Microbiome manipulation for health: building a shared narrative
Theo Murphy meeting organised by Professor Debby Bogaert, Dr Chrissie Jones, Professor Robert Read and Dr Anastasia Theodosiou.
Can we manipulate the microbiome to improve human health? Join this exciting interdisciplinary workshop for clinical, laboratory, bioinformatic and social science leaders. We will explore opportunities and threats in interventional microbiome research, discussing state-of-the-art science alongside broader societal and One Health perspectives. Our goal is to build a unique shared narrative, and expand a cross-disciplinary network committed to future collaboration.
Poster session
There will be a poster session on Monday 21 October.
Programme
The programme, including the speaker biographies and abstracts, is available to view below.
Attending the meeting
For information about attending this event, please contact the Scientific Programmes team.
Image credit: nopparit
Organisers
Schedule
09:00-09:05 |
Welcome by Royal Society and lead organiser
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09:05-09:40 |
Microbiome manipulation through four lenses
As the meeting organiser, Anastasia will introduce the aims, agenda and cross-meeting themes, including interventional microbiome research models, microbiotoxicity, social and political perspectives, and specific issues in early life. Touching on each of these themes, she will then give an overview of her own research, involving commensal inoculation in pregnancy as a novel model for studying mother-to-infant microbiome transmission. Her work has demonstrated that nasal inoculation in pregnancy using the harmless commensal Neisseria lactamica is safe, acceptable, and effective at inducing maternal respiratory colonisation. However, mother-to-infant transmission of the inoculation strain was not observed, despite evidence of broader microbiome sharing and strain-level transmission of other commensals. These findings challenge conventional perceptions of infants as passive recipients of maternal microbes, suggesting that commensal acquisition is species- or even strain-specific. Dr Anastasia TheodosiouUniversity of Glasgow, UK Dr Anastasia TheodosiouUniversity of Glasgow, UK Anastasia is a clinical academic trainee specialising in Medical Microbiology and Infectious Diseases. Her research focuses on the early life microbiome, including the world’s first perinatal human challenge model, using nasal inoculation with commensal Neisseria in pregnant women to study microbiome transmission in mother-infant pairs. She is passionate about the role of the microbiome in novel therapeutics and antimicrobial stewardship. |
09:40-09:50 |
Discussion
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09:50-10:25 |
Title tbc
Dr Feehily will discuss the impact of pregnancy and early life on the vaginal microbiome. |
10:25-10:35 |
Discussion
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10:35-11:00 |
Break
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11:00-11:35 |
Antibiotics and the microbiome
Professor Lindsay Hall will discuss the impact of antibiotics on the gut microbiome. Professor Lindsay Hall, University of Birmingham, UKUniversity of Birmingham and Quadram Institute Professor Lindsay Hall, University of Birmingham, UKUniversity of Birmingham and Quadram Institute Lindsay Hall is the Chair of Microbiome Research at the University of Birmingham since 2023. She obtained a BSc in Microbiology from the University of Glasgow and a PhD in Microbiology and Immunology from the University of Cambridge (Wellcome Trust Sanger Institute). Her postdoctoral fellowship at the APC Microbiome Institute at University College Cork, Ireland, kindled her deep interest in gut-associated microbial communities. Subsequently, she took on her first independent role as a lecturer at the University of East Anglia, Norwich, where she and her new team honed their focus on the gut microbiota, particularly during early life. In 2015, Professor Hall moved to the Quadram Institute in Norwich, where the team's research expanded significantly. They established clinical cohort studies that advanced knowledge of the role of the gut microbiota in human health. Alongside research, she engaged with the public through outreach and educational initiatives, centred around the theme of 'Guardians of the Gut'. Before joining the University of Birmingham, she held the position of Chair of Intestinal Microbiome at the Technical University of Munich, Germany. Here, she continued her team's pioneering work in beneficial microbes and developed innovative therapies to enhance infant health. |
11:35-11:45 |
Discussion
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11:45-12:20 |
The social dimensions of microbiome manipulation for health
This paper places an interest in microbiome manipulation for human health in historical, political and geographic context. It comes in three parts. It first presents the rise of probiotic approaches to microbiome manipulation as a response to growing concerns about the unintended consequences of modern antibiotic modes of managing microbes. It documents a probiotic turn in microbial management across a range of policy domains extending from human, to animal, to environmental health. Second, it explores concepts and methodologies for engaging publics with the microbiome, to harness the growing popular interest in microbiome manipulation. It focuses on approaches for building forms of microbial citizenship aware of the differences between popular and microbiological understandings of viruses, fungi and bacteria. Finally, it identifies a set of social challenges that will need to be addressed to ensure the emergence of just and democratic approaches to microbiome manipulation for human health. It identifies political questions about unequal social access to microbiome science and healthcare across a range of spatial scales, as well