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A Microbiome Odyssey Across Asia in 10 days

Biose Editor — Thu, 05 Jun 2025 06:35:51 +0000

by Richard Ellis

As all good adventures begin, mine started with… a delay. Toulouse to CDG went from “on time” to “technical difficulties” faster than failing to connect to the flight wifi, which meant I missed my original connection to Singapore. Grrh.

Thankfully, years of airline travel (and platinum status with Air France) have taught me to anticipate chaos. I phoned in a lifeline mid-delay and secured a seat on a later flight via Hong Kong. Crisis managed – sort of. I landed in Singapore fashionably late, just in time for my morning presentation at the Microbiome Business Collaboration event by Global engage. Nothing quite like going from jet bridge to spotlight with nothing but a power nap and a prayer.

Now, I’m not a natural-born for the conference as a non-scientist I have an imposter syndrome thing going on. Put me in a partner meeting or a business dinner and I’m at home. Put me on stage, sleep-deprived and sweating through Singapore’s 200% humidity index, and I’m… less at home. But with a deep breath and a mild existential crisis, I made it through. My talk on LBP & NGP development (featuring highlights on strain CMC development and production, and lessons from over 30 clinical and commercial projects) was well-received – or at least, no everybody got up and left mid-sentence.

The rest of the event was a rewarding blend of science, networking, and a solid reminder that the microbiome world never sleeps – even if I desperately needed to.

Some presentations that I found particularly insightful from this whirlwind of a trip include:

Bridgette Wilson, PhD – Dietary Impact on Gut Microbiome in Health and Gastrointestinal Disorders

Focusing on gastrointestinal disorders like IBS, Dr. Wilson’s presentation explored how diet shapes the gut microbiome. She explained that while a low FODMAP diet shows efficacy in managing IBS symptoms, it also depletes beneficial gut bacteria such as Bfidobacterium – leading to concerns about its long-term use. To address this, Dr Wilson explained different approaches including probiotic and prebiotic supplementation. Wilson showed that in one trial supplementation of a multi-strain probiotic increased numbers of Bifidobacterium species in patients on low FODMAP compared to the control – a positive result. However, prebiotic supplementation with B-GOS, while improving symptoms, did not prevent the loss. Wilson closed by emphasising the need for personalised dietary solutions for IBS and cautioned against long term low FODMAP use.

Prof. Maurice van Steensel – The Case for Selective Microbiome Control

Opening by describing the importance of the skin microbiome in maintaining skin health, Prof Steensel presented the case for selective anti-bacterials in managing acne and body odour. Steensel explained that existing treatments for skin dysbiosis wipe out all bacterial populations, not distinguishing between the helpful strains such as S. epidermis and the pro-inflammatory ones like C. acnes. To overcome this, Steensel’s company ArrowBiome are developing targeted solutions based on lysins. Steensel introduced SmartArrow™, a precision payload delivery system, and ArcherZyme™, an engineered lysin, designed to clear harmful bacteria without irritating the skin. Data presented indicated SmartArrow™ could achieve bacterial clearance at significantly lower concentrations than conventional products.

Cherry Li – Large-scale Skin Metagenomics Reveals Extensive Prevalence, Coordination, and Functional Adaptation of Skin Microbiome Dermotypes Across Body Sites

Presenting data from one of the largest studies to date on the skin microbiome, Cherry Li revealed that analysis of over 3,500 metagenomes from 200 healthy individuals across 18 body sites identified 17 distinct “dermotypes” – unique microbial community types. Interestingly, these dermotypes were not restricted to specific sites but were consistently observed across different regions of the body. Li highlighted that certain dermotypes were linked to increased skin sensitivity and itch, even in individuals without diagnosed skin conditions. Li closed by highlighting emphasising how these findings could lay the groundwork for personalised dermatological therapies based on dermotype, moving beyond the current one-size-fits-all approach.

