Microbiome Insights

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In anticipation of the upcoming Skin, Microbiome & Probiotics R&D and Business Collaboration Forum, I had the privilege of speaking to some speakers to get their thoughts about the issues confronting microbiome research.

Challenges in Microbiome Therapeutics

Celine Druart, Executive Director, Pharmabiotic Research Institute (PRI) offered her insight into the primary challenges faced in translating microbiome research into effective therapeutic interventions.

She writes “Translating microbiome research into effective therapeutic interventions is a complex endeavor that faces several significant challenges, with regulatory uncertainty being a major obstacle. Microbiome-based therapies often involve living organisms, which do not align neatly with traditional categories of drugs or biologics. Regulatory agencies such as the FDA, EMA, and MHRA are actively refining guidelines to assess these therapies’ safety, efficacy, and quality.

 

Additionally, the regulatory framework is undergoing significant changes, such as the introduction of the new Substances of Human Origin (SoHO) Regulation. This regulation will include human microbiomes within its scope, representing a major shift that will profoundly impact human microbiome research and development. These changes create uncertainties and introduce additional hurdles for researchers and companies as they navigate the development and approval processes for microbiome-based therapies.”

Celine Druart,  Executive Director, Pharmabiotic Research Institute (PRI) will explore Microbiome Regulation at the meeting.

 

Dylan West, Director of Strategy & Business Development, Concerto Biosciences says that the microbiome as a therapeutic modality – as with all therapeutic areas of research – faces a significant translational challenge: How can we be sure that in vitro results will translate into efficacious treatments that help patients live healthier, longer lives? For live microbial products in particular, different environmental & ecological contexts can result in dramatically different product performance, as microbes often express different phenotypes when isolated in a petri dish compared to when interacting with other microbes in real-world communities (like on a human’s skin).

 

Concerto Biosciences is building a solution: Using our high-throughput coculture platform (kChip), we can measure microbial phenotypes across millions of combinations of microbes, simulating real-world communities to ensure that the desired, therapeutic behaviour is robust to different real-world contexts.

 

Integration of AI and Machine Learning

Addressing the challenges encountered when integrating AI tools into microbiome research, Dylan said that “to discover live microbial products, we must reconcile with the fact that the activity we care about – the real-world function of a particular microbe or defined consortium – is highly dependent on its context, including the chemical environment and the other microbes that interact with it and modulate that activity. In principle, AI/ML models could help us address this complex ecological puzzle if we had enough training data—large quantities of high-quality, accurate, cleanly-labelled data, describing both the target variable we want to predict and its relationship to various features that predict it.

To unleash AI on this problem, Concerto Biosciences has developed the only high-throughput coculture apparatus (kChip) that generates phenotypic data (not just metagenomic data) on microbial communities. This dataset, with 20+ million communities constructed and measured to date, is uniquely large enough to accurately train a model that predicts the efficacy and robustness of a desirable microbial activity across various contexts.”

Dylan West, Director of Strategy & Business Development, Concerto Biosciences will share his thoughts on From Discovery to Clinic: Rigorous Development of Microbial Interventions for Skincare.

 

Recent Breakthroughs in Microbiome Research

Clémentine Thabuis, Nutrition and Health Senior Research Manager, Roquette believes that the most significant breakthrough in microbiome research is the understanding of the trophic networks that coexist within the gut microbiota. For a long time, gut microbiota was considered a “black box”. The development of high-throughput methods of ex vivo colonic fermentations allowed a deeper understanding of the cross-feeding mechanisms between strains. We now know that the presence or absence of a specific strain in a microbiota will not determine the response of the whole microbial community to a specific substrate. Indeed, as a prebiotic producer, one of our main concerns is the responder/non-responder ratio when a general population is supplemented with a specific prebiotic. Today the combination of ex vivo experiments and artificial intelligence permits a deep analysis of experimental readouts to predict an ingredient’s effect on a general population, taking into account the various compositions of gut microbiota worldwide. These different technological developments will allow ingredient producers to elaborate either large-range prebiotics for the general population or precision prebiotics for specific populations.

 

Microbiome and Personalized Medicine

Clémentine goes on to say that “as an ingredient producer, our main concern looking at the development of new prebiotics is the ratio of responder/non-responder. When we look at probiotic and prebiotic intervention studies in humans, we can see that the level of responders varies between 25 and 50% depending on the supplementation. Consequently, the intervention studies to investigate an impact on gut microbiota always must recruit large populations and are consequently really costly. As a result, the use of predictive tools before entering the clinical phase could be efficient for the food industry. On the contrary, if we consider precision prebiotics that target a specific effect in a specific population, these ex vivo, in vitro predictive tools are mandatory to develop personalized prebiotic solutions depending on the composition and functionality of each gut microbiota. In theory, the ideal prebiotic solution can be found for everyone. In practice, the complexity of individualized treatment will be the production and the distribution of personalized solutions without reaching incredible costs for the final consumers.”