as epistemic questions about whose knowledge counts in microbiome manipulation. Dr Jamie LorimerUniversity of Oxford, UK Dr Jamie LorimerUniversity of Oxford, UK Jamie Lorimer’s research explores public understandings of nature and how these come to shape health and environmental governance. Past projects have explored the histories, politics and cultures of nature recovery, ranging across scales from elephants to the microbiome. He uses participatory and ethnographic methods to engage publics in research practices. His current work examines the probiotic turn that is underway in important parts of the Western world in which citizens and scientists are using life to manage life: reintroducing species and managing ecologies to deliver desired functions and services. This probiotic turn is a response to the blowback caused by the excessive application of antibiotic modes of managing life in the Anthropocene. It can be detected across spatial scales from the microbial to the planetary. In the context of the microbiome, it is evident in ongoing efforts to recalibrate modern hygiene practices and to conserve and restore valued microbiota. Dr Beth GreenhoughUniversity of Oxford, UK Dr Beth GreenhoughUniversity of Oxford, UK Beth Greenhough’s research explores the social implications of scientific innovations in the areas of health, biomedicine and the environment. Employing a range of participatory, ethnographic and archival methods, Beth seeks to understand the social, cultural and ethical processes which shape how publics and patients engage with biomedical research. Previous work has explored the ethics of biobanking, factors shaping breast cancer awareness and cultures of care in animal research. Her current work looks to develop collaborative and participatory approaches to public engagements with key emerging issues in health and wellbeing, including the impacts of industrial pollution, patient experiences of Long Covid and lay engagements with the human microbiome. She is co-author of Bioinformation (Polity, 2017) and Researching Animal Research (Manchester University Press, 2024). |
12:20-12:30 |
Discussion
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13:30-14:05 |
An overview of ZOE microbiome science
Professor Tim Spector FMedSci OBE will discuss the work of his company, ZOE. Professor Tim Spector FMedSci OBE, King’s College London
Professor Tim Spector FMedSci OBE, King’s College LondonTim Spector is a Professor of Genetic Epidemiology at King's College London and honorary consultant Physician at Guys and St Thomas' Hospitals. He is also an expert in personalised medicine and the gut microbiome and started the famous UK Twin Registry in 1993. Through his work he has been given many awards and prizes, and is a Fellow of the Royal Society of Biology and the Academy of Medical sciences. He has published over 900 scientific papers and is ranked by Google as being in the top 120 most cited scientists in the world. He has published four popular books- including the best-selling Diet Myth and recently Spoon-Fed, he writes health blogs, which have been read by ten million people and appears regularly on the TV and Media round the world. |
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14:05-14:15 |
Discussion
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14:15-14:50 |
Microbiome interventions for tackling Clostridioides difficile infections and gut colonisation with antibiotic resistant bacteria
The role of the gut microbiome in the development of recurrent Clostridioides difficile infections (CDI) has been well-established since the early 2010s. CDI is primarily linked to antibiotic use, which disrupts the gut microbiome by reducing protective bacterial communities involved in bile acid metabolism. Restoring the gut microbiome through Fecal Microbiota Transplantation (FMT) from healthy donors has proven effective in curing patients with recurrent CDI and has become a routine treatment. To standardise FMT, (national) stool banks were established, and both commercial and non-commercial companies have entered the field of therapeutic microbiota interventions. Recently, the FDA approved two commercial FMT products in USA, but EMA has not (yet) been involved. In Europe, the European Commission has designated "Substances of Human Origin" (SoHO) to regulate transplants involving blood, tissues, cells, organs, and human-derived materials, including breast milk and intestinal microbiota. A new proposal is currently under review by both the Council and the European Parliament, aiming to regulate FMT and allow stool banks to continue their operations. Industry collaboration with stool banks has led to the development of various Life Biotherapeutic Products, some of which are now in phase 2 and phase 3 clinical trials. At the same time, new anti-CDI antibiotics with a narrow spectrum have been developed, helping to preserve the gut microbiome and reduce recurrence of the disease. These advancements are expected to expand the therapeutic options and reduce the need for full gut microbiome transplant. In contrast, the role of the gut microbiome for colononisation with antibiotic resistant bacteria is less well established. However, interventions targeting the gut microbiome appear to reduce bacterial load in the intestinal tract, potentially lowering the risk of infection. Professor Dr Ed J KuijperLeiden University Centre for Infectious Diseases, the Netherlands Professor Dr Ed J KuijperLeiden University Centre for Infectious Diseases, the Netherlands Professor Dr E J Kuijper previously led the Experimental Microbiology division and the Reference Laboratory for Clostridioides difficile at Leiden University Medical Centre, as well as the Centre for Infectious Disease Control at the National Institute of Public Health. In 2015, he co-founded the National Donor Feces Bank for patient treatment, followed by the establishment of the Centre for Microbiota Analysis and Therapeutics in 2017. Dr Kuijper has authored over 500 peer-reviewed journal articles and book chapters. Until 2016, he served as president of the European Study Group on Clostridium difficile (ESCGD) of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Since 2018, he has chaired the ESCMID Study Group on Host and Microbiota Interactions (ESGHAMI). |
