People often complain of recurring stomach pain, frequent diarrhoea, unexplained weight loss or constant fatigue, brushing these symptoms aside as ‘gas’, food intolerance, or stress. But for many, these early signs mark the onset of a far more serious condition.
A new international study has now found that the loss of beneficial gut bacteria may play a crucial role in triggering inflammatory bowel disease (IBD), offering fresh insight into how the condition begins and how it might be detected earlier.
The study, published in the journal Gastroenterology, was led by researchers from the University of Birmingham and brings together microbiome data from multiple countries. By analysing gut bacteria changes at the moment of diagnosis, before any treatment begins, the researchers have uncovered a consistent microbial signature associated with the onset of IBD.
The findings reveal that people newly diagnosed with Crohn’s disease and ulcerative colitis experience a sharp decline in beneficial anaerobic bacteria that help digest complex carbohydrates. At the same time, there is an increase in oxygen-tolerant bacteria (many typically found in the mouth) that migrate into the gut.
Considering that nearly 4.9 million people worldwide were living with IBD in 2019, and that long-standing IBD can increase the risk of colon cancer by up to four times, these findings could mark a turning point in how the disease is detected and managed.
What is Inflammatory Bowel Disease (IBD)?
Inflammatory bowel disease, or IBD, is a collective term used to describe chronic conditions that cause inflammation in the digestive tract. The two main forms of IBD are Crohn’s disease and ulcerative colitis.
Crohn’s disease can affect any part of the gastrointestinal tract, from the mouth to the anus, and often involves inflammation that penetrates deep into the layers of bowel tissue. Ulcerative colitis, on the other hand, is limited to the large intestine and rectum and typically affects only the innermost lining of the colon.
A third category, known as indeterminate colitis, is used when features of both Crohn’s disease and ulcerative colitis are present but a definitive diagnosis cannot be made.
IBD is considered an autoimmune disorder, meaning the immune system mistakenly attacks healthy intestinal tissue. What triggers this immune response remains unclear. “Researchers are working to understand more about the mechanisms behind the condition and the impact of genetic, environmental, infectious, immune and other factors, including the balance of bacteria in the gut,” according to Johns Hopkins.
The disease can affect people of all ages, including children and teenagers. While IBD can run in families, many patients develop it without any known family history.
“According to studies, between 5 and 20 per cent of those with inflammatory bowel disease have a first-degree relative, such as a parent, child or sibling, with the condition,” Johns Hopkins noted.
Symptoms often fluctuate, with periods of flare-ups followed by remission. Common symptoms include abdominal pain, diarrhoea (sometimes with blood), urgency to pass stools, rectal bleeding, weight loss, fever, anaemia, fatigue, and malnutrition. In children, IBD can also lead to delayed growth and development.
If inflammation is not controlled over time, IBD can cause serious complications such as strictures (narrowing of the bowel), abscesses, fistulas, and an increased risk of colorectal cancer.
Are IBD and IBS the same?
The two conditions are often confused, but they are fundamentally different.
According to Johns Hopkins, “These two acronyms often get confused. Like IBD, irritable bowel syndrome (IBS) is a chronic condition that affects the intestines. But the diseases are very different.”
“IBS does not involve inflammation: People with IBS may have periods of constipation followed by periods of diarrhea. This could be caused by heightened sensitivity of the nerves in the intestines or problems with motility ― the coordination of nerves and muscles that move food and waste through the digestive system,” it added.
What the study found
Published in Gastroenterology, the study was led by researchers from the University of Birmingham and combined raw microbiome data from multiple international studies to examine gut bacterial changes at the very onset of inflammatory bowel disease (IBD). Importantly, all participants were newly diagnosed and had not yet started any treatment, allowing researchers to capture early disease-related microbial shifts without the confounding effects of medication.
The analysis included data from 1,743 children and adults across 11 countries. Of these, 678 individuals had Crohn’s disease (CD) and 399 had ulcerative colitis (UC), the two most common subtypes of IBD. The remaining participants included 130 healthy controls and 405 symptomatic controls who had gastrointestinal symptoms but were not diagnosed with IBD.
In total, 36 studies met the eligibility criteria. Of these, 18 contributed raw data for bioinformatic reanalysis, while 24 were included in a supplementary meta-analysis.
Nearly 1,000 of the analysed samples were biopsy specimens taken directly from intestinal tissue, offering detailed insights into mucosal microbial communities.
The results showed a clear reduction in microbial diversity, known as alpha diversity, among IBD patients compared to controls. This reduction was observed across multiple comparisons, including paediatric ulcerative colitis versus symptomatic controls, adult Crohn’s disease and ulcerative colitis versus healthy controls, and paediatric biopsy samples across disease groups. Beta diversity analysis, which examines differences in overall microbial composition, revealed distinct separation between stool and biopsy samples, as well as differences by geography. These distinctions were least pronounced in ulcerative colitis.
Most notably, multivariate modelling revealed a consistent depletion of anaerobic bacteria – organisms that thrive in low-oxygen environments and play a key role in maintaining gut health, alongside an enrichment of aerobic and facultative anaerobic bacteria that tolerate oxygen. The analysis also showed an increase in bacteria typically associated with the oral cavity across both Crohn’s disease and ulcerative colitis.
