Written by:

Nadine Daou, VP of US Operations

Taous Saraoui-Mazed, Head of Programs

What does co-culturing mean?

It refers to the joint fermentation of multiple bacterial strains within the same manufacturing workflow, as opposed to the classical protocol of growing each strain in individual monocultures and blending only at the end.

So why would a company working with bacterial products consider co-culture?

As microbiome products become more sophisticated, manufacturing is being pushed far beyond the single-strain model. Many live biotherapeutic products (LBPs) and next-generation probiotics (NGPs) no longer rely on one isolated microorganism, but on combinations of strains designed to work together. Following that trend, microbiome-related basic research is evolving towards defining bacterial consortia that maximise the potential benefits, all while keeping unsought bacteria out of the mix.

As a result, developers look for manufacturing strategies that can handle this growing level of formulation complexity without multiplying operational burden. In that context, co-culture has emerged as a valuable approach, allowing multiple strains to be grown within the same process in order to streamline development and help reduce manufacturing costs.

As a result, co-culture can be, if designed properly, a strategic tool to reduce manufacturing load, support product affordability, and even take advantage of the natural metabolic interactions between strains.

Challenges of co-culture techniques

➢ Nutrient competition. When several bacterial strains compete for available nutrients, they often proliferate in unequal proportions. Natural behaviours and competing principles operate, allowing only the strongest to grow and limiting the others.
➢ Differences in nutrient needs. If the media composition is not optimally designed, one strain may proliferate faster than the others, all while the rest lag because the medium does not fully support its own requirements. That would lead to one strain dominating the culture, therefore losing the intended proportion.
➢ Growth conditions. When manufacturing bacterial products, adjusting environmental conditions to maximise growth and production is essential. However, when combining more than one taxon, choosing an environmental combination that maximises the growth of all strains becomes a far more difficult task.

This combination of variables means that a successful co-culture depends on a deep understanding of each strain’s physiology: which nutrients it prefers, which metabolites it produces, which environmental conditions it tolerates, and how it is likely to behave in the presence of other strains.

It also means that the wrong manufacturing partner can turn complexity into variability very quickly. For companies developing multi-strain LBPs or NGPs, choosing a CDMO with real strain knowledge becomes a risk-management decision.

Biose’s co-culture workflow

Biose approaches co-culture leveraging their deep microbial knowledge acquired through their 8+ years of experience as a leading CDMO in bacterial products. Rather than treating mixed fermentation as a slightly different manufacturing protocol, Biose’s pipeline starts with understanding the individual strains to assess their growth conditions, media requirements, and critical process parameters. That previous expertise, built through years of work in live biotherapeutics and advanced microbial products, provides the basis for designing rational co-culture strategies.

From there, development moves stepwise. The experts at Biose study each strain’s metabolic behaviour in detail, mapping the nutrients it consumes, the compounds it releases, and the ways those compounds can be used by other members of the consortium. This allows the team to identify bacterial combinations in which the metabolic output of one strain becomes a useful input for another, creating linked growth-supporting interactions within the culture.

Rather than functioning as isolated organisms competing for the same limited resources, the strains can be selected to operate as an interconnected system that uses the medium more efficiently. This type of metabolite-sharing interaction is known as cross-feeding, and it is one of the key mechanisms Biose leverages to design smarter, more efficient, and more cost-effective co-culture processes.

Once the compatible strains have been grouped, the growth medium is adjusted to support different metabolic needs, and process conditions are tested to identify which variables may shift the balance of the population. This is particularly important in the context of co-culture because, far from just growing bacteria, the challenge is to grow the right bacteria, in the right proportions, under conditions that remain stable and scalable.

Analytical control is another decisive factor. In a mixed fermentation, standard colony-forming unit (CFU) plating may provide a total count, but it does not offer enough visibility at the strain level. For multi-strain products, that is a major limitation. Biose addresses this by using highly specific quantitative methods (qPCR-based analytical strategies) that allow teams to monitor the behaviour of individual strains within the culture. That means being able to track whether populations remain balanced over time, whether one strain is taking over, and how process changes affect the final microbial composition. For complex microbiome products, that level of monitoring is essential.

Benefits of using co-culture

For developers working with multi-strain formulations, running one separate fermentation per strain can rapidly increase cost and operational burden. A well-designed co-culture strategy can significantly reduce that burden by consolidating compatible strains into fewer fermentation workflows while maintaining control over the process. For companies targeting broader accessibility or cost-sensitive markets, this can have a direct commercial impact.

Co-culture also offers a compelling approach to designing complex but controlled microbial products. In contrast to donor-derived approaches such as faecal microbiota products, co-culture allows developers to build products with intentional microbial complexity while preserving greater control over which strains are present. For companies operating in the microbiome space, that distinction is becoming increasingly important, as the future belongs to complex, controlled formulations.

Biose’s experience positions it as a development partner capable of turning microbial complexity into a robust, industrially viable product strategy.

The science is demanding, and the market is moving fast. Choose a partner who can keep up with the pace.

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Most of my week looks like batch planning, client timelines, and coordinating between our teams and the developers we work with. That is the project manager’s world at a CDMO like Biose, and I am generally comfortable in it.

Copenhagen was a good reason to step out of it.

The 2026 Microbiome Times Partnering Forum Europe brought together two full days of presentations spanning Harvard research labs, clinical-stage start-ups, investor perspectives, and a few genuine surprises – including a session on gut bacteria that absorb PFAS, and another on soil consortia improving crop yields. I went as a listener – curious, not expert. Here is what stood out.

From 100 subjects to 100,000

The opening panel set the tone. Four voices – Denise Kelly of Seventure Partners, Curtis Huttenhower from Harvard, Jeroen Raes from KU Leuven, and Seth Bordenstein from Penn State – were each asked to say where they think the microbiome field actually stands today.

Raes put it in numbers: from MetaHIT cohorts of around 100 subjects fifteen years ago to studies now reaching 100,000 participants. The field has moved from a community under construction to one entering a serious validation phase – clinical and preclinical data converging, AI and machine learning increasingly used to turn associations into something closer to causality.

