In short — Industrialised societies host **the lowest numbers of gut bacterial genera per host of all documented primates (Moeller, 2017).** Rather than reconstructing an entire community, new entrants target the restoration of precise functions via strains or metabolites. For ingredient providers, precise microbiome shifts value from raw diversity to measurable function.
Humans in industrialised societies host the lowest number of gut bacterial genres per host among all primates documented by metagenomics. This observation comes from evolutionist Andrew Moeller, in his 2017 article «The shrinking human gut microbiome» [1]. Measured erosion: that is the starting point of the Precision microbiome. The idea is no longer to restore lost diversity, but to reactivate precise functions. This is the foundation of the Precision microbiome as an industrial approach.
Western diet, environmental contaminants, separation from the natural world: at Probiota Americas (Vancouver, 8-10 June 2026), debates aligned these factors behind a metabolic and mental health crisis fueled by chronic inflammation. For ingredient suppliers positioned in the Precision microbiome, the operational question has changed. It is no longer «how to sell diversity» but «what precise microbial function can I restore, measure and validate».
The term Biotique Here we cover probiotics (live micro-organisms), prebiotics (substrates selectively used by the microbiota) and postbiotics. The B2B challenge hinges on a shift: from a reconstructed ecosystem to a targeted function.
Pourquoi le microbiome de précision est-il préférable à la diversité brute ?
Since diverging from other great apes, humanity has lost a substantial fraction of its ancestral gut microbiota. According to Moeller (2017), this drop in diversity has progressed with fire, agriculture, industrialisation, antibiotics, and processed foods [1]. The extent and causality of functional deficit remain actively studied.
Martin Blaser, in Missing Microbes, popularised the idea that modern medicine and lifestyles are depleting beneficial microbes, with a possible link to chronic diseases. However, several leading researchers caution against too literal a transposition of classical ecological restoration to the human microbiome.
The reason is technical: microbial communities are dynamic, individualised, and context-dependent. In other words, recreating an identical «ancestral» species composition makes no universal sense – what helps one does not necessarily help another. Hence the shift towards Restoration of function.
This is precisely what the Precision microbiome try to correct: not to restore an entire ecosystem, but a specific function.
This shift has opened a space for new entrants. Instead of rebuilding an entire community, they are targeting strains engineered to activate precise signalling pathways or produce key metabolites.
Quels modèles d’ingrédients incarnent le microbiome de précision ?
The Probiota Pioneers session brought together three startups embodying the Precision microbiome, each with its targeted function strategy rather than global composition.
| Company | Approach | Intended function |
|---|---|---|
| Kioga | Reintroduction of soil bacteria (Old Friends) | Reducing low-grade inflammation by reactivating ancestral immune pathways |
| ClostraBio | Advanced metabolite delivery solutions | Mitigating «catastrophic gut bacteria loss» linked to low-fibre diets |
| Holobiome | Exploitation of his «Microbiome Vault» | «Superhero» strains for the mental health |
«Modern food systems and lifestyles have broken 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 and chronic inflammation that erodes resilience.»
The conversation now extends to gut-body axes: metabolic markers and muscle health in the GLP-1 era, cognition in the era of chronic stress, exposure to «forever chemicals» (PFAS), lead and microplastics, and hormonal regulation in the face of endocrine disruption. For ingredient brands, each axis represents a distinct functional specification.
What this means for formulators
The value moves from the displayed diversity towards provable function. Three concrete consequences:
- Target a pathway, not a species 1. An allegations file benefits from documenting a metabolite (e.g. butyrate) or a signalling pathway, rather than a generic genus count.
- Choosing the right enumeration method for the Precision microbiome, counting in UFC or dPCR-viability, is not measuring the same thing — and the «live microorganisms» claim depends on it.
- Anticipate the prebiotic framework The absence of a standardised manufacturing reference is a regulatory risk to be integrated from the sourcing stage.
In plain terms: your scientific argument must link strain or substrate to a measurable, reproducible, and defensible function to a regulator – this is the central requirement of Precision microbiome.
The enumeration: the blind spot that decides the allegation
A probiotic is defined as «live micro-organisms that, when administered in adequate amounts, confer a health benefit on the host». The claim therefore depends on an exact cell count living.