Dr. Mrinmoy Mazumder – Harnessing Beneficial Plant-Associated Microbiomes to Enhance Crop Yield, Quality, and Climate Resilience

Dr. Mazumder presented his team’s work on designing microbial consortia to boost crop yield, quality, and climate resilience. Using advanced culturomics and genome modelling, his group developed bacterial consortia that enhanced traits such as drought tolerance, sulphur uptake, and pest resistance in Arabidopsis and Kai-lan. He also highlighted how root-derived volatile organic compounds (VOCs) can stimulate beneficial soil biofilms from a distance, expanding a plant’s microbial sphere of influence and promoting growth.

Jet lag in Asia is its own special kind of torture. When your body thinks it’s 2am and the conference coffee is doing nothing, all bets are off. That said, I made the most of my Saturday in Singapore: the National Museum (blessedly air-conditioned), followed by a bold but ill-advised venture through Chinatown and Little India. After being flambéed by the equatorial sun, I beat a strategic retreat to the hotel pool.

Sunday morning: off to Korea! It’s the Asian country I visit most, yet it never ceases to amaze me. The food is a masterclass in fermentation, the people combine warmth with relentless drive, and there’s a palpable scientific energy – especially when it comes to microbiology and the microbiome. Not surprising then that Korea has been home to over a dozen clinical LBP lines we’ve worked on at Biose in the past seven years.

This Korean leg of the journey was particularly fruitful: promising discussions with long-standing partners, new collaborations emerging, and some genuinely exciting developments I look forward to sharing soon.

From the heat of Singapore to the buzz of Seoul, this trip reminded me why we do what we do – and how far microbiome science has come, from petri dish to patient. And maybe, just maybe, I’m starting to get used to public speaking. (But let’s not get carried away.)

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Next Generation Probiotics (NGPs) – The Next Era of Probiotics?

Biose Editor — Tue, 15 Apr 2025 14:15:42 +0000

What are NGPs?

The International Scientific Association for Prebiotics and Probiotics defines probiotics as “Live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.”¹

Traditionally probiotic products have comprised a narrow spectrum of micro-organisms, mostly containing strains from the bifidobacterium or lactobacillus genera isolated from fermented foods.

Recently however, scientists have turned their attention to new species that could confer benefit to the host, with the novel organisms being referred to as “next generation probiotics” or NGPs. Species within this category include Eubacterium hallii, Faecalibacterium prausnitzii, Roseburia spp., Akkermansia muciniphila, and Bacteroides fragilis or they can be innovative engineered strains designed to perform a specific function. These strains are often sourced from the gut and are anaerobic by nature.

How do NGPs differ from existing probiotics?

Contrasted with traditional probiotics, NGP species have been identified for their specific health benefits and function. These functions include short-chain fatty acid production, intestinal barrier regulation and immune system modulation.

Some NGP spp. have been associated with disease states. For instance, in 2008 the Sokol lab documented a depletion of Faecalibacterium prausnitzii in the gut microbiome of Crohn’s disease patients, with its lower abundance being linked to a higher risk of clinical flare.²

The NGP Landscape

The newness of the NGP market makes it a very exciting area of microbiome research, forecasted to more than double in size from 231 million USD in 2025 to 486 million USD by 2032.³ Companies are utilizing the unique properties of NGPs to provide consumers and patients with novel health benefits.

Pendulum Therapeutics

Based in San Francisco and founded in 2012, Pendulum Therapeutics has raised $111M to date.⁴ Pendulum therapeutics offers a variety of OTC probiotics, all containing A. muciniphila as well as other NGP strains. Naturally occurring in the gut, A. muciniphila has been associated with improved metabolic health, including a reduction in obesity risk and an increase in heart health.⁵

In March 2024, they launched their GLP-1 Probiotic, consisting of the 2 NGP strains A. muciniphila and Clostridium butyricum.⁶ Pendulum reference various preclinical studies to support their claim that their GLP-1 Probiotic can upregulate GLP-1 secretion in the host. One such study found that a metabolite secreted by A. muciniphila increased GLP-1 secretion in mice. In unpublished company data, Pendulum also reports a dose-dependent increase of GLP-1 by Clostridium butyricum in a cell-based assay. The company is currently testing their GLP-1 probiotic in a clinical trial with completion expected in 2025.⁷The company also has active trials examining the impact of their NGPs on bipolar disorder, and bone health.