Bordenstein added a dimension worth noting: the next wave goes beyond human health. A One Health framework – where host, microbiome and environment are studied as a system, not separate chapters. Two examples he gave: oral microbiome transplants being explored to prevent dental caries, and Wolbachia-based approaches to disrupt mosquito-borne viral transmission. Neither felt far away.

The question is no longer just ‘what?’ – it is ‘how?’

One of the clearest threads across the two days was the shift from composition to function. Huttenhower’s standalone session opened with a figure worth sitting with: only around 25% of microbial genes are well annotated. The rest – a functional dark matter inside every gut microbiome – remains largely uncharacterised.

His team’s Human Microbiome Bioactives Resource (HMBR) is being built to address this. One application stood out: understanding why some IBD patients do not respond to 5-ASA, one of the most commonly prescribed treatments for ulcerative colitis. The answer, in many cases, is a microbial enzyme inactivating the drug before it can act. Identifying the organisms responsible opens the door to microbiome-aware prescribing.

Andrew Bartko from UC San Diego’s Center for Microbiome Innovation took a related angle. Around 25% of tested drugs are modified by gut microbial communities – via dihydroxylation, demethylation, hydrolysis, and other pathways. Donepezil in Alzheimer’s. 5-ASA in IBD. Knowing which organisms interfere, and how, could convert non-responders into responders without changing the molecule.

The clinical data is starting to arrive

If there was one session that stopped the room, it was Nikole Kimes presenting results from Siolta Therapeutics‘ ADORED study. Their oral LBP candidate, STMC-103H, was given to at-risk infants over 336 days to prevent the atopic march – the sequential development of atopic dermatitis, food allergy and asthma. Among infants who completed one year of treatment: a 64% reduction in the risk of physician-diagnosed atopic dermatitis (23.3% vs. 43.1% on placebo) and a 77% reduction in the risk of physician-diagnosed food allergy (4.7% vs. 16.7%). Good tolerability, no major safety signal. Numbers worth remembering.

The session that followed felt closer to home. Sam Possemiers of MRM Health and Adrien Nivoliez, our CEO, took the stage together to present MH002 – and the eight years of industrial co-development that sit behind it.

MH002 is a live consortium of six commensal strains being developed for mild-to-moderate ulcerative colitis. Phase 2a results in 45 patients (randomised, double-blind, placebo-controlled, 8 weeks): clinical remission of 14% vs. 7% on placebo at week 8, and 18% vs. 0% in the per-protocol population. CRP normalisation in patients elevated at baseline: 60% vs. 25%. Faecal calprotectin normalisation: 36% vs. 15%. No antibiotic preconditioning required.

What makes this story worth telling – from where I sit at Biose – is not only the clinical signal, but the manufacturing story behind it. Producing six anaerobic strains as a single drug substance in co-culture, maintaining viability, purity and stability as you scale, is genuinely hard. Adrien walked through eight years of progressive development: fermentation to 2,000 litres at late GMP, specific analytical methods to identify and quantify each of the six strains separately, and a innovative delivery methods to protect the product and target the intestine. Phase IIb and then Phase III are next, with scale projected toward 5,000 litres. The industrial partnership starts on day one – not when the clinical trial is already running.

The gut-brain axis gets serious

The second afternoon gave considerable space to the gut-brain axis, and the perspective that stayed with me most came from Amy Kruse, Chief Investment Officer at Satori Neuro. Her message was straightforward: the space is gaining credibility not because the idea is new, but because the evidence is becoming cleaner. Biomarkers, mechanisms, a credible regulatory path – when those three are aligned, the field starts looking investable. The era of broad microbiome enthusiasm is over; what investors now want is specificity.

Bloom Science‘s Christopher Reyes backed it up with data. Their oral LBP candidate BL-001 is designed to reproduce the effects of a ketogenic diet through the microbiome, with applications in Dravet syndrome, other developmental and epileptic encephalopathies, and obesity. Phase 1 results in 32 adults showed good tolerability and, in overweight subjects, a placebo-adjusted average weight reduction of around 2.3% at day 28, with dose-dependent effects on metabolic markers consistent with the ketogenic hypothesis. Early data – but with a mechanism behind it.

Valerie Taylor of Taylored Biotherapeutics added another angle: FMT trials in psychiatric disorders – bipolar disorder, OCD, depression – as a tool to identify which microbiomes are associated with treatment response, before moving toward a more defined microbial product. Around 80% response reported with FMT in bipolar disorder in their trial data. Eighteen candidate strains are now being evaluated for the next development stage. Still early. Still striking.

The wider picture

Some of the sessions that stayed with me fell outside the more familiar therapeutic tracks – and they are worth noting.
Yolanda Sanz from CSIC presented work linking a specific strain, Phascolarctobacterium faecium DSM 32890, to a favourable metabolic profile in human cohorts – less detected in obese subjects, with preclinical data showing reduced weight gain, adiposity and glucose intolerance in a high-fat diet mouse model. A small human study in overweight and obese subjects showed signals consistent with the preclinical data, though still very early stage. The next-generation probiotic space is moving toward strain-specific, mechanism-driven candidates – this felt like a good example of what that looks like in practice.

Kevin Horgan of Melius Microbiomics presented a different kind of next-generation approach: genetically engineered microorganisms, using E. coli Nissle 1917 as a chassis. Their platform, BioPersist, transfers the ttr operon from Salmonella Typhimurium to improve colonisation in an inflammatory environment. Lead programme MMB-003 is in development for ulcerative colitis. The engineering is layered – better colonisation, targeted colonic delivery, and specific metabolic pathway modulation. Whether you find GEMMs straightforward or complex as a regulatory proposition, the science is serious.

Stephen Robinson from the Quadram Institute introduced Bioscopic, a UK spin-out developing therapeutic candidates from infant microbiota bacteria – specifically Bifidobacterium-derived compounds, not live bacteria themselves. Their lead, BIOS-001, is in preclinical development for immuno-oncology, showing around 50% reduction in tumour burden in breast cancer mouse models via dendritic cell activation and CD8 T-cell engagement. The active molecule appears to be a surface sugar from Bifidobacterium pseudocatenulatum. Still preclinical, but a genuinely different angle on what microbiome-derived therapeutics can look like.

