Integrated multiomics of host-bacteria interactions during C. elegans gut infections.

When one realises that we carry ten times more microbial cells than human cells, it is no surprise that maintaining a good relationship with our gut microbes is essential for our health. Perhaps less evident is the fact that our gut microbes not only determine our propension to obesity and cardiovascular health, they also determine our risk of developing cancers, diabetes, neurodegenerative, and auto-immune diseases. They also condition how we age, how well we recover from illnesses, surgeries or aggressive therapies, and they can even influence our moods!

Understanding how we communicate with our gut microbes has thus become a key challenge, and a potentially unlimited source of new therapies to tackle very complex disease states, and help all of us live and age much better. Yet, it is in itself a very difficult endeavor. We host thousands of microbial species organised in dynamically evolving communities. Moreover, no two microbiotas are identical, not even in twins. At the moment, despite amazing advances in biotechnology and computer sciences, it is simply too expensive and too big to solve.

Fortunately, as we did before with genome sequencing or brain mapping, we can turn to a simpler system first: C. elegans, a 1mm-long bacterium-eating roundworm that already enabled several Nobel Prize-winning discoveries. If we can solve the problem at a smaller scale, we can uncover essential principles that apply at a larger scale, and accelerate discovery of new drugs and therapies.

Like us, C. elegans has a gut microbiota, but it only colonizes its intestine during adulthood. In the laboratory, this allows us to precisely control which and how many bacteria colonize the worm gut. Because C. elegans is transparent, we can also directly look at these bacteria as they divide and move in the worm gut. To watch together different bacteria in the gut of live worms, we can further color-code them and film them by fluorescence microscopy. C. elegans is actually the most intimately known animal. We can know in real-time how active its genes and cells are, and how healthy it is. We can also switch off worm genes at will using RNA interference. We can even tell precisely when a worm dies, as it emits blue fluorescence at death. Lastly, we can make worm sick by giving them human diseases. Thanks to all this, we can use simple worm models to study complex human diseases.

This is exactly what we will do in our project. We will give the worms bacteria that are responsible for human urinary tract and lung infections. This will emulate gut dysbiosis in worms: a state where the relationship with our gut microbes goes awry, and which is frequent in ill-health and ageing. Then, combining all the approaches evolved earlier (using microscopy imaging, modifying and looking at gene activities, assessing worm and bacterial health), we will investigate and elucidate how all relevant worm and bacterial genes interact, and how it explains disease states. Knowing that, we will then test if known drugs can be used to improve worm health when dysbiosis happens.

Because worms share a lot of physiological functions, genes and diseases with other animals and humans, knowing how dysbiosis works in worms and how to prevent or correct it, will teach us a lot about our own human experience of gut dysbiosis. Hence, it will quick-start the development of new therapies, including new antibiotics and treatments to promote gut health and healthy ageing.

More than genetic make-up and lifestyle alone, our relationship with the 10^14 microbes we host in our gut, dictates our health status, how we age, respond to therapies, or even feel. In particular, imbalanced interactions with our gut microbiota (dysbiosis) promote age-associated co-morbidities, chronic infections and inflammatory diseases, cancer, metabolic and neurological disorders. Resolving them has thus become an urgent matter with the rising pressure of ageing populations and spreading of antimicrobial resistances. Yet, dysbiosis remains too complex to comprehend in humans. Its conservation across animals fortunately enables studies in simpler, solvable models such as the bacterivorous roundworm C. elegans.

