Microbiome: can we engineer healthy gut bacteria?

Written by: Dr Aathavan Loganayagam
Published: | Updated: 08/07/2022
Edited by: Laura Burgess

For more than one hundred years, we believed avoiding bugs or removing them from our system was the simplest way to improve our health.

But while tremendous public health advances have come from controlling dangerous pathogens, we now understand the trillions of other bacteria that live in our body – and in particular, our gut – perform a range of important functions.

Expert gastroenterologist Dr Aathavan Loganayagam explains whether we should re-engineer our gut bacteria when the microbiota (the microorganisms) becomes unbalanced (which is known as dysbiosis) and is associated with chronic health conditions such as autoimmune diseases.

When and how should we try to manipulate these microorganisms?

What we eat satisfies the nutrient demands of our microbiome – and subsequently shapes their capacity to further contribute to our health. But the modern lifestyle, particularly diet and hygiene changes, have altered our relationship with our microbes.

To have a healthy microbiome, the best advice is to include natural plant foods, including fibre, in your diet. Although diet has a major role in shaping our microbiome, it’s not a precise way to re-engineer it if things have gone wrong.

How can we engineer our microbiome?

There are two broad avenues for microbiome engineering: generic strategies that target large numbers of different bacteria simultaneously, such as faecal (poo) transplant and antibiotics; or specific strategies that target a small group of microbes, such as probiotics.

Although changes in our microbiome are associated with many chronic diseases, and those changes almost certainly have some contribution to the disease, they are not necessarily the main cause. Microbiome manipulation is most useful when we know exactly how microbes are involved in particular diseases.

But if you don’t have a problem, you don’t need to mess with your microbiome. This is another reason why taking antibiotics when you don’t need them is a bad idea.


Read more: Do poo transplants or probiotics affect gut health?

By Dr Aathavan Loganayagam

Dr Aathavan Loganayagam trained in medicine at Guy’s, King's and St. Thomas’ medical schools. He then underwent rigorous structured specialty training in gastroenterology and general internal medicine in the well respected South London training programme.

He then spent two years during postgraduate training as a research and endoscopy fellow at Guy’s and St Thomas’ Hospitals, London. His research was in the fields of pharmacogenetics, inflammatory bowel disease and gastrointestinal malignancy. He has received awards and grants for outstanding research work, including the prestigious NHS Innovation London Award.

Dr Loganayagam has numerous publications in peer reviewed journals on all aspects of gastroenterology. He is actively involved in clinical research. He has particular local expertise in the practice of personalised medicine and the utilisation of novel therapeutic agents in the treatment of complex inflammatory bowel disease. He is currently the lead clinician for endoscopy at Queen Elizabeth Hospital, Woolwich.

Diagnostic and advanced therapeutic endoscopy remains a major part of his clinical expertise, including assessment and treatment of inflammatory bowel disease, strictures, polyps and cancers.

Dr Loganayagam is an approachable doctor who takes pride in his communication skills with patients. He is keen to ensure that patients are fully informed and involved in all aspects of their care.

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