Peter Holme Jensen of Cambiotics presented something that felt more consumer health than pharma, but which raised questions worth taking seriously: gut bacteria capable of accumulating PFAS – the ‘forever chemicals’ present at measurable levels in most human populations. Their publicly reported strains show bioaccumulation of 25-74% of PFAS within minutes. A first human trial is planned for 2026. Whether or not this becomes a mainstream therapeutic direction, the underlying question – what else are commensal bacteria doing to environmental contaminants in our gut? – is a legitimate one.

Shelly Buffington from Baylor College of Medicine Ventures presented work tracking the infant microbiome across the first six months of life and linking specific microbial and metabolite profiles to neurodevelopmental outcomes at age two. In a cohort of 35 infants with 123 faecal samples and Bayley scores at two years, her team identified a predictive metabolite and then designed a microbial intervention to increase it – achieving more than a three-fold increase in the target metabolite and observing behavioural improvement in animal models. A reminder that the earliest developmental windows may be where microbiome intervention has the most to offer.
On the agritech side, Thomas Veje Flintegaard from Collaborome presented soil bacterial consortia being tested as biopesticides against fungal crop disease – with yields of up to 25% higher under fungal pressure in field trials. Not the core focus of most people in the room, but a useful reminder of where the broader microbiome toolkit is heading.

Two days in Copenhagen. Thirty-plus sessions. The common thread was not a single breakthrough, but a field steadily building the evidence base it needs to move from promising to proven – across therapeutics, prevention, nutrition, and now further afield than most people in the room had perhaps expected.

From our side at Biose, the manufacturing takeaway is the one we hear most consistently from our partners: the path from a promising strain to a stable, scalable drug substance is longer and more complex than it looks from the outside. The Biose-MRM Health story is one illustration of what that journey looks like when it goes well.

If you were at the Forum and want to compare notes, or if you are working on an LBP programme and want to discuss what the science means for your manufacturing strategy, feel free to reach out.

The 2026 Microbiome Times Partnering Forum Europe was held in Copenhagen. For more information: microbiomeforum.com

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Switching from a liquid medium to sold agar plates in the early 1800s was a significant change for microbiology sciences. Operational standardisation of plate counting evolved at such a rapid pace that it quickly became the default quality control (QC) method, allowing for better bacterial isolation and quantification, and significantly decreasing contamination rates in bacterial purification processes.

Colony-forming units (CFU) counting constitutes a simple method widely found in current standards, which explains why it remains the current practice in Live Biotherapeutic Product (LBP) quality control protocols throughout the production and scaling processes worldwide – despite it first being introduced over 200 years ago.

However, despite its multiple benefits, CFU-counting methodologies have inherent constraints (time and strain-wise) that have become particularly obvious with the rise of modern microbiome products such as ‘Next Generation Probiotics’ (NGP).

Some of the limitations of CFU-based enumeration include:

• Slow iteration: days-long incubation delays decisions during process development and troubleshooting.
• Undercounting or biased readings: some bacteria can enter a dormant but metabolically active state that will not form colonies in that specific culturing condition but might reactivate at a later stage. This state is known as ‘viable but not culturable’ (VBNC). As these bacteria do not properly form CFU, they can get lost throughout the isolation process, leading to falsely ignoring their presence in the original mix.
• Not fit-for-purpose for ‘next-generation’ strains: strict anaerobes and novel gut commensals can be difficult to culture consistently; in this context CFU counting becomes unsuitable as the sole enumeration method.

Many NGP candidates are based on strict anaerobe strains, with demanding growth requirements; industrial production steps (concentration, freezing, drying, storage) can push cells into VBNC states. When strains are difficult to culture, and timelines are tight, the time needed to cultivate a colony can easily become a bottleneck.

At Biose Industrie, we understand this challenge, and as a CDMO specialising in both LBP and NGP development, we are deeply committed to bringing pharmaceutical-grade manufacturing discipline to difficult-to-culture organisms and complex production workflows, all the while staying abreast with the state-of-the-art technology.

Modern microbial characterisation: AFU technology

While CFU-counting is the gold standard in microbial-based therapeutics regulatory standards, it is not the only available technique for bacterial characterisation. In the 1990s, flow cytometry (FCM)-based bacterial analysis arose as a faster alternative to CFU-counting, which bloomed in the 2000s with the development of different dyes used to discriminate between live and dead bacteria.

FCM bacterial characterisation has arisen as a robust alternative to overcome most of the limitations faced by CFU-counting for NGPs, especially since its international recognition in the regulatory landscape by ISO 19344 IDF 232 for the quantification of active and/or total bacteria in probiotic products.

According to this regulation, cells are primarily stained with fluorescent dyes that allow for live/dead state discrimination, after which they are analysed in a one-by-one manner as they pass through a laser. Further processes of fluorescent-based separation split active/intact cells from damaged/non-active cells. As the main goal is the identification and quantification of live cells, these are often referred to as Active Fluorescent Units (AFU).

Biose’s approach to become the reference in NGP manufacturing

After more than 9 years as a leading CDMO for microbiome therapeutics, we aim to offer each market segment what it requires:

• For LBPs (drug/medicinal products with microorganisms as active ingredients), bacterial specificity and quantity are critical points. Overestimation of the bacterial concentration or potential uncertainty about the mix composition becomes a drug potency issue, alongside a potential safety issue. That is why, following international regulation (FDA guidance), manufacturing is tightly controlled using CFU-based techniques. The FDA, however, does propose implementing alternative methods (see USP 1223).
• For NGPs (dietary/food supplements with microorganisms as active ingredients), the product is expected to be dominated by the intended microorganism(s), which is why ISO methodology can be acceptable as long as the QC systems effectively control for the expected purity and the method is adequately validated.

