Microbiome manipulation for health: building a shared narrative

21 - 22 October 2024 09:00 - 17:00 Doubletree by Hilton Leeds City Centre Free
Bacteria Lactobacillus in a human intestine

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

  • Dr Anastasia Theodosiou

    Dr Anastasia Theodosiou

    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.

Schedule

09:00-09:05 Welcome by Royal Society and lead organiser
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 Theodosiou

Dr Anastasia Theodosiou

University of Glasgow, UK

09:40-09:50 Discussion
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
10:35-11:00 Break
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, UK

Professor Lindsay Hall, University of Birmingham, UK

University of Birmingham and Quadram Institute

11:35-11:45 Discussion
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 Lorimer

Dr Jamie Lorimer

University of Oxford, UK

Dr Beth Greenhough

Dr Beth Greenhough

University of Oxford, UK

12:20-12:30 Discussion
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 London

14:05-14:15 Discussion
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 Kuijper

Professor Dr Ed J Kuijper

Leiden University Centre for Infectious Diseases, the Netherlands

14:50-15:00 Discussion
15:00-15:25 Break
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 Lebeer

Professor Sarah Lebeer

University of Antwerp, Belgium

16:00-16:10 Discussion
16:10-17:00 Poster flash talks
17:00-18:15 Poster session
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 Gilbert

Professor Jack Gilbert

University of California San Diego, USA

09:35-09:45 Discussion
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 Harman

Toni Harman

Alto Films Ltd, UK

10:20-10:30 Discussion
10:30-11:00 Break
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 Fady

Dr Paul-Enguerrand Fady

Centre for Long-Term Resilience, UK

11:35-11:45 Discussion
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 Guardabassi

Professor Luca Guardabassi

University of Copenhagen, Denmark

12:20-12:30 Discussion

Chair

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Dr David W Cleary, University of Birmingham, UK

13:30-15:00 Blue sky thinking: end-to-end microbiome interventions
15:00-15:30 Break
15:30-16:00 Discussion panel: meeting overview and plans for future work