The Akkermansia Company

Also leveraging the health benefits of A. muciniphila is the Akkermansia Company in Belgium. Founded in 2004, the company was founded on the discovery of A municinphila by Willem M. de Vos’ laboratory of Wageningen University and the Patrice Cani’s research from UCLouvain. To date it has raised $21.9M in funding.⁸ Notably, The Akkermansia Company utilise a proprietary pasteurised form of A. muciniphila, Akkermansia MucT. Their product “Healthy Weight” has been available in Europe since 2021 and launched into the US in June 2024.⁹

In 2019, a randomised double-blind study conducted by The Akkermansia Company, the Microbes4U® study, found pasteurized A. muciniphila improved insulin sensitivity, reduced insulinemia and reduced plasma total cholesterol compared to the placebo in human subjects – interestingly, only the pasteurised form led to reduced cholesterol versus the live form.¹⁰ Bolstering these findings, a paper in Nature identified that pasteurised Akkermansia better strengthened intestinal integrity and lipid metabolism than the live form in a tissue model. ¹¹

ClostraBio

A spin-out from the University of Chicago, ClostraBio are developing an NGP for targeted delivery of butyrate to promote gut health and intestinal barrier integrity. Butyrate is critical to gut homeostasis, as it serves as the primary carbon source for colonocytes and promotes barrier integrity by upregulating tight junction proteins¹² and increasing mucin production¹³. However, decreased butyrate levels have been observed in individuals afflicted with numerous chronic diseases^12,14 as well as those consuming a Western diet^15,16. ClostraBio’s CLB101 is an NGP that has been shown to produce high levels of butyrate from fermentation of prebiotics as well as from the lactate and acetate excreted by common gut commensals like Bifidobacteria¹⁷. Manufacture of CLB101 has been successfully scaled to commercial capacity with a planned product launch in 2025¹⁸.

Florey Biosciences

Spun out from Cubillos-Ruiz’s research in the MIT and Wyss Institute lab of James Collins, Ph.D., Florey Biosciences are developing genetically engineered probiotics to improve human health. Their lead product FLR-101, consists of a food-grade yeast strain which produces an enzyme to degrade beta-lactam antibiotics – which represents approximately 50% of antibiotics used. Antibiotic consumption significantly disrupts the fragile balance of the gut microbiome, an inconvenient side-effect of a highly useful drug class. Florey aim to eliminate this side-effect by shielding the gut microbiome with the beta-lactam degrading effects of FLR-101. As the yeast is localised to the gut, the antibiotics can still act on infection elsewhere in the body.¹⁹ Currently, Florey are pursuing a medical food designation for their probiotic product.

In a 2022 proof of concept paper, the team demonstrated in vivo that an engineered strain of Lactococcus lactis could effectively degrade beta-lactam in the gut of mice, without impacting the serum levels of the antibiotic. The paper notes that the beta-lactamase gene does not confer antibiotic resistance to the host strain and is not susceptible to horizontal gene transfer.²⁰

Looking to develop an NGP?

In addition to our world-leading LBP manufacturing solutions, Biose Industrie have fully anaerobically sealed industrial production lines for NGPs with over 600 different strains being manufactured for the different clients around the world!

If you are interested in manufacturing a NGP product, get in touch here.

Sources:

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Microbiome Wrapped 2024 – A Year in Review & What’s Next

Biose Editor — Mon, 30 Dec 2024 10:09:08 +0000

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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Our highlights from Global Engage’s 12th Microbiome & Probiotics R&D and Business Collaboration Forum

Biose Editor — Thu, 05 Dec 2024 12:13:39 +0000

On October 17 – 18 the Biose team travelled to San Diego for Global Engage’s 12th Microbiome & Probiotics R&D and Business Collaboration Forum. Covering everything from the gut-brain axis to microbiome market trends, the team enjoyed two days of meetings, interesting talks and networking.

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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