Irritable bowel syndrome (IBS) and your gut bacteria

Written by: Dr Aathavan Loganayagam
Edited by: Bronwen Griffiths

Within our digestive tract, we all have a complex community of gut bacteria or gut flora. This mix of bacteria lines the length of your gut and are said to affect your metabolism, your immune system, and even your mood. Dr Aathavan Loganayagam, a leading gastroenterologist, discusses the recent findings that link your gut flora with irritable bowel syndrome (IBS).

Are bacteria to blame for your symptoms of IBS?

Recent findings suggest that IBS is linked to clearly detectable gut microbiota alterations. Thanks to new diagnostic insights and a rapidly growing knowledge about the role and function of the microbial communities living inside our guts, our view on IBS and its causes has changed considerably.

Your gut is home to a huge community of bacteria, some beneficial or ‘friendly’ and some potentially pathogenic or ‘bad’ bacteria. In a healthy balanced gut, our friendly bacteria dominate and prevent the overgrowth of bad bacteria.

What is dysbiosis?

Intestinal dysbiosis is a condition in which the bacteria in your gut are out of balance, and pathogenic (bad) bacteria begin to dominate, creating symptoms of digestive disturbance. There is more and more evidence accumulating that dysbiosis may play a key role in the development of IBS.

You are an ecosystem

We have over 100 trillion microbes living inside our bodies, most of them residing in our colon; these microbes are known as your microbiota. Your gut is home to a complex ecosystem of 800 different species of microbiota, which include 7000 different strains. Amazingly, our bodies contain 10 times more bacteria than we have cells!

The composition and balance of our gut microbiota differ a lot amongst people, but certain bacteria should dominate and act to suppress the overgrowth of harmful or pathogenic bacteria.

The Bad Guys

Although most of the bacteria in our gut are beneficial to us, some bacterial species, such as B.fragilis, C.difficle and Shigella, may colonise the gut and are potentially harmful. These species, referred to as opportunistic bacteria, when in small numbers and under control fulfil some important functions in the gut, like assisting in the digestion of food, breaking down fats and bile acids.

In a balanced, healthy gut, the amount of these bacteria is limited and kept under control by the beneficial flora. However, if the beneficial flora are somehow weakened, for instance by antibiotics, poor diet and/or stress, the opportunistic bacteria can grow out of control and lead to a number of gastrointestinal symptoms including, bloatingabdominal pain, diarrhoea and constipation.

Your gut bacteria just aren’t that into you

Imbalances and disruptions in the gut microbiota are beginning to be recognised by the medical community as the missing link in understanding how IBS develops in the body.

Latest research has shown a clear distinction between the microbiota in the gut of patients with IBS and that of healthy people. Healthy individuals appear to have a more diverse gut microbiota than individuals who suffer from IBS. Put simply, this means the composition of the bacteria in the gut of someone with IBS is different from that of someone without digestive symptoms.

Studies have found a distinct imbalance between beneficial and pathogenic bacteria in the microbiota of people with IBS, with:

  1. Decreased counts of bifidobacteria.
  2. Increased levels of Clostridia spp.
  3. A decrease of coliforms, lactobacilli and bifidobacteria.
  4. Reduced Bacteroides.
  5. A two-fold increase in the ratio of Firmicutes to Bacteroidetes.

What are the symptoms of dysbiosis?

  • Bloating, abdominal pain and cramping
  • Constipation, diarrhoea, or alternating
  • Indigestion, reflux, heartburn
  • Food intolerances
  • Fatigue, brain fog, lowered mood
  • Joint pain
  • Skin conditions

What are the causes of intestinal dysbiosis?

Factors that may disrupt your gut microbiota include:

  • Antibiotics
  • Diet
  • Chronic stress
  • Gastrointestinal infections (food poisoning, travellers’ diarrhoea, gastroenteritis)
  • Medications such as NSAIDs, proton pump inhibitors
  • C-section birth
  • Exclusive bottle feeding
  • Altered gastric secretions (gastric acid, pancreatic enzymes, bile)


The use of antibiotics is by far the most common and significant cause of intestinal dysbiosis. The alteration and disruption of the normal level of flora caused by antibiotics has been known for a long time. Antibiotics do this by inviting a secondary infection by harmful yeasts and pathogenic bacteria to take hold.

Antibiotics kill all kinds of bacteria, both good and bad. They are indiscriminate in this regard and this causes many short-term as well as long-term side effects.

Studies have shown that, by taking a single course of antibiotics, you can lose the biodiversity and balance of your gut flora within as little as 3 – 4 days. Although broad-spectrum antibiotics are formulated to kill systemic infections, they also alter the gut flora. A study was carried out showing that the use of broad-spectrum antibiotics was linked with the development of IBS.

How is dysbiosis treated?

Correcting dysbiosis by taking probiotics/prebiotics and dietary manipulation. Patients with resistant symptoms may require a course of very specialised gut-specific antibiotic (rifaxamin) to kill the bad bacteria.

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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