14:50-15:00 |
Discussion
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15:00-15:25 |
Break
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15:25-16:00 |
Isala: implementing citizen science and vaginal microbiome research to explore microbiome-based therapeutics to advance women’s health
Understanding the composition and function of the vaginal microbiome is essential for advancing women’s health. In this context, Dr Lebeer and her team established the Isala citizen-science project, which in a first phase involved 3,345 women across Belgium (aged 18–98 years) who contributed self-sampled vaginal swabs and completed extensive questionnaires. Lactobacillus species dominated 78% of these samples, with overall microbiome composition strongly influenced by factors such as age, childbirth, and menstrual cycle phase. Network correlation analysis with methods such as SparCC revealed specific bacterial modules or guilds of collaborating bacteria, including a module containing Lactobacillus crispatus, L. jensenii, and Limosilactobacillus, which was positively correlated with health estrogen levels and contraceptive use, and negatively correlated with childbirth and breastfeeding. Other modules, characterised by Gardnerella, Prevotella, and Bacteroides, were linked to multiple partners, menopause, menstrual hygiene, and contraceptive use. Building on these findings, Dr Lebeer and her team are now developing microbiome-based therapeutics (or live biotherapeutic products, focusing on isolated Lactobacillus strains and their combinations. Preliminary results indicate that these microbial therapeutics hold promise for maintaining vaginal health and preventing infections. By integrating citizen science with cutting-edge microbiome research, the Isala project not only aims to enhance our understanding of vaginal microbiome dynamics but also paves the way for novel interventions to improve women’s health. Professor Sarah LebeerUniversity of Antwerp, Belgium Professor Sarah LebeerUniversity of Antwerp, Belgium Sarah Lebeer is the principal investigator and head of the Laboratory of Applied Microbiology and Biotechnology at the University of Antwerp since 2011. She studies the microbiome of the gut, vaina and upper respiratory tract and is especially fascinated by the beneficial members of our microbiome such as lactobacilli and how we can apply them as probiotics or live biotherapeutic products. She obtained her Masters in Bioscience Engineering in Cell and Gene Technology (2004) and PhD (2008) within the Faculty of Bioscience Engineering of the KU Leuven. She is the vice president of the International Scientific Association on Probiotics and Prebiotics (ISAPP) and coordinator of a Centre of Excellence (named U-MaMi) on ‘Advancing Health Equity Through Microbiome-Centric and Multidisciplinary Research’. She is also involved in several citizen-science projects such as the Isala project on women’s health. |
16:00-16:10 |
Discussion
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16:10-17:00 |
Poster flash talks
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17:00-18:15 |
Poster session
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09:00-09:35 |
Translating the microbiome in to Clinical Practice
The human microbiome is a high dimensional and dynamic part of our physiology that plays a key role in managing health and individualised responses to diet and medicine. The immune system controls our interaction with the microbial world, and the microbial communities in our bodies are central to modulating the immune response. Changes in the human microbiome and their metabolism have substantial influence on atopy, neurological disorders, metabolic disorders, and a range of complex conditions and disease states. Diet is incredibly important in shaping human health and the microbiome, altering both composition and metabolic activity, resulting in changes in immune, endocrine, and neurological systems. Microbiome-Wide Association Studies (MWAS) combined with novel quantitative multi-omic approaches are enabling us to use AI techniques to determine personalised responses to nutrition that drive diseases states and treatment efficacy. Through these innovations we are finally realising the paradigm of precision medicine for facilitating patient care. Professor Jack GilbertUniversity of California San Diego, USA Professor Jack GilbertUniversity of California San Diego, USA Professor Jack A Gilbert earned his PhD from Unilever and Nottingham University in 2002 and completed postdoctoral training at Queens University, Canada. He was a senior scientist at Plymouth Marine Laboratory and later led Microbial Ecology at Argonne National Laboratory and the Microbiome Center at University of Chicago. In 2019, he joined UC San Diego as a Professor in Pediatrics and at Scripps Institution of Oceanography, where he directs the Microbiome and Metagenomics Center. Professor Gilbert co-founded the Earth Microbiome and American Gut Projects and has authored over 450 publications. He is founding Editor-in-Chief of mSystems and co-authored Dirt is Good. He also founded BiomeSense Inc and leads the $200M NIH Nutrition for Precision Medicine program. He is the current President of Applied Microbiology International the oldest society for applied microbiology in the world. |
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09:35-09:45 |
Discussion
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09:45-10:20 |
Parent demand: a shortcut to close the gap between what scientists know and what clinicians do?