Building on the breadth of genetic and microbiological tools and knowledge, recent discoveries on C. elegans natural microbiota, Omics technologies, new high-throughput screening techniques developed in our lab, and a network of world-class collaborators, we will:

1- develop new amenable experimental models of gut dysbiosis for the parallel study of host, bacterium and host-bacterium dynamics;
2- combine transcriptomics, proteomics, targeted metabolomics, spectroscopy and bioimaging phenomics to gain an inclusive view of the interactions between an animal (C. elegans), and two human opportunistic pathogens (Gram+ E. faecalis, Gram- P. aeruginosa) in wild type vs long-lived IGF1/insulin-receptor mutants with extended gut healthspan;
3- elucidate conserved, bacterial group- or strain-specific dysbiosis mechanisms for application to human opportunistic infections;
4- identify host susceptibilities to gut dysbiosis to be exploited for new anthelminthic development;
5- identify host and bacterial mechanisms that promote microbial balance and gut healthspan;
6- test the ability of host-/bacterium-targeted interventions to prevent/correct gut dysbiosis in worms; with the long-term objective of promoting gut health in human ageing and diseases.

This project will provide new knowledge, methods and models to tackle host-microbe interactions & gut dysbiosis.

Beneficiaries include:
1- academics (microbio-, biogeronto-, nemato-, bacterio-, neuro-, immuno-logists, systems and evolutionary biologists) via the models, methods and knowledge developed via this project;
2- undergraduate (UG) and post-graduate (PG) students working in my lab, or whom I teach;
3- the higher- education sector via production of new knowledge and training of future educators;
4- Lancaster University (LU) and NHS academics, biomedical scientists and clinicians I (will) collaborate with to translate the findings of the project;
5- the local community (wider public, school teachers and pupils) via outreach activities;
6- Lancaster University, through teaching, research and engagement activities, contributing to its missions and reputability;
7- the agro-industrial sector through identification of new drug targets for antibiotic and anthelminthic design;
8- local (Bionow network) or larger companies (GSK, Syngenta, Astra-Zeneca, Johnsons&Johnson, Bayer etc.) interested in optimizing screening pipelines, developing new antibiotics, pesticides or 'anti-ageing' treatments;
9- the health sector affected by antimicrobial resistance, via development of new antibiotic strategies;
10- patients affected by gut dysbiosis (elders, gut surgery patients,etc.) via development of corrective abiotic and probiotic treatments;
11- third-world countries struck by economically and socially ravaging helminth-transmitted diseases;
12- the society as a whole through the reduction of healthcare costs, improvement of health and education.

Dissemination (0-6 years, groups 1-8)
Through Biomedical & Life Sciences (BLS) thematic groupings, the Centre for Ageing Research (C4AR), Material Science Institute (MSI), and Health Innovation Campus (HIC), updates from this project will be discussed at departmental and institutional seminars & symposia on a two-monthly basis, benefiting from regular inputs from academics across departments and NHS staff. Through public events organised by LU, the HIC, C4AR, and MSI, we will touch the wider public, local Biotech companies (Bionow), HIC partners, LU students and staff. As members of the BSRA, Physiological and Biochemical societies, we will present the project at further public events and international conferences. We will publish findings in leading Open-access peer-reviewed journals, LU & BLS social media accounts, and press releases (coordinating with LU & BBSRC press offices). Data will be deposited in public repositories, and a project website with regular updates will be created.

Training (0-many years, groups 1-4)
Out of 8 UG and PG students trained in my lab, 3 already contributed to this project, 3 pursue a PhD, 1 a MD. Students produce publishable data and co-author articles. When teaching on UG/PG courses, engaging with UCAS or 3rd form pupils, I instil elements of my own projects to relate student education to ongoing research and current societal issues. I foster a multidisciplinary culture, promote good laboratory practices and encourage creativity. It forms enthusiastic, open-minded and polyvalent young scientists able to work as part of team, adapt to exacting standards (industrial, clinical), intellectual challenges (academia), and interpersonal issues (anywhere).

Translation (4-15 years, groups 8-12)
Leveraging collaborations (gut and cancer immunologists, microbiologists, nematologists, and chemists at LU and Manchester University), we will confirm project findings in mammalian models, establish pilot drug screening pipelines, and apply for further funding. New collaborations with NHS pathology (at the HIC) will allow translation into human health (clinical trials). Links with industries will be established via LU Research & Enterprise Services, MSI and HIC, to produce and commercialize drugs and health products arising from the project.