Baby steps toward better probiotics with Bonface Gichuki

Bonface initially trained as a biochemist in Kenya, before taking on a research assistant job at the KEMRI-Wellcome Research Programme (KWRP). "At the time, I was working on a large study called the CHAIN Network," Bonface explains. "CHAIN stands for the Childhood Acute Illness and Nutrition Network. It's a study based in six countries: four in Africa, and two in South Asia. The main goal of CHAIN was to try and understand the underlying factors of death in children with malnutrition." During his time at CHAIN, he met his current supervisor, Dr Trevor Lawley, through a shared interest in gut microbiome research. Following the study, Bonface received a master's fellowship from the Wellcome Trust to spend time in Dr Lawley's lab learning microbiology, which he completed while finishing his postgraduate studies at the University of Aberdeen.

Bonface first became interested in the field of gut microbiome research when reading a study by Dr Jeffrey Gordon, the 'father of the microbiome', about Kwashiorkor, a form of severe protein malnutrition. Dr Gordon's study was the first to confirm that the microbiome has a causal role in malnutrition, not just simply lack of food. "I think that's what hooked me in the field," Bonface says.

Recent research has dramatically expanded the understanding of the gut as a vital organ that functions as a central communication hub, influencing everything from immunity and metabolism to brain function and behaviour. Populations from different geographical settings have their own microbiome fingerprint, which is shaped by diet, environment, and lifestyle. By studying these, scientists can tell which microbes are common between populations, and those that are unique to particular areas. Together with an international team from Wellcome's Lawley Lab, Bonface worked on compiling a global atlas of over 4,000 genomes from 48 countries which aimed to understand the genetic diversity of two dominant types of bacteria across infant populations all over the world.

“What we found was that one of the bacteria, the Bifidobacterium infantis, was particularly missing in babies from Western populations, but it was very dominant in babies from Africa and South Asia. These bacteria were also missing in the current infant probiotics on the market.”

The global microbiome atlas is fifteen times larger than previous resources, with more representation for lower-middle income countries across Africa and Asia. 

The missing bacteria, absent in babies from countries like the UK, helps the body to digest the complex carbohydrates in breast milk and plant-based diets. "They're very crucial when babies are growing up," Bonface says. "They help to fight off infections and the immune system to mature. When babies miss these microbes from when they're born, that puts them at a higher risk of developing health complications like allergies, asthma, or others."

Crucially, the study found that all commercial infant probiotic strains can be traced back to three historical bacterial strains which are no longer present in today's infant populations. Despite being marketed under different names, these strains are highly similar genetically. Probiotic drops are often given to premature babies in the UK within 24 hours of birth to aid gut health and are highly recommended during or after antibiotic treatment.

"You're actually giving a probiotic containing bacteria that doesn't even exist in your gut ecosystem. So it raises the question of whether these probiotics will actually work, or if we need to develop a better probiotic."

One of the key takeaways for Bonface is the potential for improving health outcomes for children. "I think it's a wake-up call to manufacturers and people working in the probiotic industry to rethink which is the best approach to create more effective probiotics so it's not a one-size-fits-all approach."

When he's not at the lab, Bonface is one of the coordinators of Wolfson's Global Health Network. "I think it's helped me to meet students worldwide, and also to balance my academic and social life, which has made my time at Wolfson very enjoyable." The Network's recent Global Health conference at Wolfson's Lee Hall, Global Health in a Changing World, took place in March, with over 200 attendees registering for the sold-out event. Topics ranged from the double burden of disease and equitable access to technology, to climate change and the evolving landscape of global health funding.

When asked about what advice he would give to current students, Bonface says that the main thing is to be curious. "Don't be afraid to ask big questions, but also be open to coming across unexpected findings, because some of the greatest discoveries in science have come from following unexpected results."

Read more about Bonface's work on the Wellcome Sanger Institute website.