Probiota Pioneers: Trilliome on using lesser-known plants for precision microbiome outcomes

Co-founded by microbiome and technology expert Dr. Tim Mak and molecular biologist Dr. Patrick Guye, Trilliome distinguishes itself by isolating bioactive compounds from Asian fruits, offering an alternative to more conventional approaches that rely on generic fibers or common probiotic strains for broad-spectrum applications.

Ahead of his Probiota Pioneers presentation at the upcoming Probiota Americas in Vancouver, Dr. Guye discusses the founding and growth of Trilliome, the vision driving its innovation strategy, the non-negotiable nature of sustainability and ethical sourcing, and the key areas he believes will shape the future of the microbiome space.

NutraIngredients: What was the driving force behind the founding of Trilliome?

Patrick Guye: Tim and I initially connected in 2019. While consulting for microbiome start-ups and venture capitalists interested in the sector, we gained a unique panoramic view of the industry—observing firsthand what was succeeding and, crucially, where significant gaps remained in translating fascinating research insights into commercially viable, impactful solutions. We both possess a strong entrepreneurial drive, so founding our own venture felt like a natural progression.

As we grow older, we naturally place greater value on our health. With our deep expertise and proven experience, we see a powerful opportunity to give back — by driving microbiome innovations to market that not only improve lives but also unlock significant growth potential in a rapidly expanding industry. After extensive brainstorming, prototyping and invaluable discussions with potential clients, Trilliome was born. Our driving force was the opportunity to harness the therapeutic potential of the gut microbiome in a novel way, focusing on natural, plant-based bioactives with a rich history of traditional use, now validated by modern science. We quickly established collaborations with leading academic partners and Contract Research Organizations to generate the foundational data for our vision.

NI: What has gone into developing the flagship product (R&D, funding) and creating a pipeline precision extracts?

PG: From Trilliome’s inception, our R&D has been guided by key principles: scientific rigor, scalability and sustainability. We strategically focus on upcycled materials from food plants—exotic, nutrient-rich fruit extracts sourced from Asia—which have overlooked byproducts of food production, minimizing our footprint on the supply chain and also permitting for low COGS.

In collaboration with institutions like the University of Basel’s Department of Pharmacology, we employ smart fractionation techniques to isolate and characterize extracts with distinct compositions and properties. These are then rigorously tested for bioactivity using highly translatable ex vivo human gut experimental models through specialized CROs.

Our flagship extract, derived from these efforts, was selected for its exceptional ability to modulate the gut microbiome. Specifically, it has demonstrated up to a 4,500% increase in certain beneficial, neuroprotective bacteria that reside deep in the gut. These bacteria are often negatively correlated with cognitive decline, neuroinflammation and mood disturbances. This extract also significantly boosts the production of short-chain fatty acids (SCFAs), molecules critically linked to brain and metabolic health. This pioneering work is supported by our initial funding rounds and a filed patent protecting our innovations.

NI: Where are you now in your evolution and what is the next step for Trilliome?

PG: We are currently at an exciting juncture, pursuing a multi-pronged strategy. Our immediate focus is efficiently bringing our lead gut-brain axis ingredient to market with further validations in clinical studies and through B2B partnerships with nutraceutical, functional food and wellness companies. Simultaneously, we are advancing the development of additional proprietary prebiotic formulations from our pipeline, each identified for specific microbiome-modulating activities. We’re also exploring synergistic combinations of our extracts and further dissecting them to identify novel chemical entities with potent effects on the gut microbiome.

Our overarching goal is to solidify Trilliome’s R&D platform, enabling us to rapidly and efficiently develop precision prebiotic solutions that can reliably shift diverse gut microbiomes towards enhanced health and cognitive performance. We are actively engaging with potential clients and preparing for market entry in North America and key Asian markets.

NI: What are some of the challenges you‘ve encountered in the first years of the business?

PG: Bootstrapping Trilliome and developing novel, science-backed ingredients with a lean team has been both exhilarating and demanding. Constantly switching hats —from scientist to strategist to business developer— is part of the start-up journey. However, our small team size has been a distinct advantage, allowing for efficient alignment, rapid decision-making, and agility—crucial in a fast-evolving field. Moreover, our cross-industry experience has helped us build a strong network of experts, advisors, and supporters who offer valuable insights, guidance, and ongoing support.

One significant challenge has been effectively communicating our unique positioning at the intersection of food and medicine. Many investors are traditionally more comfortable in either the consumer wellness space or the strictly pharmaceutical therapeutics zone. However, we’ve seen a tangible shift over the past couple of years. There’s a growing recognition from new investors and accelerator programs, like EIT Food’s ‘Food as Medicine’ track, of the profound value in this integrated approach. It’s becoming increasingly accepted that healthy nutrition, especially through science-based precision nutraceuticals like ours, can play a vital role in offsetting, compensating for, and even correcting imbalances incurred through modern lifestyles, processed diets, and medication use.

