These themes, among others, emerged at this year’s Probiota Americas conference in Vancouver, as academia and industry continued to fine tune the role biotics might play in countering the modern insults that have contributed to a global metabolic and mental health crisis fed by chronic inflammation.
Discussions also contemplated the persisting question of what constitutes a healthy microbiome and how next-gen solutions might best be used to reverse microbial extinction and restore precision functions linked to the ancestral microbiome while navigating the inherent complexities of biotic enumeration, manufacturing, translation and regulation.
Targeting the capacity of the ancestral microbiome
Humans have lost a substantial fraction of their ancestral gut microbiota since diverging from other great ape lineages—a process driven by major dietary, ecological and behavioral changes.
The loss of diversity—which progressed with the use of fire, advent of agriculture, acceleration of industrialization, introduction of antibiotics and increasing consumption of processed foods—has led to changes in immune and metabolic function, though the extent, causality and impact of functional loss remain actively studied.
“Industrialized lifestyles have led to greatly reduced levels of gut bacterial diversity, such that humans living in industrialized societies harbor the fewest gut bacterial genera per host of any primate for which metagenomic data are available,” evolutionary biologist Andrew Moeller noted in a 2017 paper titled “The shrinking human gut microbiome”. “This observation suggests that the depauperate state of the gut microbiota in industrialized human populations is unprecedented in the history of primate evolution.”
While microbiome science did not start with an ecological restoration framework, it has gradually evolved toward one as the field began to understand microbial communities as complex ecosystems. In the last decade or so, scientists like Martin Blaser, particularly in his book Missing Microbes, popularized the idea that modern medicine and lifestyles may be causing a loss of beneficial microbes and that this microbial depletion could be contributing to the rise of many chronic diseases.
Leading microbiome researchers, however, have also cautioned against applying classical ecological restoration too literally to the human microbiome. Unlike many environmental ecosystems, microbial communities are highly dynamic, individualized and context-dependent, leading some to suggest that restoring function may matter more than recreating a specific species composition, which may not always be beneficial.
This shift in thinking has created opportunities for new entrants in the biotics space. Rather than attempting to rebuild an entire microbial community, these companies focus on restoring function through targeted strains designed to activate precise signaling pathways or produce key metabolites.
No place else on the Probiota program was this more pronounced that during the Probiota Pioneers session, which gathered startups ClostraBio, Holobiome and Kioga—each recognized for their pursuit of a next-generation of biotic solutions.
Kioga, for one, is reintroducing soil-derived bacteria, also known as “Old Friends”, to reduce low-grade inflammation by reactivating ancestral immune signaling pathways.
“Modern food systems and lifestyles have severed our relationship with the natural world including with our Old Friends,” said Justin Whiteley, CEO of Kioga. “The result is an over-reactive immune system leading to a rise in chronic inflammation that erodes resilience and exasperates aging.”
On its quest to commercialize the next wave of commensal strains, Clostrabio is pioneering advanced metabolite delivery solutions to address what it describes as the “catastrophic loss of bacteria” due to low-fiber diets, and Holobiome is mining its massive Microbiome Vault for “superhero microbes”, currently focused on unlocking strains that can support mental health.
As the conversation continues to evolve from broad concepts of gut health to the functions along gut–body axes and within the intestinal lumen, sessions also explored how specific strains might mitigate key metabolic markers and muscle health in the age of GLP-1, cognitive function in the age of chronic stress, exposure to contaminants in the age of “forever chemicals”, lead and microplastics, and hormonal regulation in the age of endocrine dysfunction.
Addressing the inherent complexities
Probiota presentations also surfaced some of the challenges in the rapidly expanding field, considering that biotics are not single, stable, uniformly measurable substances but biologically dynamic systems whose identity, activity and measurability depend on factors like replicable methods, selective contexts and viable counts.
Here, precision function requires precision infrastructure.
Trevor Kirby, principal research scientist at supplement brand AG1 and this year’s Scientific Frontiers industry award winner, presented preliminary findings on how probiotic cell counts are measured and why traditional plate-counting methods may not fully capture the number of live microorganisms in probiotic products.
He explained that while colony-forming unit (CFU) counts remain widely used, they can miss viable but non-culturable cells (VBNC)—microbes that are alive but do not grow under standard laboratory culture conditions—and offered viability Digital Polymerase Chain Reaction (dPCR) as a promising alternative because it uses dyes to distinguish live, metabolically active cells with intact membranes from dead or damaged cells before DNA amplification.
Where probiotics are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host,” health claims depend on accurate enumeration and therefore clinically applicable dosing of live microorganisms.
“[T]he enumeration method does influence how cell counts should be interpreted, so if you are using plate counting and you’re counting in colony-forming units, you’re likely referring to the total culturable cell counts, whereas if you are using a more nuanced method like the viability dPCR, you’re likely referring to the total viable cell counts, and those do ultimately matter in the context of the definition of a probiotic, because again, it is live microorganisms, not just culturable microorganisms,” Kirby said.
Rachel Asbury, a PhD student in the Department of Chemical Engineering and Applied Chemistry at the University of Toronto, received the Scientific Frontiers student research award for her in vitro exploration of how prebiotics selectively influence gut microbial communities.
Because predicting which microbes will utilize specific carbohydrates within complex and shifting microbial communities remains a significant challenge, her research highlights the wide variability in individual responses to prebiotics and demonstrates that not all prebiotics are equally effective food sources for resident bacteria.
“Just as there are many different types of fertilizers to support the growth of different plants, there are also many different types of prebiotics,” she said. “In fact, the structural diversity of carbohydrates is immense, and it’s impossible for all of these to be utilized in the same way at the same rate by the same microbes. Selectivity is a defining characteristic of prebiotics.”
By screening at the gene level, Asbury’s work links prebiotic utilization to particular bacterial enzymes and carbohydrate-binding machinery to help identify patterns in how prebiotics influence the growth of different microbial groups, including suppressing some less desirable bacteria while promoting families associated with beneficial metabolites such as butyrate.
During his presentation, Bradley Saville, professor at the University of Toronto and one of Asbury’s academic advisors, spoke to another layer of complexity: the critical role of industry-scale manufacturing methods in determining prebiotic product functionality, safety, reproducibility and credibility. These attributes, in turn, are essential for regulatory approval, clinical research and commercial success.
His remarks centered on the need for labeling and manufacturing guidelines in the prebiotic sector, like those developed for probiotics by the International Probiotics Association (IPA). The association recently submitted its “Technical Aspects of Commercial Prebiotic Manufacturing” manuscript to Beneficial Microbes, detailing the differing processes for the production of some of the more common prebiotics.
Previewing that work, Dr. Saville noted that prebiotics are more complex to standardize because they include a wide range of compounds and production methods, from enzymatic transformations to precision fermentation, membrane separation, purification, concentration and drying.
“As you heard from Rachel this morning, you have a very diverse array of compounds—they’re all fermented in a dramatically different way,” he said. “Importantly, the decisions that are made regarding manufacturing influence the composition of those prebiotics. They influence the structure of the prebiotics. They influence their fermentability, selectivity and functionality.”