Increasing evidence points to harms to the early life microbiome associated with common maternity practices, including overuse of antibiotics, caesarean sections, and formula feeding. It seems clinical practice has not quite caught up with the latest microbiome research. This perhaps isn’t surprising given the oft-cited estimate it can take 17 years for original research to be incorporated into clinical practice. What if… there was a shortcut? Filmmaker Toni Harman proposes a radical solution to fast-track change. Toni makes a case that activating consumer demand coming directly from expectant parents could help shorten the time lag between scientific discovery and clinical implementation. If there was a dedicated public education campaign aimed specifically at expectant parents involving film screenings, live events, and evidence-based messages conveyed on social media, this could provide expectant parents with accurate up-to-date information about the microbiome, early in pregnancy. This could help expectant parents make informed decisions about their diet, lifestyle, birth and infant feeding choices that were more 'microbiome-mindful.' This could generate demand from service users, expectant and new parents, for maternity care that was more 'microbiome-mindful.' To help meet this wave of parent demand, continuing professional development programmes and other clinical training initiatives could help bring health professionals up to speed with the latest microbiome research. What if…. these parent- and clinician-facing microbiome narratives led to fast-track changes to regional, national and even international health policies? Toni suggests this radical solution of activating parent demand isn’t just possible. It’s cost-effective and already starting to happen. Toni HarmanAlto Films Ltd, UK Toni HarmanAlto Films Ltd, UK Toni Harman is the producer of the award-winning documentary Microbirth (Alto Films Ltd) about the origins of the human microbiome. Microbirth won top prize at several science film festivals, had over 1,000 premiere public screenings around the world on the same day, and has been broadcast internationally. Toni is the co-author of the books, The Microbiome Effect (Pinter & Martin Publishing) and Your Baby's Microbiome (Chelsea Green Publishing). In 2017, Toni set up Microbiome Courses, an online school offering continuing professional development courses about the microbiome, now with over 43,000 health professionals enrolled as students. Toni has hosted two international virtual conferences about the infant microbiome, the last one held in February 2024 was attended by 3,500 health professionals. |
10:20-10:30 |
Discussion
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10:30-11:00 |
Break
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11:00-11:35 |
Microbiome science in politics and policymaking
The political establishment is almost entirely unaware of the microbiome. A search of Hansard, the official record of all things said in Parliament, shows that it has only been mentioned 22 times total across both Houses. One Parliamentarian is single-handedly responsible for over half of these mentions. Prior to the general election, only 1 in 6 MPs had any level of interest or background in STEM or medicine. Scientific literacy in Parliament remains low, and engagement with the microbiome almost non-existent. So how can the microbiome research community begin to speak to policymakers in a way which has cut-through and lasting impact? How can microbiome scientists and clinicians best communicate the opportunities and challenges inherent in widening the adoption of pre-, pro-, and post-biotics? This talk will explore 'lines of attack' which are likely to resonate with Parliamentarians and policymakers in the UK when discussing the latest findings in microbiome research and their potential translation into clinically relevant products. It will also highlight key stakeholders in Government and Parliament whose support will be key to driving engagement with the microbiome under the new administration. Dr Paul-Enguerrand FadyCentre for Long-Term Resilience, UK Dr Paul-Enguerrand FadyCentre for Long-Term Resilience, UK Dr Paul-Enguerrand Fady undertook his doctoral research in Pharmaceutical Science as part of the London Interdisciplinary Doctoral Programme, supervised by Professor James Mason at King’s College London as well as Profesor Mark Sutton and Dr Lucy Bock at the United Kingdom Health Security Agency. His thesis focused on antimicrobial resistance; specifically, the risk posed to human innate immunity when Gram-negative bacteria are exposed to antiseptics. Prior to this, he obtained a BSc in Microbiology and Immunology (with a minor in Linguistics) from McGill University. He has worked across disciplines ranging from Newborn Medicine (Harvard Medical School), Applied Physical Chemistry (Institut Français du Pétrole energies nouvelles), and Chemical Engineering (McGill University). Paul-Enguerrand has recently started a new role as a biosecurity policy manager at the Centre for Long-Term Resilience. This comes on the heels of several years of Parliamentary work, advising senior policymakers on One Health, infectious disease, AMR, the microbiome, and more. |
