Next wave of microbiome solutions pairs AI and big data, Plug and Play finds

Plug and Play’s new research has found that investments in AI and data-led technologies have expanded in the microbiome market, where successful start-ups are creating personalized, holistic health solutions. 

The innovation platform finds that new businesses are taking holistic approaches that go beyond single-strain treatments to target inflammation, metabolism, and cognitive health comprehensively.

For instance, Jona, Holobiome, and Concerto Biosciences are businesses that are using large datasets for developing targeted therapies and improving public health.

“Corporations are not just buying products,” comments Arthur Jamon, ventures analyst at Plug and Play France. “They are buying datasets and clinical validation.”

Additionally, the industry is introducing consumer-facing microbiome testing platforms to make gut health analysis accessible at home, on a scale, and more cheaply, the report points out. “While the scientific rigor of these platforms varies widely, the gap between consumer accessibility and clinical credibility remains a key tension in this space.”

Microbiome as a whole system

The “Microbiome longevity: Top start-ups rewiring how we age” report concedes that the first generation of microbiome therapies “failed,” suggesting that succeeding solutions will pair AI with clinically validated, long-term data. 

“The first generation of microbiome drugs treated one strain as one drug for one disease,” explains Jamon. “The microbiome does not work that way. It affects inflammation, metabolism, cognition, and skin at the same time.”

Plug and Play stresses that the microbiome should be viewed as a whole system and that advances in AI and sequencing are enabling this more holistic approach. Using these tools, innovators can map individual microbiomes in detail and stimulate the effects of specific interventions.

It adds that personalized benchmarks are going beyond generic probiotic recommendations.

The report also points out that, unlike the genome, the microbiome is modifiable, making it one of the most actionable targets in longevity science.

Microbiome and longevity start-up categorized (Image credit: Plug and Play). Authors note that scientists intervening more precisely can go beyond managing disease toward preventative approaches that prevent health decline — potentially before it begins, in some cases.

Stand out start-ups

Start-ups are emerging across the market, with innovations targeting more specific disease markers, says Plug and Play. Technologies, such as data infrastructure, sequencing platforms, and microbiome certification tools, are becoming more common. 

Plug and Play analyzed over 30 start-ups and categorized them based on the biological issues they addressed and how explicitly their solution was rooted in longevity and healthspan, rather than general gut health or disease treatment.

For instance, Jona’s microbiome analysis platform, powered by AI, scans around 220,000 peer-reviewed studies to match findings to single test results, the report points out. The platform also has a second engine that can stimulate interventions before recommending them.

As another example, Holobiome is a company developing gut-brain axis therapeutics that target depression, anxiety, and central nervous system issues. It has used two million bacterial genomes and multi-omic data from 80,000-plus people. Also, Plug and Play notes that it has partnered with Fortune 500 companies like Unilever and Ingredion to translate its database into functional food ingredients at scale.

Another standout start-up that Plug and Play spotlights is Concerto Biosciences, which uses a robotic platform that builds and tests millions of microbial combinations daily. The company is known to design combinations of microbes precisely to help restore damaged skin microbiomes.

To collect and examine start-up data in the microbiome and longevity space, Plug and Play used Crunchbase, PitchBook, LinkedIn, company websites, and its internal database called Playbook. 

The companies were filtered based on a microbiome-first thesis, scientific credibility, active operational status, and relevance to at least one of four biological levers: inflammaging, metabolic health, the gut-brain axis, or the gut-skin axis.

Evolving microbiome field

Plug and Play says that the microbiome field is still evolving, with the most scientifically mature players focused on inflammaging and metabolic health — where clinical evidence is strongest. Meanwhile, the gut-skin axis is noted to be the “most dynamic frontier” but has a gap between a small number of clinical-stage players and growing early-stage activity.

Plug and Play says that the microbiome field is still evolving, with the most scientifically mature players focused on inflammaging and metabolic health — where clinical evidence is strongest.Notably, the platform points out that very few companies carry explicit healthspan claims today. Instead, the start-ups rely on microbiome health, disease biomarkers, or consumer wellness positioning. 

However, this is beginning to change, Plug and Play observes, as some of the most recent start-ups in the field are positioning themselves explicitly in longevity.

Furthermore, the report finds that inflammaging and immune function are the main levers of start-ups in the microbiome field.

“The start-ups targeting the inflammaging lever represent some of the most technically ambitious approaches in the microbiome space, moving well beyond generic probiotics toward gene editing, precision binding proteins, and compound-level targeting of aging pathways,” the report details. 

“We are seeing a growing number of European players emerging in this therapeutic segment, reflecting a broader pattern. While the US leads in diagnostics and consumer platforms, Europe is building some of the most scientifically rigorous companies in the space. No two companies here use the same mechanism, which tells us the field is still searching for the most effective way to address chronic inflammation at its microbial root.”

Other levers are metabolic health and aging, and Plug and Play finds investors believe this segment is growing amid GLP-1 triggering conversations. The report finds that in metabolic health, the entry is narrowing for start-ups as established players deepen their clinical and commercial bases.

The third lever is the gut-brain axis, with clinical science in the space still maturing as the field is more research-led than commercially driven, notes Plug and Play. Lastly, the fourth lever is the gut-skin axis, which the report says is where microbiome science meets one of the world’s largest consumer markets. Players targeting this axis are gaining funding to build clinical trials. 

Plug and Play venture experts will be sharing the report findings at the company’s Longevity Event on Oct 22 in Paris, France.