Trevor Kirby, AG1’s Principal Investigator and 2026 Scientific Frontiers industry award recipient, presented preliminary findings on the limitations of classical enumeration. Colony Forming Units (CFUs) remain the standard, but they miss viable but non-culturable (VBNC) cells – alive, yet unable to grow under standard laboratory conditions.
Its objective result: digital viability PCR (dPCR) distinguishes, using dyes, viable cells with an intact membrane before DNA amplification. «If you are counting CFUs, you're talking about culturable cells; with viability dPCR, you are talking about viable cells - and that's what counts regarding the definition of a probiotic,» Kirby clarified.
The business implication is clear: two batches displaying the same «live» count can represent different realities depending on the method. For a supplier, aligning their enumeration method with their claim is no longer optional.
Prebiotics: selectivity as a defining characteristic
Rachel Asbury (University of Toronto), the student prize winner, explored in vitro Prebiotics selectively influence microbial communities. His work shows that not all prebiotics are equivalent food sources for resident bacteria.
«The structural diversity of carbohydrates is immense; it is impossible for all of them to be used in the same way, at the same rate, by the same microbes. Selectivity is a defining characteristic of prebiotics,» she explained. Her genetic-level screening links the use of a prebiotic to precise bacterial enzymes and identifies the families that produce beneficial metabolites. Selectivity is thus the hallmark of the Precision microbiome side substrates like butyrate — while suppressing certain less desirable bacteria.
Bradley Saville, a professor at the University of Toronto, added another layer: industrial-scale manufacturing conditions the functionality, safety, and reproducibility of the prebiotic product. Prebiotics are more difficult to standardise — enzymatic transformations, precision fermentation, membrane separation, purification, concentration, drying. Each process decision alters the final composition.
The International Probiotics Association has submitted its manuscript «Technical Aspects of Commercial Prebiotic Manufacturing» to Beneficial Microbes. For the next-generation prebiotics, the current absence of labelling guidelines equivalent to those for probiotics is a grey area to watch.
What Precision Microbiome Demands of Your R&D
The lesson from Probiota can be summed up in one equation: precision function = precision infrastructure. A biotic is not a stable and uniformly measurable substance. It is a dynamic biological system, whose identity and activity depend on reproducible and viable counting methods.
For nutrition stakeholders, three priorities emerge from the material presented:
- Document the function : signalling pathway activated or metabolite produced, rather than claimed global diversity.
- Lock the method aligner UFC or dPCR-viability on the claim made.
- To industrialise cleanly : trace how each process step modifies the prebiotic composition.
The market will no longer reward just being «good for the microbiota». R&D oriented Precision microbiome will reward the strain or substrate capable of proving What it restores, how much from living cells it delivers and how it was made.
References
- Moeller, A. H. (2017). The shrinking human gut microbiome. Current Opinion in Microbiology.
- Valensa International. Emerging Science: Why Improving Urinary Performance is the Next Frontier in Men's Healthy Ageing. NutraIngredients.
- Ashwagandha: Science, regulation and transparency. NutraIngredients.
- The Business of Longevity: Market Data, Consumer Demand and Innovation Gaps. NutraIngredients.
- NutraIngredients. Official LinkedIn page.
- NutraIngredients. Official Facebook page.
- NutraIngredients. Official X Account.
- NutraIngredients. Google News.
- Please clear. Apply to re-use our content.
FAQ
What is precision microbiome for an ingredient supplier?
This is the approach that targets the restoration of precise microbial functions — a signalling pathway or a metabolite like butyrate — rather than the reconstruction of complete species diversity. For the startups presented at Probiota 2026 (Kioga, ClostraBio, Holobiome), the value lies in demonstrable function, not overall composition.
Why does the enumeration method impact the probiotic claim?
According to Trevor Kirby (AG1, 2026), UFC counting measures culturable cells and misses viable but non-culturable (VBNC) cells. Viability dPCR distinguishes between live cells with intact membranes. As a probiotic is defined by its live microorganisms, the chosen method determines the validity of the claim.
Pourquoi les prébiotiques sont-ils plus difficiles à standardiser que les probiotiques ?
According to Bradley Saville (University of Toronto), prebiotics encompass a wide diversity of compounds and processes — enzymatic transformations, precision fermentation, membrane separation, drying. Each manufacturing decision alters the final composition, and the absence of labelling guidelines equivalent to those for probiotics remains a regulatory risk.