Microbiomes under the microscope

The smallest bacteria can make their presence felt in our everyday lives and APC plans to bring microbiome science to a new level of scientific discovery

Killing 99.99 per cent of bacteria is not necessarily a good thing and part of the future for microbiome research is to come up with antimicrobial solutions that target just harmful bacteria while being friendly to microbiomes

We all know that there is strength in numbers and sometimes a collection of the smallest things combined can have the most powerful impact. This is very true of bacteria which, while invisible to the naked eye, can certainly make their presence felt in our everyday lives.

We live in a microbial world where most bacteria live in large communities – and scientists have discovered that by influencing and manipulating these bacterial communities, it enables us to tackle some of the major challenges facing humankind and the planet ranging from obesity, infection, to food security and methane emissions.

Based in University College Cork and Teagasc, APC Microbiome Ireland (APC) is Ireland’s national microbiome research institute and is a world-leading SFI research centre.

With 300 scientists, clinicians and research support staff, it partners with several other academic institutes including NUIG, UCD, UL, TCD and MTU. It also has strategic partnerships in the food, pharma and biotech sectors and Paul Ross, director of APC, says the institute nurtures a “strong international network of academic, community and industry partnerships”.

“APC collaborates extensively with stakeholders to explore how to harness and manipulate microbes for the good of human and planetary health,” he said. “It is widely recognised that the gut microbiota plays an important role in human health and has become one of the most dynamic, complex and exciting areas of research in both food and pharmaceutical arenas.

“Over the last decade, the APC has established itself as one of the leading global centres in gut microbiota research – and has made several landmark discoveries, publishing over 3,000 research articles in peer-reviewed journals.”

Recent research areas being led by APC include the development of new diagnostics, biomarkers of health or risk of disease based on analysis of the microbiota; exploring the mechanisms by which the microbiota may be favourably mobilised or manipulated to promote health including mental health, and “mining” the microbiota for new drugs and functional food ingredients.

Set up in 2003, APC has established a global reputation for scientific excellence built on 19 years of pioneering work on microbiome science.

This has had a broad impact not just in scientific terms, but also in educational, economic and industrial terms – and the stage has been set for a new chapter. One where APC will build microbiome science together with its stakeholders to a new level of scientific discovery and opportunity in terms of human and planetary health.

APC’s many areas of microbiome research include cancer; here APC have developed a screening tool for colorectal cancer based on profiling the oral and gut microbiomes. One of the most advanced areas of microbiome research is developing a microbiome solution for infectious diseases which are resistant to antibiotics.

Gut health and nutrition enhancement is also an important area of research, while sustainability is another big focus.

“One of our passions is to support gut health in early life,” Ross said. “In this respect, APC Microbiome Ireland has recently joined with Friesland Campina Innovation in a four-year research collaboration focused on the gut microbiota, which will investigate the impact of oligosaccharides, including complex sugars found in mothers’ milk on the growth and metabolic activities of early life microbes.”

“The insights generated from the project will contribute to our ever-growing knowledge on how specific oligosaccharides can impact the microbiota in early life to support a healthy gut.”

There are also a number of other projects under way including MASTER (Microbiome Applications for Sustainable food systems through Technologies and Enterprise), which is a Horizon 2020 Innovation Action project being coordinated by APC Principal Investigator Professor Paul Cotter at Teagasc.

There is also a collaborative research project between APC and International Flavors & Fragrances Inc (IFF) which investigates the rebalancing of babies’ gut bacteria after either antibiotic exposure or a Caesarean section birth.

The centre has also been involved in the recent pandemic with research into changes in gut microbiome of people who contracted Covid-19, how the virus impacted on immune development, sequencing and tracking new viral variants in Ireland and helping the national pandemic response roll out.

APC’s research remit is multifaceted and the director says the future of microbiome research will be far-reaching.

“Together with our industrial partners and stakeholders, APC continues to grow as a focal point for microbiome research and collaboration on the Island of Ireland,” he said. “We are expanding our reach through the development of key international collaborations with like-minded world leading microbiome centres and in so doing build a global critical mass in key areas of strategic importance to this country.

“We have established APC as the leading centre for impactful translation of microbiome science in terms of generating intellectual property, attracting foreign direct investment in R&D, and providing a cohort of high calibre research trainees for Irish industry.

On top of that, APC continues to be a hive of activity with regards to the development of high potential spin-out companies. So far, Ross says there are “five thriving companies already in existence and more in the pipeline.”

“This culture of partnership and entrepreneurship would be greatly enhanced through the development of the APC Innovation Centre, “ he said. “Which will be a new building dedicated to translating our science at the interface of food and medicine, embracing new areas such as precision medicine and personalised nutrition.”

“In the last two decades, we have come to realise how communities of bacteria shape the biology of our planet in so many ways including our own health and wellbeing.”

"So killing 99.99 per cent of bacteria is not necessarily a good thing and part of the future for microbiome research is to come up with antimicrobial solutions that target just harmful bacteria while being friendly to microbiomes, unlike broad spectrum antibiotics and chemical disinfectants.”