NI: As one of our pioneers, could you outline your approach or ethos in treading a path or direction that no other firm has gone before? How do you weigh up the risks and benefits here?

PG: Our pioneering ethos is rooted in bridging ancient wisdom with cutting-edge science to unlock the untapped potential of natural, exotic botanicals for gut and cognitive health. Unlike many who rely on common probiotic strains or generic fibers, we delve into regions known for rich biodiversity and traditional healing practices, specifically focusing on unique Asian fruit extracts.

The ‘path less traveled’ involves identifying plant-based bioactives that have a history of safe dietary use but whose precise microbiome-modulating effects are only now being uncovered through advanced science. The risk lies in the novelty —these aren’t currently mainstream ingredients. However, the benefit is immense: truly differentiated, high-impact solutions that address unmet consumer needs for natural, effective cognitive and gut health support.

We mitigate risks through rigorous scientific validation, collaborating with world-class academic partners like the University of Basel and ETH Zurich. Our R&D integrates smart fractionation, advanced gut modeling and pharmacogenomic insights.

Sustainability and ethical sourcing are non-negotiable and integral to our business model from day one. Our ingredients are primarily derived from upcycled plant materials, minimizing waste and our impact on the food chain. We are committed to sourcing these materials in compliance with ecological best practices. As we establish supply chains, we are actively working to integrate fair trade principles and tailor fitting Access Benefit Sharing methodologies to ensure value is shared equitably with local communities and partners in the regions from which these botanicals originate. For us, pioneering means not just scientific innovation, but also responsible and ethical business practices.

NI: In the probiotic, prebiotic and microbiome space, what would you say is the next research area that the industry needs to keep its eye on?

PG: Beyond the continued exploration of new microbial strains and basic fiber prebiotics, we believe the next frontier lies in understanding and harnessing the power of complex plant-derived bioactives and their specific metabolites produced by the gut microbiome. We see increasing interest in validated nutraceuticals —food as medicine.

The industry needs to focus on:

1. Restoring damaged gut microbiomes through consumer products: We are beginning to understand how our modern lifestyles damage our gut microbiome and which species are contributing to modern health challenges, either by being underrepresented or overrepresented. We believe it’s possible to design corrective precision prebiotic solutions that move gut microbiomes toward more healthy states.
2. Deep mechanistic understanding: Moving beyond general ‘good for your gut’ claims to precisely understanding how specific natural compounds interact with distinct microbial populations and pathways and how these interactions influence host physiology, particularly along the gut-brain axis.
3. Synergistic formulations: Investigating the synergistic effects of combining different bioactives with specific probiotics or other prebiotics to achieve more potent and targeted health outcomes. Nature rarely works in isolation, and well-designed combinations could unlock next-level efficacy.
4. Advancing prebiotics for broad efficacy through personalized insights: The concept of personalized nutrition, including tailored prebiotic interventions, is a vital research avenue. Understanding how diverse microbial ecosystems respond to different prebiotic substrates is fundamental to our R&D and product development. We leverage these insights to identify common beneficial pathways and mechanisms. However, for prebiotic solutions to truly reach and benefit the mass market, we believe they should not typically depend on individual diagnostic testing, which can introduce costs and friction many consumers wish to avoid. Our approach, therefore, is to use the deep understanding gained from studying individual variations to design prebiotic formulations that are robustly effective across a wide spectrum of gut microbiomes, delivering benefits to as many people as possible without requiring prior testing.
5. AI, ‘omics, and advanced in-vitro models: Leveraging artificial intelligence and multi-omics data (genomics, transcriptomics, metabolomics) to accelerate the discovery of novel plant bioactives, predict their effects on the microbiome, and design and identify winning active compounds and combinations, as well as tapping into the emerging field of human in-vitro 3D models (Organ-on-a-Chip models such as gut, liver, simplified gut-brain models) to de-risk and speed up the identification of prebiotics that will truly be active in human beings.

NI: Finally, what is the significance for Trilliome of being named one of our 2025 Probiota Pioneers, and how do you think it helps your profile in such an innovative, ever-changing industry?

PG: Being named a 2025 Probiota Pioneer is a tremendous honor and a significant milestone for Trilliome. For us, it serves as powerful external validation of our innovative approach, our scientific rigor and the potential of our mission to revolutionize healthy aging and cognitive performance through natural gut health solutions.

In such a dynamic and rapidly evolving industry, this recognition provides invaluable credibility and visibility. It helps elevate our profile among key industry stakeholders, potential partners and future investors. The ‘Pioneer’ title resonates deeply with our ethos of exploring novel botanical sources and scientifically uncharted territory within the microbiome space.

We believe this award will open doors to new collaborative opportunities, accelerate our engagement with industry leaders and ultimately help us bring our unique, science-backed prebiotic ingredients to a wider global audience. It energizes our team and reinforces our commitment to pushing the boundaries of what’s possible in microbiome science for tangible human benefit.