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By Adrien Nivoliez

Chief Executive Officer, Biose Industrie

As the year draws to a close today, I’d like to reflect on the microbiome landscape in 2024:

Unfortunately, conditions remained particularly challenging for pre-revenue biotechs raising funds for microbiome-based therapeutic programs, and this was felt by the market with several programs discontinued, a handful of biotechs closing their doors, and even some microbiome industry-specific service providers shutting down.

Despite this, 2024 was an extremely significant and historical year for the field as we had indisputable scientific evidence that defined Live Biotherapeutics work!

Infant Bacterial Therapeutics’ Phase 3 readout demonstrated a 27% reduction in all-cause mortality for infants with necrotizing enterocolitis. Beyond its significance for the market as potentially the first FDA and EMA-approved single-strain LBP, Infant Bacterial Therapeutics’ product saves babies’ lives!

This, for me, is far more important than any short-term hurdles our industry is currently facing and is what should also be more important for everyone else too. At the end of the day, it is now a fact that defined LBPs have the potential to save lives, and IBT’s Phase 3 study comprising 2,153 premature infants is testimony to just that.

Of course, there were other important milestones reached by a number of companies progressing microbiome science in and out of the clinic, some sizeable fundraises, new spin-outs, and important clinical data. Furthermore, it was great to see some very sizeable public investment commitments.

Below, I share some highlights throughout 2024 and some of the things that I am particularly excited about coming up in 2025:

Fundraising in the Microbiome

Despite 2024 being a difficult year for early-stage biotechs, there were some significant investments across the microbiome field, such as:

• $12M raised by Kanvas Biosciences, Siolta Therapeutics, and Z-Biotics.
• A $10.4M strategic grant from the Bill & Melinda Gates Foundation into Freya Biosciences.
• £27M raised by EnteroBiotix.
• Additional funding rounds: $9M for Holobiome, $4.2M for Ancilia Biosciences, and $2M for Neobe Therapeutics.
• €20M funding for SNIPR Biome from the European Innovation Council.

On the public funding side, the Dutch government allocated €200 million specifically for microbiome research through the establishment of the Holomicrobiome Institute.

M&A and Partnerships in 2024

2024 also witnessed strategic mergers and acquisitions:

• The formation of the Cmbio brand through the merger of Clinical Microbiomics, CosmosID, MS-Omics, DNASense, and Microba’s Research Services Unit.
• Probi’s acquisition by Symrise.
• Lactobio’s acquisition by L’Oréal.

One standout partnership was between the Novo Nordisk Foundation, Wellcome Trust, and the Bill & Melinda Gates Foundation, with a $300M commitment aimed at advancing global health equity. Notably, the microbiome was highlighted as a key area of focus for addressing nutritional and immunological health challenges.

Clinical read-outs

As already mentioned, Infant Bacterial Therapeutics (IBT) reported positive Phase 3 results for their candidate targeting infant necrotizing enterocolitis, showing a 27% reduction in all-cause mortality. If approved, this would represent the first FDA approval of a single-strain Live Biotherapeutic Product (LBP).

• Maat Pharma presented positive 18-month data for MaaT013, showing a clear overall survival advantage in acute Graft-versus-Host Disease (aGvHD) for 140 patients at the 2024 Annual congress of the European Society for Bone and Marrow Transplantation. As we enter 2025, I am particular excited for MaaT Pharma’s official phase 3 Ares read-out!
• MRM Health announced positive Phase 2a results for pouchitis and ulcerative colitis, significant indications with substantial market potential.
• EnteroBiotix reported successful Phase 1b results for their program in liver cirrhosis.
• Seres Therapeutics shared positive Phase 1b safety and clinical results.

Additionally, during the Microbes in Women’s Health Congress in Copenhagen (April 2024), I had the opportunity to present alongside leading KOLs Caroline Mitchell and Jacques Ravel on the development of two multi-strain LBPs, LC106 and LC115, targeting bacterial vaginosis (BV). These drug products, each containing multiple Lactobacillus crispatus strains, were designed based on insights from stable vaginal microbiomes.

2024 also saw two landmark Nature publications:

• Eligo Bioscience’s study on genetically modifying bacteria in the gut with nearly 100% efficiency.
• Immunobiome’s research on microbiome-based cancer therapies, focusing on iron deprivation in the tumor microenvironment.

Some other promising 2025 clinical read-outs I am excited about include:

• Genome & Company’s Phase 2 trials for GEN001, targeting stomach cancer and biliary tract cancer
• Microbiotica’s Phase 1b trial for MB097, targeting advanced melanoma in patients who have failed to respond to immunotherapies
• Biomica’s Phase 1 trial for BMC128, focused on patients with non-small cell lung cancer (NSCLC), melanoma or renal cell carcinoma (RCC) who previously progressed on immunotherapy
• CJ Biosciences’ Phase 1/2 trial for CJRB-101, investigating its efficacy in solid tumours including NSCLC and melanoma
• Everimmune’s Phase 1/2 trial for EV997, evaluating safety and preliminary efficacy in combination with immune checkpoint inhibitors for solid tumour
• Exeliom Biosciences’ Two additional Phase II studies evaluated EXL01 in hepatocellular carcinoma in combination with an ICI and one in postoperative Crohn’s disease.

New spinouts on the scene

Despite the challenging fundraising landscape, 2024 saw the emergence of several promising biotech spinouts:

• Ostia Biosciences (University of Toronto) – Developing probiotics producing novel antimicrobials, with trials starting in early 2025.
• 32 Biosciences (Ginkgo Bioworks) – Focused on diagnostics and therapeutic modulation of bacterial virulence.
• Taylored Biotherapeutics (UCalgary) – Targeting the gut-brain axis for mental health applications.
• Florey Biosciences (Harvard Wyss) – Innovating with engineered yeast strains to address antibiotic-induced microbiome disruptions.
• Concordance Therapeutics are developing smart bacteria that localize to disease sites in the gut, consuming toxic metabolites and converting them into anti-inflammatory compounds.