How we include AFU in our processes

AFU fits naturally across three manufacturing phases:

1. Upstream growth & scale-up: providing rapid confirmation that concentration and population “fitness” are on track to continue with the seed train process.
2. Downstream recovery & concentration: bacterial collection and concentration are known to severely affect bacterial viability and integrity. Applying AFU-based enumeration between the independent steps is paramount when identifying potential bottlenecks in optimisation processes, improving overall bacterial recovery rates.
3. Formulation & finishing: using AFU enumeration to track how the active fraction survives the drying stage and evolves during storage allows for the improvement of shelf-life and process robustness.

Operationally, the goal is efficiency with confidence. Clients can request AFU tracking between steps to confirm targets and verify final batch quality, but they can also ask for AFU application to multiple small samples to confirm a given batch is truly consistent.

At Biose, we have a strong commitment to providing the best quality standards while making use of the most innovative technology. This is why we have incorporated AFU bacterial characterisation for several strains among our services to ensure our clients have more accurate and faster feedback times, smaller sampling burdens, and an instantaneous with higher accuracy in-process control. We are now leveraging our deep expertise in microbiome products to optimise the QC processes of NGP production and scaling, so our clients can continue to innovate in the field, knowing their products are compliant with the latest regulatory requirements.

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Despite a continued challenging economic environment across biotech, the past 12 months have brought meaningful progress for the microbiome field. We have seen encouraging developments in microbiome therapeutics, alongside impressive resilience from companies committed to addressing unmet medical needs for patients.

At the same time, new patterns are emerging with the rapid development of — and growing demand for — Next-Generation Probiotics.

Here at Biose Industrie, I am proud of how our teams navigated these dynamics while delivering strong results. In 2025, we onboarded more than 200 new client strains across our U.S. and EU facilities, produced 450 certified active-substance batches, and delivered 250 certified finished-product batches.

With early signs of renewed investor interest and new European public-funding initiatives building momentum into 2026, I am optimistic that our industry is preparing for a new wave of opportunity — not only next year, but well beyond.

Clinical and Regulatory Milestones

If there is one feature that has truly defined 2025 for the microbiome field, it is the strength of the Phase II and III therapeutic readouts.

MaaT Pharma’s Xervyteg® (MaaT013) demonstrated a three-fold increase in one-year survival among patients with GI-aGvHD in the pivotal ARES Phase III trial creating waves for the microbiome field and making headlines globally. These results supported submission to the EMA under an MAA — positioning Xervyteg® as potentially the first microbiota therapeutic in hemato-oncology.

Siolta Therapeutics announced positive topline results from the Phase 2 ADORED study of STMC-103H, its lead oral microbial therapy. Infants completing one year of treatment showed a clinically meaningful reduction in the risk of developing atopic dermatitis and food allergy, including a 77% reduction in physician-diagnosed food allergy, with consistent benefits across secondary endpoints.

In the metabolic space, Bloom Science reported that BL-001, an investigational oral therapy, achieved statistically significant placebo-adjusted weight loss at 28 days in a Phase 1 study.

We also saw compelling long-term data published in Nature Communications. In a cohort of adolescents originally enrolled in an FMT study eight years earlier, participants in the treatment arm were, on average, 11 kg lighter than placebo recipients four years post-intervention.

Looking ahead, 2026 is poised to be a milestone year, with anticipated topline data from Vedanta’s Phase 3 RESTORATiVE-303 study, potential EMA marketing authorization for Xervyteg®, and possible FDA accelerated approval for Infant Bacterial Therapeutics’ IBP-9414 in the United States.

In addition, the EMA’s positive Pediatric Investigation Plan decision for AOB Pharma’s B244 in atopic dermatitis and pruritus enables AOBiome to move toward an initial MAA submission following completion of its pivotal and extension studies.

Finally, Exeliom Biosciences continues advancing multiple Phase 2 programs evaluating a Faecalibacterium prausnitzii-derived LBP to prevent post-surgical recurrence in Crohn’s disease and as an adjuvant across several oncology indications with data expected in early 2027.

Promising Financial Indicators

2025 also brought encouraging financial signals for the microbiome and next-generation probiotics sector:

MRM Health successfully closed a €55M Series B round — a landmark raise that drew widespread attention across the European biotech ecosystem. SNIPR Biome likewise completed its Series B at $35M, bringing its total funding to more than $90M to continue advancing its pipeline.

The acquisition of The Akkermansia Company by Danone in July marked a significant inflection point for the next-generation probiotics market, underscoring growing strategic interest from major consumer health players.

Beyond these transactions, we observed several early-stage financings as well as two announcements with important implications for the years ahead:

• Novo Nordisk and Novonesis entered into a partnership to explore the role of the gut microbiome in metabolic health — with the dual aim of informing product development and identifying predictive biomarkers for obesity prevention.
• Wellcome Leap launched the FORM (Foundations of a Resilient Microbiome) program — a $50M initiative designed to investigate the causal link between early-life microbiome dysfunction and neurodevelopmental conditions such as autism.

Together, these developments reinforce gr owing investor confidence and highlight the strategic relevance of microbiome science across pharma and consumer health.

The EU Biotech Sector

As the CEO of a company with facilities in France and the US and Treasurer of the European Microbiome Innovation for Health, I have been well-positioned over the past years to monitor both the EU and US markets closely.

The EU has traditionally controlled the biotech market through tighter regulations and reduced market exclusivity periods, a strategy that inadvertently signalled a ‘hostile’ environment for R&D and drove significant capital migration to the United States. This ‘production drain’ was starkly validated by the recent Draghi report, which identified the chronic investment gap as a primary threat to European stability within the biotech industry.

However, it is great to see important steps being taken that will greatly increase the EU’s competitive position moving in to 2026 with the announcement of The Biotech Act and the €10 billion BioTechEU initiative. By introducing regulatory sandboxes, simplifying clinical trials, and creating a massive capital injection, the European Commission aims to strengthen the EU biotech sector with the objective to restore a regulatory and industrial environment capable of sustaining innovation within Europe.