You can hear Clémentine Thabuis, Nutrition and Health Senior Research Manager, Roquette explore Pectic oligosaccharides from potatoes exhibiting different bioactivities based on structural details such as molecular weight and degree of methylation for health benefits

 

Future Directions in Microbiome Research

Eric (Chun-Ming) Huang, Professor, Arizona State University, USA was asked to look ahead and suggest promising areas of microbiome research that could revolutionize healthcare in the next decade.

He said “Fecal microbiota transplantation (FMT) has been used in clinics for treatments of human digestive disorders. Bacteria isolated from human healthy stool are transferred to the colon of patients by FMT. In the near future, the same concept will be used by isolating probiotic bacteria from different human locations including skin to do “microbiota transplantation” against human diseases.”

 

Next-Generation Probiotics

Eric also elaborated on next-generation probiotics’ development and potential impact in treating or preventing diseases. Refereeing to his work he said “We are developing next-generation probiotics which are those electrogenic bacteria. We isolated these bacteria from different locations of the human body. These bacteria can eliminate the free radicals. In the elderly, the abundance of these probiotic bacteria is significantly reduced. Without these bacteria in the skin or gut, many free radical associated diseases are developing in senior publications.”

Eric (Chun-Ming) Huang Professor, Arizona State University, USA presentation is on Electron-driven future ingredients for cosmetics and foods using a synthetic microbiology approach

 

Advice for Emerging Researchers Interested in Specialising in the Human Microbiome

Guenolee Prioult, Senior Director, Nutrition Science and Technology, Nestle Health Sciences offered this advice to emerging researchers interested in specializing in the human Microbiome.

 

She said: “To all emerging researchers in human microbiome: Embrace resilience and champion interdisciplinary teamwork alongside technological progress. Remember, it will take time to prove the impact of microbiome advances on human health, and even longer to educate and persuade consumers and healthcare professionals about these novel concepts. The significance of the microbiome in overall wellness, particularly its gut-level influence, is undeniable. Yet, its effects on cognition, weight management, anxiety, skin and beyond remain complex and elusive to the public. Our mission is to bridge the gap—integrating scientific breakthroughs, clinical data, compelling narratives, and innovative manufacturing to deliver precise solutions that resonate with consumers and healthcare providers alike. Stay passionate and persistent; your work is pivotal.

Guenolee Prioult the Senior Director, Nutrition Science and Technology, Nestle Health is also speaking in the Hague this April. Her presentation is on the Effect of L. reuteri DSM 17938 & GOS synbiotic on gut- microbiome, bone & muscle development: from ex vivo to clinical studies.

 

Looking ahead

Colette Shortt, Visiting Professor, University of Ulster was asked to look to the future. One promising area is the tremendous commercial opportunity and demand for direct-to-consumer (DTC) microbiome testing. However, she said that ” the clinical evidence for DTC microbiome diagnostic tests is sparse and a clear regulatory framework is warranted. In particular, to build confidence in DTC microbiome testing there is a need for standardisation and validation of testing kits. We need to ensure the tests are accurate, reliable, and clinically relevant and that the consumer receives clear and understandable information. Realisation of these development aspects, which will take research effort, would ensure a robust pathway for the development and exploitation of DTC microbiome tests to benefit health.”

 

Ethical Considerations in Microbiome Research

 

Thinking about ethical factors, Colette notes that there are several regulatory considerations regarding personal data related to microbiome work involving human subjects. She highlights the importance of informed consent as one of the founding principles of research ethics. “It is essential that subjects can partake in microbiome research freely /voluntarily with full understanding and information about what it means for them to participate, and that their consent is given and recorded before they enter into the research.” In Europe, a key regulation to adhere to when conducting clinical research with human subjects is that of the General Data Protection Regulation (GDPR). This she says means that “much care is required in sharing or transferring data (particularly across regulatory jurisdictions or between legal entities) and in the storage of personal/medical data.”

Colette Shortt, Visiting Professor, University of Ulster is leading a panel discussion in the Hague this April.  Take part in the debate on Advancing Sustainability and Health: Innovations in Food Ingredients, Precision Medicine, and the Microbiome.

 

 

Visit our upcoming Microbiome event page