pathway, at this dose, in this population. That gap is where the next decade of credible products gets built. Companies that connect a specific microbe (or set of microbes) to one or more mechanism to an outcome that matters for consumers and patients will do well.
Second, the integration of food, microbiome and host biology at population scale. Most of what’s known about food’s effect on the microbiome comes from small studies of single ingredients in homogeneous populations. The real opportunity is to assemble matched datasets—diet plus microbiome plus metabolome plus clinical outcomes—across thousands of diverse participants and use that to build models that can predict who benefits from what. Personalized nutrition has been a marketing concept for a decade; the data to actually make it real is finally within reach. We’re making a big bet here in 2026.
NI: What’s the significance for Holobiome of being named a 2026 Probiota Pioneer, and how does the company see it helping its profile?
JK: It is genuinely meaningful. The microbiome field is currently grappling with a significant credibility gap—an issue Holobiome did not create but must certainly navigate. After a decade defined by over-promising, inconsistent clinical readouts, and an increasingly noisy marketplace, skepticism is high. Being recognized as a Pioneer by a publication that has scrutinized this space with such care and rigor for years serves as a critical signal; it suggests that those who have actually seen the receipts believe we are doing things the right way.
On a practical level, this recognition serves as a catalyst for growth. Our business model is built around corporate partnerships. So being chosen as a top-microbiome and probiotic player in the space adds to the validation Holobiome has already received from investors, government agencies and corporate partners.
On a practical level, this recognition serves as a catalyst for growth. Since our commercial architecture is centered on long-term corporate partnerships, being recognized as a premier innovator in the probiotic and microbiome space reinforces the existing validation we have earned from our venture backers, government institutions and global industry collaborators.
As we continue to scale, we are actively seeking elite talent to join our merry band of “super-nerds.” We are architecting a future where microbiome modulation is executed with first-principles precision to fundamentally improve human health, and we invite those with equal passion to join us in this mission.