The Consolidation of Live Biotherapeutics Products & Next Generation Probiotics

To properly understand the current microbiome landscape, it’s essential to understand how it now spans two converging and increasingly interconnected sectors:

Live Biotherapeutic Products (LBPs) are fully regulated biological medicines developed under stringent GMP conditions and supported by advanced CMC packages, and multi-phase clinical trials.

Next-Generation Probiotics (NGPs) by contrast, are positioned within the Consumer-health space but are increasingly underpinned by strain-specific clinical data, multi-omics characterisation, and precision formulation strategies. Companies such as Pendulum, Design for Health, Verb Biotics, and Clostra Bio are generating robust real-world datasets feeding therapeutic discovery.

Increasingly, microbiome companies are considering a dual strategy, leveraging their expertise in LBPs to launch NGPs. This approach allows companies to generate early revenue and gather solid scientific evidence while navigating the lengthy pathway for biological drugs.

Despite distinct regulatory frameworks, both LBPs and NGPs rely on shared biology and industrial foundations such as fermentation and formulation technologies, analytical methods, manufacturing infrastructure, supply-chain management, and downstream quality and data systems. This convergence is giving rise to a unified industrial ecosystem, and ample market opportunities for Biose. making NGPs a primary focus area for our company’s strategy moving forward.

It’s all about the Science

Albeit I am writing this letter as Biose’s CEO, I am a scientist at heart and especially excited to see recent advances in both basic and population-level research.

What were once viewed largely as associative “gut–organ” links are now increasingly supported by mechanistic evidence, moving the field from correlation toward causality.

Studies published this year have shown that specific gut-derived metabolites do not merely circulate through the body, but actively influence immune function in peripheral tissues such as the skin and lungs, effectively acting as systemic signalling molecules.

At the same time, researchers are beginning to characterise microbial communities in biological sites that were long considered sterile or biologically marginal. Emerging data indicate that low-biomass environments — including intratumoral niches and the ocular surface harbor distinct microbial signatures capable of modulating disease progression and influencing responses to existing therapies.

As research increasingly moves beyond the gut, women’s health has emerged as one of the most compelling areas where microbiome science is now delivering robust, mechanistic insights.

Over the past years, several academic groups and industrials— including work conducted by Seed Health, Freya Biosciences, Biocodex, and teams at Massachusetts General Hospital — have significantly contributed to elevating vaginal microbiome research to the level of global health priorities, with initiatives that have reached major institutional stakeholders such as the Gates Foundation.

Recent publications have moved the field beyond descriptive abundance profiling, demonstrating how Lactobacillus crispatus–dominated ecosystems form structured, protective biofilms that actively reinforce epithelial integrity and limit pathogen invasion. These findings provide a mechanistic framework explaining why L. crispatus–rich microbiota is consistently associated not only with protection against bacterial vaginosis, but also with improved reproductive and gestational outcomes.

In parallel, growing clinical and translational evidence continues to strengthen the rationale for strain-specific approaches in women’s health. Recent peer-reviewed studies published in 2024–2025 have further documented the functional properties of Lacticaseibacillus rhamnosus Lcr35, including its capacity to modulate host–microbe interactions across multiple indications, from mucosal protection to systemic metabolic and inflammatory pathways, moving away from generic probiotic concepts toward well-characterized, clinically validated strains.

Conclusion

The microbiome field is coming out of a transition period, being defined by in-human data, industrial maturity, and clear regulatory pathways. With some important milestones expected and signs of a recovering financing landscape I remain bullish entering 2026.

At Biose we look forward to another year of continuing to support leading microbiome companies around the world with their mission of developing the next generation of microbiome products for patients with unmet medical needs.

Supporting our clients with this mission is the very foundation of our business and as such, I’d like to close this year’s wrap-up with the words of Adam Wilkinson, Vice President of Pre-Clinical Development at Microbiotica:

“Working in partnership with the Biose team, we are delighted to have successfully navigated the challenges of process development and scale-up of two LBPs in parallel. Manufacturing of biologics can be challenging at the best of times, but the development of multiple processes to be scaled up to cGMP standard poses significant challenges, and seamless open collaboration between our project teams has been essential to success”

Wishing everyone a very Happy New Year filled with joy and success.

Yours Sincerely,

Adrien Nivoliez

Chief Executive Officer, Biose Industrie

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Working to scale microbial strains from the gut microbiome can be a challenging feat. Selecting the right culturing conditions requires extensive experience, the right equipment, and a finely tuned approach. For some, without the right know-how it might even seem impossible.

Now imagine the challenge of having to simultaneously scale two products consisting of over 17 separate strains…which is exactly what Microbiotica had to do with it’s two live biotherapeutic programs: MB097 and MB310.

Biose had the privilege of working with Microbiotica to overcome this challenge and get these programs to clinical scale for Phase 1b clinical trials.

Microbiotica precisely links bacterial signatures to clinical outcomes

Microbiotica is a spin-out from the world-renowned Wellcome Sanger Institute, drawing on 10 years of microbiome research experience. The compositions of their defined live biotherapeutics are selected from bacterial signatures found in successful clinical outcomes in defined patient groups.

MB097 boosts immune checkpoint inhibitor response and MB310 modifies ulcerative colitis

• MB097 is a nine strain LBP, made up of strains identified in clinical responders to ICI in multiple melanoma patient datasets. In mice tumour models combined anti-PD1 and MB097 therapy shows significantly higher survival rates compared to anti-PD1 therapy alone.

• MB310 is an eight strain LBP composed of bacteria identified from patients who responded well to FMT in a placebo-controlled Ulcerative Colitis trial. Assays using human immune cells and epithelial cell lines suggest that MB310 may work by promoting intestinal barrier repair and inducing immune homeostasis to modify the harmful proinflammatory responses in the gut of UC patients.

The journey to scale was resource intensive and difficult

When Microbiotica approached Biose Industrie, they needed to scale-up these two candidates ready for their respective phase 1b clinical trials. The collaboration was challenging, but ultimately successful.

During transfer of materials from client to Biose it was identified that the process needed to be adapted for scale-up and GMP.