The Consumer Microbiome Market

In 2024, the consumer microbiome market experienced significant momentum, driven by groundbreaking innovations and product launches from key players in the field. Next-Generation Probiotics (NGPs) continue to gain traction, offering targeted solutions for metabolic health, gut health, and women’s health.

Companies like Pendulum Therapeutics have showcased the potential of precision probiotics with products designed to address metabolic pathways. Similarly, Z-Biotics has expanded its footprint with innovative GMO-based probiotic solutions, addressing emerging consumer needs in metabolic health. Seed Health, on the other hand, has made notable progress in women’s health with their vaginal synbiotic, setting new standards for efficacy in microbiome-focused solutions.

These developments underscore the growing maturity of the NGP market, where science-backed innovation continues to drive both clinical and commercial success on a global scale.

Biose’s year in review

Reflecting on 2024, I am incredibly proud of the achievements of our team at Biose Industrie:

• 600+ bacterial strains manufactured.
• 80+ drug substance batches and 25+ clinical drug product batches produced.
• 10 million finished products delivered globally.
• New major and fantastic clients onboarded, reflecting our growing global reputation.

Looking ahead, we are actively preparing for a Pre-Approval Inspection (PAI) by the FDA. This preparation is closely aligned with the clinical advancements of our clients’ programs and represents a critical milestone in enabling commercial manufacturing of approved therapies.

We will also be expanding of our Boston laboratory in 2025 to serve as a small-scale GMP Phase 1 product manufacturing suite, complementing its state-of-the-art R&D services.

Furthermore, we are heavily investing in cutting-edge technologies to enhance both efficiency and scalability. This includes advanced fermentation techniques, optimized anaerobic production processes, innovative lyophilization strategies, and real-time quality monitoring systems to guarantee precision at every stage of production.

Signing off

Despite difficulties and challenges faced by the microbiome field, 2024 will remain for me as a pivotal and extremely significant year for our industry, as it is the year in which defined LBPs showed therapeutic reality.

With significant clinical trial results, significant investments from the public and private sectors, new company formations and good science continuing to emerge, it is important that stakeholders of the industry continue to focus on their end goal, which is ultimately bringing new therapies to patients in need.

I can say with certainty that this is the goal which continues to drive the team at Biose Industrie to maintaining the gold standard in bacterial manufacturing.

With this, I would like to wish all our friends, colleagues, clients and collaborators a very successful 2025!

Yours Sincerely

Adrien Nivoliez

CEO

Biose Industrie

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This edition signified an expansion of the event’s coverage of women’s and infant health areas. A highlight of which was undoubtedly UCSF’s Craig Cohen who gave an insightful keynote on the development of live biotherapeutic products for bacterial vaginosis and HIV susceptibility.

Other subject areas covered at this year’s forum included “gut microbiota for health & disease”, “gut-brain axis”, “regulation and manufacture”, “probiotics, personalised nutrition & cardiometabolic diseases”.

On the morning of day one, Biose’s, CEO, Adrien Nivoliez was honoured to present on the CMC challenges for LBP and next-generation probiotic manufacturing. He was also pleased to contribute Biose’s expertise on a LBP manufacturing panel, alongside Bharat Dixit of Adiso Therapeutics and Ryan Garrett of Vedanta Biosciences.

We spoke to the event team to get their personal highlights from the forum:

• “Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease”, Xin Zhou, Research Scientist, Snyder Lab, Stanford

Zhou described his work tracking the human microbiome over a six-year period in 86 individuals across four body sites. His results revealed stable, individualised, bacterial signatures that varied in stability depending on site. Additionally, his work found a relationship between host insulin-resistance and microbiome compositions, with insulin resistance resulting in disrupted stool and skin microbiome stability.

• “Trials To Testimonials: A Probiotic for Autism”, Noelle Patno, Chief Scientific Officer, Bened Life

The applicability of psychobiotics to alleviate autism-associated symptoms was at the centre of Patno’s talk. Patno described several trials conducted with Bened Life’s lead probiotic product, PS128, that found it reduced ASD-symptomology in children through increased attention, improvements in social communication skills, and a reduction in anxiety.

• “My Baby Biome Study: A DataDriven Approach to Infant Probiotic Development”, Pedro Torres, Director, Bioinformatics and Data Science, Persephone Biosciences

Torres outlined Persphone’s development of new infant probiotics, powered by its “my baby biome” study to identify biomarkers for infant gut microbiome health. From this study, Persephone identified three distinct infant enterotypes: one Bifidobacterium dominated, one Bacteroides dominated, and one Proteobacteria/Firmicute dominated . The research also found microbiome composition influences the microbial-beneficial impact of breast milk. Torres stated Persephone will launch an infant synbiotic in early 2025, developed with the information gathered through this study.

• The Potential of Live Biotherapeutic Products to Optimize the Vaginal Microbiome to Improve Reproductive Health”, Craig R. Cohen, Professor, Department of Obstetrics, Gynaecology & Reproductive Sciences, University of California San Francisco

Cohen addressed the limitations of current bacterial vaginosis (BV) treatments and explored novel treatments. He described the high recurrence rates of BV and the potential for live biotherapeutic products to treat it. The development and clinical trials of L. crispatus CTV-05 were discussed, showing promising results in reducing BV recurrence and maintaining vaginal colonization. A randomised, placebo-controlled phase 3 clinical trial is in the pipeline.

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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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