11:35-11:45 |
Discussion
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11:45-12:20 |
Microbiome manipulation to combat post-weaning diarrhoea and reduce antibiotic dependence in pigs
Post-weaning diarrhea (PWD) is an economically important disease and the most important indication for antimicrobial use in pig production. Professor Guardabassi's research group has conducted several longitudinal studies to understand the changes in the gut microbiota of piglets affected by PWD using 16S rRNA metabarcoding and shotgun metagenomics. Their aim is to develop new strategies to identify piglets predisposed to PWD and to test interventions to modulate their gut microbiota. Machine learning analysis using Random Forest revealed distinctive microbial signatures related to health status that could be further exploited as prognostic or diagnostic biomarkers. Specifically, piglets that remain healthy after weaning display a different community structure with a higher abundance of amplicon sequence variants (ASVs) and metagenome-assembled genomes (MAGs) associated with beneficial bacteria such as Lachnospiraceae, Oscillospiraceae and Lactobacillaceae. Furthermore, we have developed and tested various interventions in newborn piglets based on fecal microbiota transplantation (FMT) or the administration of a synbiotic mix of probiotics and prebiotics. These interventions resulted in a lower occurrence of PWD and better feed efficiency. Piglets treated with synbiotics displayed increased levels of Lactobacillaceae and Prevotellaceae, while those treated with FMT showed higher levels of Oscillospiraceae and Lachnospiraceae. Altogether, this research highlights the probiotic potential of bacteria belonging to certain and provides insights into the microbial dynamics of PWD, along with new strategies to reduce the impact of PWD and reliance on antibiotics for treatment of this disease. Professor Luca GuardabassiUniversity of Copenhagen, Denmark Professor Luca GuardabassiUniversity of Copenhagen, Denmark Luca Guardabassi graduated in veterinary medicine from the University of Pisa in 1994 and completed his PhD in veterinary microbiology at the University of Copenhagen in 2000, where he works as professor of One Health AMR since 2012. He is an internationally renowned One Health microbiologist with more than 200 peer-reviewed publications (H-index 71). His research covers a broad range of topics interlinked with AMR, from epidemiological and evolutionary studies on multidrug-resistant bacteria to testing new drug targets, alternatives to antibiotics, and rapid diagnostic tests for guiding antimicrobial use. He is a pioneer in veterinary antimicrobial stewardship and has served on numerous national and international committees to develop guidelines for rational antimicrobial use in animals. Among his honorary offices, Luca is vice-chair of the Scientific Advisory Board in the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) and member of the Quadripartite Technical Group on the Economics of AMR. |
12:20-12:30 |
Discussion
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Chair
Dr David W Cleary, University of Birmingham, UK
Dr David W Cleary, University of Birmingham, UK
Dr Cleary is an Assistant Professor in Microbial Genomics at the University of Birmingham. He previously held positions at the University of Southampton and before that was a Senior Scientist at the Defence Science Technology Laboratory (DSTL) Porton Down. His current research focuses on the application of genomic, metagenomic and microbiome approaches to the understanding of colonisation of the upper respiratory tract by bacterial pathobionts such as Streptococcus pneumoniae and Haemophilus influenzae.
13:30-15:00 |
Blue sky thinking: end-to-end microbiome interventions
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15:00-15:30 |
Break
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15:30-16:00 |
Discussion panel: meeting overview and plans for future work
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