Careful tweaking and iterations led to a hard-to-scale microbe achieving exponential growth

One key step in this was figuring out how to culture a completely novel strain discovered by Microbiotica, MI10. This obligate anaerobic strain showed very little growth under initial culturing. Microbiotica and Biose worked closely together, running 12 production runs over a 5-month period. The process required assessment of multiple variables including raw materials, culture conditions, anaerobic gas, and process parameters to get it right. Eventually, the collaboration identified a robust and reproducible process, ready for clinical batch manufacturing

Biose integrated brand-new equipment to ensure scale could be reached

Another difficulty Biose faced in scaling-up the production was that some of the strains were not growing under the existing anaerobic cabinets. Biose took action to integrate brand new equipment into the facility to overcome this. This included the integration of new solid plates in a temperature regulated and hygrometric environment, which allowed the growth and handling of these strains.

Biose and Microbiotica overcame the manufacturing challenges and are ready for the Phase 1 trials

Through a close working relationship with Microbiotica, extensive experience in microbial manufacture, and an agile approach to getting these candidates ready for clinical batch scale, the manufacturing projects for MB097 and MB310 have been a success. Both clinical batches are ready for the Phase 1b European clinical trials, produced by Biose’s and Microbiotica’s jointly created manufacturing process.

Biose looks forward to the clinical read-outs from both trials and is excited about its continued partnership with Microbiotica

Having trouble scaling up your live biotherapeutic product? Contact us for a chat here.

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At Biose Industrie we are proud that half of our employees are women – watch the video below to hear their thoughts on gender challenges within biotech.

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2023 was a tough year for everyone in drug development, including us in the microbiome field!

Despite the challenges presented by the financial markets and investment landscape, I was proud to see how microbiome biotechs persevered and what many achieved. 

Whilst we saw several biotechs downsize/close down their microbiome operations in 2023 (Finch Therapeutics, Seres Therapeutics, Evelo Biosciences), we also saw some promising investment rounds, (Eligo Bioscience’s $30M, Vedanta’s huge $106.5M and Freya’s $38M) and acquisitions such as Boehringer Ingelheim’s acquisition of T3 Pharma. 

These successful fundraisers should serve as beacons of promise for the industry, and act as examples of great leadership, science, and adaptability to market forces.

Of course, we were all happy to hear 2023’s many positive clinical read-outs and the market authorization of Seres Therapeutics’ donor-derived product, VOWST, which along with REBYOTA’s approval in 2022, demonstrated commercialized microbiome therapeutics as a reality. And VOWST’s reported net sales of $7.6 Million sales in Q3 demonstrated commercialized microbiome therapeutics as a revenue-generating reality too!

I was particularly excited to see Vedanta’s and MRM Health’s positive clinical readouts in 2023, which are both paving the way for the next generation of microbiome therapeutics!

So, what can we expect 2024 to have in store?

On the investment side, with inflation expected to decrease in the coming year, I predict a surge in investment within the biotech sector which will positively impact the microbiome biotech landscape. With government initiatives set to support the growth of innovative biotech markets, like those in South Korea, and France, the microbiome field is sure to see a boost in 2024. 

Clinical read-outs will also play a role in boosting economic interest in the microbiome sector.

As the field gears up for the next generation of microbiome therapeutics, key read-outs will include

• Sweden’s Infant Bacterial Therapeutic’s Phase 3 candidate indicated for infant necrotizing enterocolitis, expected in Q2;
• Everimmune’s Phase 1/2 findings for their immunotherapy-enhancing candidate Oncobax AK, expected in Q4; and
• MRM Health’s Phase 2/3 development  trial forMH-002.

Other clinical read-outs I am excitedly anticipating include Biomica, Bloom Science, and Siolta Therapeutics.

Regarding regulation, I do not expect any significant change, rather I expect 2024 to be a year of regulatory stabilization. The US FDA’s growing number of IND dossier approvals will continue to clarify expectations for manufacturing, and testing. Whilst the SoHO regulation will clarify material origins, GMP requirements for developing LBPs will remain unchanged.

The role of Biose Industrie in the future of the field

CDMOs, like Biose Industrie, play a crucial role in powering the microbiome drug development field by ensuring timely manufacturing, and precise regulatory compliance.

Our 2023 achievements, including a significant increase in production capacities and analytical capabilities, position us to lead the field in 2024.

Biose Industrie has strategically invested in enhancing its facilities and capabilities. Key investments include a new manufacturing line for drug substances, scaling up to 5000L, and expanded drug product manufacturing. In 2023, the company produced an impressive number of capsules, sachets, and tablets. Additionally, Biose has bolstered its analytical capabilities, conducting over 130,000 in-house analyses across various disciplines, crucial for IPC, release tests, and stability studies. The company’s technological advancements now allow the manufacturing of over 250 strains, catering to both oral, vaginal applications and new adventures into topical and lung delivery. Furthermore, Biose has continued to elevate its analytical technology with continuous developments in its analytical methods developments and QC laboratory and expanded these capabilities at its Boston applied Tech transfer laboratory.

Biose’s 2024 strategy is focused on anticipating market needs by expanding our industrial and analytical capabilities. Our acquisition of new land (an additional 7000m² to add to our existing 45 000m² in total at our center of excellence in France) for facility expansion solidifies our position as the world’s largest LBP GMP CDMO, ready to meet the growing demands of the microbiome sector.

Best Regards,

Adrien Nivoliez

The post The Year Ahead for Microbiome Therapeutics – Food for Thought for 2024 appeared first on Biose Industrie.

Head of Programs for LBP Development & Manufacturing

A few weeks back, Nadine, Richard, Adrien, and I had the pleasure of attending the Boston-based microbiome drug development conference “Microbiome Connect USA 2024”. Spanning 3 days the event promised the chance to connect with the microbiome field, and learn about its latest innovations, and it did not disappoint!

Women’s & Infant Microbiome Pre-day

Arriving at the conference, November 14^th, we attended the Women’s & Infant microbiome pre-day, a day of talks and panels dedicated to the work being undertaken to improve women’s health treatments and outcomes for infants. The talks ranged from regulatory considerations for microbiome-based technologies in paediatric use from the FDA to discussions on single-strain vs multi-strain approaches for vaginal dysbiosis.

