Improve your social microbiome: ‘Live with other people, live in a rural environment and have a dog’

Microorganisms help us digest our food, train the immune system and support all body systems

For far too long, we’ve focused on the dangers of microbes – the bacteria and viruses that make us sick and some of which can kill both humans and animals. A new graphic book by multiple award-winning gastroenterologist, Prof Fergus Shanahan and graphic designer, Laura Gowers wants us to turn our attention to how microbes help to keep us alive and even contribute to the survival of planet Earth.

So, let’s start at the very beginning.

“Humans wouldn’t exist if ancient microbes had not mutated such that they could split water and produce oxygen. There would no food, no plants and therefore no animals without microbes,” explains Shanahan, who is the founder and former director of APC Microbiome Ireland, a University College Cork research centre into the study of how the microorganisms in our guts impact on numerous diseases and even our mental health.

The community of microorganisms (bacteria, viruses, fungi and archaea) that live in and on humans are known as the microbiome. Not only do our personal microbiomes vastly outnumber human cells, but stretching right along our digestive tract from the mouth to the anus, they help us digest our food, train the immune system and support all body systems.


“When I first qualified as an immunologist, I realised that we were only looking at half of the story if we only looked at the gut without understanding the microbes,” says Shanahan. The discovery that stomach ulcers were caused by the helicobacter pylori bacteria was an epiphany for me.”

Although Australian researchers Barry Marshall and Robin Warren were awarded the Nobel Prize for their discovery in 1982, the study of the gut microbiome is still not widely taught in medical schools. “Microbes make fibre digestible for humans and when digested, they become short-chain fatty acids which are important for the immune system, the brain and nervous system, the endocrine system and much more,” says Shanahan.

But, while the helicobacter pylori can cause ulcers and stomach cancer is some people, it can protect against cancer of the lower oesophagus and other chronic diseases in others. Some strains of Escherichia coli (E.coli) promote food digestion, whereas others may cause food poisoning and inflammatory disease. “We can’t think of microbes in a binary way – as good or bad bugs because they adapt themselves to the situations they find themselves in,” explains Shanahan.

So how do you ensure that you have a healthy microbiome?

“Have a diversified diet – eat a little bit of everything – particularly fibre,” says Shanahan who agrees with what American writer, Michael Pollan said – “eat real food, not too much and mostly plants”.

Research also points to how mothers pass more microbes to their babies during a vaginal birth and through breastfeeding. “But if you were born via a Caesarean section and you weren’t breastfed, you can improve your “social microbiome” by living with other people, living in a rural environment and/or having a dog,” says Shanahan.

Too many antibiotics in childhood can also disrupt the role of the microbiome in developing a healthy immune system and lead to allergies and autoimmune diseases while increasing the risk of obesity. A diverse gut microbiome is also advantageous for people about to have chemotherapy.

And although the Covid pandemic instilled global fear of new viruses, the use of viruses (so-called viral vectors) to deliver life-saving vaccines to vulnerable individuals is a scientific wonder. “The vast majority of microbes are not pathogenic. We can’t live without them,” says Shanahan.

And while he is cautious about overstating the role of gut health in curing mental health problems, Shanahan has great hope that microbiota will be mainstreamed as treatment options for various conditions in the near future. “Saying that you can eat your way out of depression risks the microbiome being besmirched but faecal microbial transplants are already used in the treatment of antibiotic associated diarrhoea,” he explains. Novel foods are currently being developed to reduce deterioration of the gut microbiome in older adults.

Now with their new book, Listen to Your Microbes (Liberties Press), Gowers and Shanahan want to share this “public health message told from the microbiome perspective”.

“The book is designed for anyone who cares about their personal microbiome with information which isn’t dumbed-down, drawings showing the beauty and majesty of the microbiome and humour,” explains Shanahan.

There are also QR codes in the book which lead readers to interviews with experts on everything from fermented foods to probiotics to bacteriophages (viruses that infect bacteria).

The author and designer encourage us to mind our microbes. “Almost every aspect of human lifestyle affects gut microbes. Food, sleep, drugs, physical and social activity influence the composition and function of gut microbes. In turn, the microbiota reflects human health and wellbeing,” writes Shanahan.

And, he also sees a role for microbiota in solving some aspects of the climate crisis. “Microbes can be used to clean up oil spills and plastics in the ocean but climate change is also influencing the spread of infectious diseases around the world yet bacteriophages may have a role in dealing with the growing problem of antimicrobial resistance,” says Shanahan who is adamant that regional and international collaboration in both science and politics will be the key to solving these issues.

Sylvia Thompson

Sylvia Thompson

Sylvia Thompson, a contributor to The Irish Times, writes about health, heritage and the environment