Image Credits: Ben McDade Photography for Wellcome Connecting Science

Categories: Sanger Science22 May 2023

Empowering microbiome research in underrepresented countries

Mentoring and training early career scientists; building technology that can adapt to humid and hotter countries; finding a way of transporting anaerobic microorganisms. The pathway to accelerating microbiome research isn’t lacking challenges.

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To date, the majority of research on the human microbiome has focused on high-income countries, particularly European and North American populations. A retreat, co-organised by Sanger researchers and partners in Kenya, Pakistan and the US, aimed to address this power imbalance. Supported by Wellcome Connecting Science, as part of their Learning and Training programme, and the Gates Foundation, it brought together more than 40 leaders in gut microbiome research, funding and policy from over 20 different countries in April 2023. They discussed how to accelerate microbiome research to improve the health of children in Asian, Latin American and African countries.

There is a growing body of evidence that suggests that the microbiome plays a role in health and disease. It is associated with the development of respiratory and gut illnesses such as cholera or pneumonia, and in vaccine response through interactions with the immune system. It has also been recognised as a target for therapeutic interventions to improve malnutrition and other diseases (obesity or inflammatory bowel disease, for example).

“Our microbiome is like a fingerprint. It has an enormous variation and the majority of microbiome research has been focused on richer countries and has been neglected in other parts of the world.”

Hilary Browne,
Senior Staff Scientist at the Host-Microbiota Interactions lab at the Sanger Institute and co-organiser of the retreat.

How should we address this research imbalance? Everyone agreed that building capacity, networks and collaboration was key. Exactly how that materialises was a theme of the retreat. Attendees shared knowledge of their work in their own countries. Tahmeed Ahmed, from the International Centre for Diarrhoeal Disease Research, explained how his team is treating young infants with malnutrition in Bangladesh with a set of gut bacteria abundant in early life, called Bifidobacterium. Denise Fonseca from the University of Sao Paolo described how intestinal infection can impact tissue homeostasis in the mesentery (the membrane that holds the intestine in place). Her work aims to better understand the role of infection in the microbiome during childhood.

At the Sanger Institute, Dr Trevor Lawley leads the Host-Microbiota Interactions Lab which explores the relationship between humans and their microbiome. Since 2019 the team has been focusing on early life, to map how gut bacteria and viruses influence long-term growth, development and disease resistance.

“Early life is an area in which we can have the biggest impact on microbiome science and research. My team is focused on microbiome and health, and this needs a long-term strategy, a network and collaboration. This retreat is part of this effort to increase capacity and collaborate with countries around the world, helping to build capacity in African, Asian and Latin American countries.”

Trevor Lawley,
Senior Group Leader of the Host-Microbiota Interactions lab at the Sanger Institute.

Several global initiatives were also presented during the gathering, such as a spinout from the Massachusetts Institute of Technology, OpenBiome, a microbiome library that aims to build and share a globally representative collection of samples and strains for microbiome science. CHAIN (Childhood Acute Illness and Nutrition), a multinational research group the Sanger is part of, was also discussed. CHAIN is looking to improve the management and care of highly vulnerable children in resource-limited settings and help improve survival, growth and healthy development.

The retreat purposely brought together a mix of established researchers, including Jeff Gordon, known as the “father of the microbiome”, from Washington University, and early career researchers from countries in which microbiome research is underrepresented.

Bonface Gichuki, soon to be a joint Sanger and University of Cambridge PhD fellow, is currently working within Dr Lawley’s lab studying the gut microbiome of children readmitted to hospital in Africa and South Asia. It was precisely Jeff Gordon who inspired him to venture into microbiome research. He has a long-term vision:

“The network that we’ve built within the past two days if it can be maintained, will give us a great foundation for training and in the future, once I have my own trainees, it can be a network I can signpost them to.”

Bonface Gichuki,
Soon to be a joint Sanger Institute and University of Cambridge PhD fellow.

“One of the challenges for me, especially coming from Kenya, is to look at infrastructure. We need to build up the correct kind of labs that will enable us to carry out microbiome research. Secondly - training. Building a critical mass of trained people who are able to do the research, all the way from sample collection to processing and storage in readiness for microbiome analysis, and thereafter, being able to analyse the data.”

Caroline Tigoi,
PhD fellow at the University of Oxford pursuing a Dphil in clinical medicine, co-organiser of the retreat.

Caroline, who prior to her PhD worked at KEMRI / Wellcome Trust as the Laboratory Lead for the CHAIN network overseeing laboratory activities in its nine sites, also highlighted collaboration and mentoring. “To have senior leaders mentoring scientists from African, Latin American and Asian countries and giving them the opportunity to lead in some areas, and even apply for funding or grants together [is vital],” she said.

For Najeeha Iqbal, Associate Professor at the Aga Khan University, Pakistan, and co-organizer of the retreat, career development for early-stage researchers was a priority:

“We hope that some of the attendees of this meeting will emerge as future scientists of microbiome research and will be able to benefit from this event - this retreat was fundamental in my career development pathway.”

Najeeha Iqbal,
Associate Professor at the Aga Khan University, Pakistan, and co-organizer of the retreat.

“We were inspired to bring this retreat together because we see immense potential for the field of microbiome science to impact child health globally. We hope this meeting serves as a catalyst for new equitable research partnerships and collaborations that can accelerate the field and deliver innovations for child health.”

Majdi Osman,
Co-organiser of the retreat from OpenBiome.

Following the retreat a group will be formed to develop an institutional model for microbiome innovation in global child health, and the sharing of best practices.

What’s next?

The organisers intend to publish the outcomes of the event in a scientific journal to share their findings - and unknowns - with the wider community. The slack channel that was set up for the retreat will keep the dialogue open between global scientists and available to anyone interested in the topic.

Find out more