Caroline Mitchell’s presentation was a personal highlight of the pre-day, providing a detailed analysis of microbiome interventions for bacterial vaginosis (BV). Mitchell described the lack of efficacy and innovation for existing bacterial vaginosis treatments, pointing out that options have remained stagnant since the 1980s, with antibiotics being the main treatment. Antibiotic usage leads to high rates of BV recurrence and rarely restores the vaginal microbiota to a healthy L. Crispatus dominance, Mitchell explained. The presentation explored a range of research projects which are developing antibiotic, microbiome-modulating alternatives, mentioning work by her eponymous lab as well as the Kwon Lab, Freya Biosciences, and the VMRC. It was exciting to see Biose’s partnership with the VMRC to develop an L. Crispatus derived LBP for BV be mentioned. The LBP is currently being tested for safety and efficacy in a phase 1 trial with results expected in 2025.

Day One – A Post Regulatory Approval Microbiome Market

On the morning of Day 1, we entered the buzzing conference room where Vedanta kicked off the official day one with a presentation on the future of the microbiome drug landscape. Dan Couto, Vedanta’s Chief Operating Officer, explored the field’s recent events including the closure of several developers, significant investments, and M&As. This led nicely into a panel discussion with MTIG, Rebiotix, BiomeBank, and Seres Therapeutics who discussed the field’s future in the context of the recent regulatory approvals.

Following the morning session, the agenda split into two tracks: “Emerging Pipeline & Therapeutic Updates” and “Bioprocessing & Data Strategies”. Emerging Pipeline & Therapeutics Updates covered a range of modalities for targeting a range of microbiomes, including a multi-strain product for targeting the lung microbiome from Biose partner Alveolus to a small molecule regulator of the gut microbiome by Axial Therapeutics. On the other track, Bioprocessing & Data Strategies presentations focused on the manufacturing side of microbiome drug development exploring CMC and cGMP manufacturing considerations and challenges, including one I was privileged to give on Biose’s world leading expertise in drug manufacturing.

My presentation described our global customer base, and how we leverage EU and US based facilities to ensure a close working relationship with our clients. I explained our end-to-end services, which extend from WGS data analysis for strain identification to regulatory support for CTD filing. A key focus of the talk was a scale-up case study on one of our clients. This project begun at our technology transfer facility in Boston. Where we worked to scale an extremely oxygen sensitive microbe from our clients’ flask-scale up to a 2000L reactor. This journey took several iterations, working up increasing scale and regulating the process until the microbe grew reliably and robustly. This kind of speciality work is only possible due to our extensive experience working with microbes, beginning in 1951!

The day ended with a screening of “Designer Shit”, followed by a panel discussion of the film. The movie followed the journey of Director Saffron Cassady, as she examined the world of faecal microbiome transplantation as a potential treatment for Ulcerative Colitis.

Day Two – Money, Microbiome and Manufacturing

At a time of uncertain investment for the biotech field at large, the morning panel of day two felt appropriate, focusing on what biotechs can do to engage investors and ensure their financial future in the market. Joyance Partners, Seventure, and Corundum Systems Biology all gave their input on this question giving a rounded view of investment strategy to the room full of microbiome researchers.

Once again, the program split into the two tracks, with Emerging Pipelines and Therapeutics continuing to showcase the diverse modalities biotechs are using to improve health outcomes, this time broadening to include clinical reads-outs for indications including rare liver disease, eczema, and cancer. Bioprocessing & Data Strategies shifted its focus to cover the “data” side of the track, with talks on multi-omics, proteomics, and biomarker development.

After three days of meeting with existing and new clients, listening to leading researchers discuss their work, the event came to a close. We all had a wonderful experience at Microbiome Connect and we cannot wait to return next year.

Presentation highlights:

Presentations we particularly enjoyed included:

• “Ambition to Provide Premature Infants With Approved Medication” – Robert Molander, COO, Infant Bacterial Therapeutics. Molander opened by describing the market opportunity for an effective infant necrotising enterocolitis (NEC) treatment, highlighting the high economic burden of the disease along with the high frequency. Their phase 3 candidate IB-9414 leverages reuteri to reduce inflammation and prevent dysbiosis in premature infants to prevent NEC development. Their phase 3 is currently the largest preterm randomised trial to date, IBT expect results for IB-9414 in 2024.
• “Development of AX -5006, a Small Molecule Inhibitor of CsgA Aggregation as a Potential Disease -Modifying Treatment for Parkinson’s Disease” – Becca Senter, Ph.D, Vice President, Head of Preclinical Research and Development, Axial therapeutics – Senter discussed Axial’s work on gut-brain candidates including small molecules to target autism-associated irritability, parkinson’s disease, and oncology. The presentation focused mostly on their lead candidate, AX-5006. Senter presented compelling results from Axial’s preclinical work which indicated that AX-5006 inhibits CsgA aggregation in mice models to alleviate Parkison’s motor-related symptoms. AX-5006 plans to enter the clinic in 2024.
• “AI-enabled, Metabolomics-based Drug Discovery Engine for Inflammatory Disease” – Hannah Wastyk, CEO, Interface Biosciences – Wastyk introduced Interface’s platform of AI-powered drug discovery, which combines the cultivation of important microbes in a proprietary growth media with an AI tool “CausalVision” to screen for microbe-produced metabolites with casual relationship to disease phenotypes. Interface’s first candidate is a topical Rx small peptide, RC13, which targets atopic dermatitis. Wastyk presented pre-clinical results which showed improved wound-healing in a scratch model and in vivo antibiotic activity.
• “Reinventing Humanity’s Relationship with Microbes” – Cheri Ackerman, CEO, Concerto Biosciences. Ackerman opened with a description of Concerto’s kChip technology, a high-throughput discovery platform for measuring microbe-microbe interactions. Ackerman explained the application of the kChip to discover a new candidate, ENS-003, to target vulvovaginal candidiasis. The LBP will modulate albicans, by down-regulating it’s virulence and shifting it to a commensal state. Concerto are currently screening the top performing bacterial combinations which regulate C. albicans.