The findings reveal that people newly diagnosed with Crohn’s disease and ulcerative colitis lose beneficial anaerobic bacteria that help with the digestion of complex carbohydrates.
“While previous research has suggested that a shift toward oxygen-tolerant bacteria and a loss of beneficial anaerobes may be involved in IBD, this is the first study to demonstrate these changes so clearly at the onset of disease – and across multiple international datasets,” said Dr Peter Rimmer from the University of Birmingham and Consultant Gastroenterologist at University Hospitals Birmingham NHS Foundation Trust, and joint lead author of the study.
“This research gives us a clearer picture of what’s happening in the gut at the very start of IBD. Our findings suggest that changes in gut oxygen levels and the migration of bacteria from the mouth to the gut may play a key role in triggering inflammation – and these patterns could pave the way for earlier diagnosis and new treatments for IBD patients,” added Dr Rimmer.
The study supports the ‘oxygen hypothesis’, which is the idea that increased oxygen levels in the gut lining disrupt the delicate balance of the microbiome, allowing harmful bacteria to thrive and drive inflammation. It also highlights the presence of oral bacteria such as Granulicatella and Haemophilus in the gut, which may represent new targets for treatment or prevention.
Professor Tariq Iqbal, joint senior author of the study and Director of the University of Birmingham’s Microbiome Treatment Centre, said, “This study demonstrates the value of collaborative research in the microbiome field. By combining global data and advanced bioinformatics, we’re moving closer to personalised, non-drug therapies that could transform how we treat chronic gut conditions like IBD.”
Professor Morris Gordon, Co-director of the Biomedical Evidence Synthesis and Translation to Practice (BEST) unit at the University of Lancashire, added, “This unique study combined significant clinical, scientific and evidence synthesis expertise to identify the unique conditions in the gut at the time of diagnosing this condition. This opens up avenues to investigate regarding screening, diagnosis and therapies.”
Reflecting on the broader implications, the authors wrote, “While historically relevant, enrichment of oxygen-tolerant bacteria and depletion of anaerobes has not previously been demonstrated so starkly at disease onset and across multiple studies.”
“Research targeting such perturbations at diagnosis might alter subsequent disease course and should be a priority,” they said.
The study also acknowledged certain limitations. “Some studies contributed disproportionately, with sequence data and high-quality metadata from others unobtainable. The scarcity of treatment-naïve metagenomic data in the literature meant analyses lacked the granularity to go beyond genus level or comment on microbial function.”
Why it matters
The implications of these findings are particularly significant for India, where IBD is emerging as a growing but under-recognised public health challenge. A 2025 study titled ‘Burden of inflammatory bowel disease in India: analysis of the Global Burden of Disease study from 1990 to 2019’ highlights a rapidly changing epidemiological pattern of IBD in the country. While India’s age-standardised incidence rate (ASIR) in 2019 remained lower than the global average, the annual rate of increase between 1990 and 2019 was higher than the global trend, indicating a steady acceleration of cases.
The study notes that IBD incidence in India is higher among men, but the rate of increase is greater among women, signalling a shifting gender pattern. Incidence was highest in the 50–74 age group, with the fastest rise seen among those above 75 years, pointing towards an ageing IBD population. Mortality rates in India were higher than the Asian average, though lower than the global figure, a gap the authors attribute partly to “poor access to healthcare and the lack of dedicated centres for the management of such patients.”
Despite rising incidence and prevalence, disability-adjusted life years (DALYs) linked to IBD have declined, possibly due to earlier diagnosis and improved treatment options. However, the authors caution that this improvement may mask deeper systemic gaps. “Despite having a lower incidence rate compared to the global population, the annual rate of change is higher in the Indian population,” the study notes, warning that India’s future disease burden could be underestimated.
“Quick diagnosis and better access to health care in suburbs and rural areas could rapidly increase the numbers of IBD in India,” the study added.
This shift is already visible in clinical settings. A study examining over 30,000 patients with lower gastrointestinal symptoms across rural and urban India found that IBD accounted for more than 5 per cent of cases, surpassing infectious colitis—traditionally the dominant cause of such symptoms. Notably, the proportion of IBD cases was similar in rural and urban populations, challenging the assumption that IBD is primarily an urban disease and underscoring the need for broader awareness and diagnostic capacity beyond cities.
The consequences of delayed diagnosis are illustrated by another 2025 hospital-based study that tracked IBD patients over four years. The study found that 10 per cent developed dysplasia, a precancerous condition, with rates exceeding 11 per cent among ulcerative colitis patients. “Periodic endoscopic surveillance biopsies are a must in IBD patients to rule out dysplasia and prevent progression to the development of colorectal carcinoma and morbidity and mortality associated with it,” the authors concluded, highlighting the importance of long-term monitoring.
In 2022, the Indian Council of Medical Research (ICMR) launched the IBD NutriCare smartphone app on World IBD Day to support dietary management, an essential component of long-term IBD care. Available in eight Indian languages, the app provides culturally relevant nutrition guidance and tracking tools, improving accessibility for patients across regions.
This story is done in collaboration with First Check, which is the health journalism vertical of DataLEADS.