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An Internal Ecological Crisis Is Unfolding Inside Our Guts

In his new book, Dr James Kinross explains how gut bacteria are fundamental to global health – and they're in deep trouble.


Tom Hale


Tom Hale

Senior Journalist

Tom is a writer in London with a Master's degree in Journalism whose editorial work covers anything from health and the environment to technology and archaeology.

Senior Journalist

3D artwork of Colorful Gut bacteria, good and bad bacteria microbiome healthy gut bacteria, bacteria in digestive system

The good, the bad, and the ugly: humans harbor hundreds of bacterial species in their intestinal tracts.

Image credit: CI Photos/

Global health is in a dramatic state of flux. As the world becomes ever-more globalized, we’re becoming buried by a tsunami of preventable diseases: obesity, cardiovascular disease, countless cancers, and allergies, to name but a few. While we might imagine that humans are the main character behind this change, the real star of the show may actually be the trillions of microorganisms that inhabit our guts. 

Speaking to IFLScience, Dr James Kinross explains how many of the problems facing global health have a fundamental link to the gut microbiome – the bustling hive of bacteria, archaea, fungi, and viruses that live in our digestive tracts – and its decimation in the modern world.


“I'm a clinical scientist, I'm a surgeon, and I treat people with problems in their gut all of the time,” Dr Kinross explains.

“I am sick and tired of treating preventable chronic diseases that are driven by our microbiomes. Or, perhaps I should say, by the destruction of our microbiomes,” he adds.

Dr Kinross is a Senior Lecturer in Colorectal Surgery and a Consultant Surgeon at Imperial College London who’s just written his first book – Dark Matter: The New Science of the Microbiome – in which he spills his knowledge on the profound importance of the gut microbiome to physical health and mental wellbeing. 

As the name of the book suggests, he sees gut bacteria as a kind of dark matter of human biology: we know it's there and we know it's important, but we're struggling to grasp its true nature and often fail to appreciate its pervasive influence. 


The problem is that lifestyles over the past century have proved disastrous for our internal ecosystems and, in turn, our immune systems. 

Effectively, we're living through an internal climate crisis.

Dr James Kinross

Overuse of antibiotics, especially in agriculture, has dramatically altered the composition and abundance of certain bacteria in the microbiomes of some populations. Homogenized diets of over-processed, low-fiber foods are a similar problem, as well as increasing urbanization and changes in migrations. 

“You've got really big forces that are that are creating a catastrophic loss in the microbiome,” explains Kinross.

“We are experiencing a global pandemic of crippling chronic disease that is driven by a generational destruction in our microbial ecosystems that live within us,” he added.


“Effectively, we're living through an internal climate crisis.”

In the public consciousness, it’s pretty well known that a healthy gut is invaluable for a healthy body. Most people appreciate that a diverse diet, full of leafy greens and fiber, plus the odd probiotic, is an integral part of staying fit. 

a set of fermented food great for gut health - top view of glass bowls against grunge wood: cucumber pickles, coconut milk yogurt, kimchi, sauerkraut, red beets, apple cider vinegar
Probiotic foods - like pickles, kimchi, miso, sauerkraut, yogurt, and kefir - are an easy (often delicious) way to support the gut microbiome.
Image credit: marekuliasz/

That’s certainly true, but the odd kombucha or side of kimchi is not a silver bullet. If the fragile ecosystem of gut bacteria is disrupted in early life, perhaps by poor diet or over-exposure to antibiotics, then the microbiome can effectively become “scarred” and struggle to return to its original state, says Kinross.

One example is how gut bacteria are helping to fan the flames of the ongoing mental health crisis. Diet and lifestyle in adult life, plus 21st-century culture, are undoubtedly a major influence, but a significant part of the issue originates in our early development and the microorganisms that forge our immune systems.


“The gut microbiome maintains and optimizes our health from birth to death. It controls the development and function of many of our organs that are not typically associated with microbes – like the brain,” he adds.

“The bacteria in our gut are very, very important in setting up the basic structure of nerves in early life. So, for example, bacteria are important in coating some of our nerves with myelin, which is a sort of layer of fat that allows nerve fibers to fire efficiently. If those bacteria are missing at critical moments in development, those people in whom they're missing are more likely to become anxious and to have higher states of anxiety and anxiety awareness,” Kinross tells us.

Likewise, a fundamental upset of the gut microbiome can have a colossal impact in later life too. 

“If you damage it before puberty, that will be very important in determining your sex-associated risk of chronic disease state. If you damage it when you're susceptible later in life, as you start to become frailer, that might knock you into the care home much, much faster than you'd otherwise be,” he notes. 

The maternal microbiome should be a human right.

Dr James Kinross

To tackle this intestinal crisis, Kinross suggests a paradigm shift is needed. The outdated idea that bacteria are always the "bad guys" needs to change from the top down. Scientists, doctors, and healthcare authorities need to grasp the importance of the gut microbiome and its baseline role in the global health problems we face. 

“I think we should be thinking about how we can have more effective healthcare policy to protect the microbiome, we need to bring it into standard healthcare practice,” notes Kinross.

In fact, Dr Kinross believes that protecting gut microbes is so influential to a person’s health and happiness, perhaps we should consider giving legal protection to the gut microbiome. It might sound like a far-out idea. However, if the gut bacteria of mothers are protected, he argues, then benefits for people and the planet could be monumental.

“I think the maternal microbiome should be a human right,” Kinross states.


“Children born to women who have microbiomes that are not optimally programmed to maintain the development of the gestating baby are disadvantaged and the implications may be significant or lifelong for their children,” he divulges. 

“The importance of the maternal microbiome is that it is modifiable, both in good and bad ways. Pregnant mothers who are socially disadvantaged are more likely to have a poorer diet and greater exposure to environmental drivers that cause harm to themselves, their microbiomes, and their developing babies. By saying ‘the maternal microbiome is a human right’ it reframes health policy around healthcare prevention in the most vulnerable people in our society or in low- and middle-income countries,” Kinross added. 

His new book – Dark Matter: The New Science of the Microbiome – is available now.


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