Preclinical showcase presentation – Dr. Egle Katkeviciute, CSO and co-founder, Recolony – Katkeviciute presented their work to develop two anti-cancer candidates. The first is an LBP, RCLBP01, based on commensal bacteria which modulates T-cell activity to aid tumour clearance. Due to the approach only using commensal bacteria the therapeutic has high tolerability compared to other anti-cancer approaches. The company will be filing for an IND in 2025. Along with this LBP approach, Recolony are also developing a small molecule based on a RCLBP01-produced metabolite. Recolony forecast filing an IND for their small molecule late 2026.

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South Korea has emerged as a leading hub for innovative microbiome research and development, with a thriving biopharmaceutical industry and cutting-edge research institutions. In this article, we will highlight seven South Korean microbiome developers that are poised to make significant advancements in 2024.

Korean Microbiome Developers

1. Genome & Co

Located in Seongnam-Si, Genome + Co is a global biopharma company which develops microbiome pharmaceuticals, along with consumer products and novel immune checkpoint inhibitors. Their discovery platform, GNOCLE™, combines a library of real-world clinical data, with multi-omic analysis and in vitro/vivo assays to identify novel microbiome targets.

Genome & Co’s pipeline consists of programs including stomach cancer, biliary tract cancer, autism spectrum disorder, infertility, and cancer rash. Collaborators for these programs include Merck, LG Chem, MSD, and Genome + Co’s subsidiary: Scioto Bioscience.  Genome & Co’s lead candidate, Gen-001, is a phase 2 single strain live biotherapeutic (LBP) to treat stomach cancer and biliary tract cancer. In May 2023, the company reported positive results from interim analysis of their phase 2 trial for Gen-001 combined with Avelumbab to treat stomach cancer. The company expects the full data to be released in late 2023, and stated they are seeking a licensing agreement for the candidate.

2. ImmunoBiome

ImmunoBiome is a North Gyeonsang Province-based biotech company seeking to develop novel LBPs to treat incurable disorders. In 2020, the company signed a CDMO contract with Biose Industrie. ImmunoBiome has two candidates listed on their public pipeline, with 10 domestic and 5 international patents to date. Their lead candidate, IMB001, is a patented single strain LBP with unique polysaccharides (RHP) on its’ surface which targets human melanoma and colon cancer. IMB001’s anti-cancer effects are facilitated through T-cell activation, sequestering of iron ions in the tumor microenvironment, and synergetic effect with immuno-oncology drugs. Their second candidate, IMB002 is a patented single strain LBP with different unique polysaccharides on its’ surface (CSGG) which targets inflammatory disorders (IBD, RA, Orphan disease).

3. CJ Biosciences

Founded as an independent subsidiary of CJ CheilJedang’s Red Bio, CJ Bioscience utilises it’s Ez-Mx platform to develop LBPs across a range of diseases. CJ Biosciences have 17 programsspanning the immune-oncology, gastrointestinal, liver, and neurological categories. In March 2023 CJ acquired 11 drug candidates from the UK-based biotech 4D-Pharma. The company’s lead candidate CJRB-205 is in phase 2 and targets irritable bowel syndrome.  In December 2022, CJ Biosciences’ submitted phase 1 clinical trial protocols for CJRB-101, an immuno-oncology asset to target solid tumours.

4. AtoGEN

Working to develop drugs, and functional food materials, the 2012 founded AtoGEN have 6 programs in development. Their pipeline consists of drugs to target bacterial vaginosis, cancer cachexia, NASH, asthma, and lung disease. In July 2023, AtoGEN completed a phase 1 clinical trial for Labthera-001, a single strain candidate, targeting bacterial vaginosis. The randomised control trial found 0 serious adverse events across 24 treated women. The trial protocol for this candidate described the drugs mechanism as temporary colonisation of the vagina to encourage a more normal microbiome.

5. GI Biome

Founded in 2018, GI Biome is a drug developer based in Seongnam-si, which aims to “lead the future of disease treatment by developing innovative microbiome” therapies.  GI Biome has 4 programs in its development pipeline, developed from their “GI-SCOVERY” platform, which include targets such as: cancer, metabolic disease, autoimmune disease, and inflammatory disease. In June 2023, their lead candidate GB-X01 combined with bevacizumab, a drug for colorectal cancer entered the clinic.  This single strain candidate has shown anti-tumour effects in a mouse model. The trial will be operated as a decentralised clinical trial. Biose are working with GI Biome to manufacture GB-X01.

6. HealthBiome

Based in Daejeon, and founded in 2017, Healthbiome is a bioventure company specialised the research and development of strict anaerobes as LBPs. Currently, all candidates are in preclinical stage and target the indications IBD, dementia, sarcopenia, and cancer. Two of HealthBiome’s candidates are single strain Akkermansia muciniphila strains (for cancer, IBD, and sarcopenia), and the other is a strain of Agathobaculum butryiciproducens (for dementia). HealthBiome has established its own GMP factory for the manufacture of their LBPs.

7. Liveome

Established in 2021, Liveome, a subsidiary of Medytox, are working to develop next-generation microbiome therapeutics. Liveome have 6 programs in development, targeting gastrointestinal disease, solid cancer, transplant related disease, and autoimmune disease. LIV001, Liveome’s lead candidate, targets gastrointestinal disease and entered the clinic in September 2023. In January 2023, Liveome won a patent for their engineered-LBP platform in Japan, which utilises gene editing to impart specific therapeutic function onto bacteria.

Conclusion

South Korea has positioned itself as a global leader in microbiome research and development, driving remarkable advancements in the field. As we look ahead to 2024, it is clear that South Korea will continue to shape the future of microbiome-focused innovations, furthering our understanding of the intricate relationship between the microbiome and human health. Biose will continue to contribute to and engage with South Korea’s microbiome industry as it furthers itself as the global microbiome CDMO.

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