Microscopic Colitis: What Your Biopsies Really Show (From an NHS Lab Scientist)

My name is Chris. For the last decade I worked as a Senior Biomedical Scientist in a busy NHS hospital testing everything from Full Blood Counts (FBC), Faecal Calprotectins, to biochemical analytes such as CRP.

I was diagnosed initially around 2014 with Ulcerative Colitis, but it is my goal to try and empower and educate patients as much as i can around what the lab test results mean, which ones are important and what we can learn from them.

I wrote this post specifically for patients of Microscopic Colitis. While, from a lab perspective we monitor it the same as any other IBD condition, microscopic colitis presents very unique challenges. I wanted to try and focus my attention on this niche part of the IBD spectrum.

What Is Microscopic Colitis?

At risk of preaching to the choir here (there is a wealth of information out there). Perhaps this section is written only to educate myself fully - this will be a basic overview.

Microscopic colitis (MC) is a chronic inflammatory condition of the colon. Microscopic, meaning it generally cannot be identified to the naked eye. Even on a colonoscopy, there may be no visual evidence - rather down a microscope with ‘histological examination’ it is diagnosed.

Histology is a specialised department within the medical lab. Their job is to study the microscopic anatomy of biological tissues. They are a smart team, with an important responsibility. Quite often many of the team have doctorate degrees.

Based on what is observed by the histology team, microscopic colitis exists in two subtypes:

• Collagenous colitis CC: A thickened layer of collagen (a structural protein) builds up beneath the lining of the colon.
• Lymphocytic colitis LC: There is an increased number of lymphocytes (a type of white blood cell) within the lining of the colon.

MC has seen a rise in incidents in recent years. The incidence is 2 to 8 times higher in women than in men. This difference is greater, the older the age at diagnosis and is higher in CC than in lymphocytic.

The estimated prevalence of MC is 119 cases/100,000 population, being 50.1 per 100,000 population for CC and 61.7 per 100,000 population for LC [2]

So you are not alone. As isolating as it might feel. Facebook groups provide a great community space for anyone dealing with this.

Although the exact cause is still unknown, research has identified several risk factors from genetic, to environmental, see figure 1.

How is it diagnosed?

Biopsies are placed in a formalin preservative and sent to the lab for processing.

Biopsies taken from a colonoscopy are sent to the histology department, where the tissue is preserved, embedded in wax, sliced into ultra-thin sections (using a microtome see image below) and stained.

Under the microscope, pathologists examine the architecture of the colon lining at a cellular level. They are looking for subtle inflammatory changes, often patterns that are completely invisible to the naked eye during the procedure itself.

In microscopic colitis, this may include an increased number of inflammatory cells (lymphocytes) within the lining of the bowel, damage to the surface epithelium, or in some cases a thickened collagen band beneath the surface layer.

What are doctors looking for?

A normal colon above can be seen above. This image shows an extremely thin slice of tissue stained and embedded in paraffin wax. Typically around 3-5 micrometres thick (or 0.003mm - thinner than a human hair!)

To the untrained eye, it is fairly hard to know what we are looking at. To an expert though, they know exactly what's normal, and the abnormal (inflammation or cancer etc). With specialised stains, they can differentiate and highlight certain abnormal features such as collagen or lymphocytes.

Lymphoctic Colitis (LC) is diagnosed when there are 20 or more lymphocytes per 100 surface epithelial cells. Lymphocytes are immune cells (a subtype of white blood cell) and in this condition, too many of them accumulate within the lining of the bowel.

The glands (crypts) still look normal. This helps doctors distinguish it from Crohn’s or ulcerative colitis.

The CD3 stain is primarily used to highlight T lymphocytes. By making these immune cells clearly visible, it allows pathologists to accurately count them within the lining of the bowel when confirming a diagnosis.

Collagenous Colitis: The defining feature here is the collagen band >10 micrometres. This thickened collagen layer reflects altered collagen turnover in response to inflammation. Mechanically this interferes with water absorption by disrupting communication between cells.

We use a trichrome stain here to highlight collagen: Collagen → stains blue (depending on protocol), Muscle → stains red, Nuclei → dark.

Again, the glands look normal - helping differentiate with crohn's and colitis.

The good news is, current evidence shows no increased risk of colorectal cancer associated with microscopic colitis. Problems stem from these subtle anatomical changes which can affect absorption - in particular, absorption of water. Up to 40% of microscopic colitis patients will experience bowel incontinence and watery stools [2].

Blood Results

Normally with IBD patients (particularly Crohn's and Ulcerative Colitis) there are several biomarkers used to monitor disease progression. While a colonoscopy with histological examination is still the gold standard for diagnosis. We use FBC, ESR, CRP, and Faecal calprotectin.

I discuss each one at great length in this post: Inside the Lab: What Your IBD Tests Really Tell Us

The challenge with MC: While the symptoms are life changing, the biomarkers in the blood we usually use for monitoring and diagnosing tell a different story. In microscopic colitis, inflammation is localised to the mucosal surface. It does not always trigger a strong systemic inflammatory response. That’s why CRP and ESR are often within normal limits.

However, having your blood monitored regularly is still very important in MC. Haemoglobin (as part of the full blood count) and Ferritin (as part of the Iron Studies) are important to monitor - especially if you are experiencing fatigue. B12/Fol is less of an issue, as this is absorbed higher up in the small intestine (more of an issue with crohns). However, again for overall health this should be checked routinely.

Microscopic colitis can be linked to other auto-immune conditions such as thyroid disease. This is quite often overlooked. It is worth requesting your Thyroid Function Tests (TSH and TFT) as part of regular health checks.

Other tests: Screen for celiac disease. This is something worth excluding out early on. To do this, the doctor should request the tests: Tissue transglutaminase (tTG IgA) and Total IgA.

Vitamin-D: Something that should be monitored in the general population much more often. Chronic inflammation, steroid use (budesonide maintenance) and concerns over bone density, this should be monitored.

Dealing with Bowel Incontinence

While understanding the science is important, for many people the day-to-day challenge is managing urgency and incontinence.

A little of my story. This is a symptom I've dealt with for a long time. It’s a horrible symptom. Shame inducing, isolating and very difficult initially to accept and manage life with it. Truth is though: life doesn't stop with incontinence and it can be learned to live with.

My bowel/faecal incontinence is related to ulcerative colitis. However, from my own personal experience, the anxiety of having an accident, or being away from a toilet is often the trigger in itself.

For me pads are a great way to minimize this anxiety. Recently, I had a music festival - Download 2025. My problem was though, the only pads I could find were not discreet in any way. Nor did pictures of the elderly and hospital styled pads and diapers reduce my anxiety wearing them.

I was determined to go to the festival. However, port-a-loo to port-a-loo I decided I was going to create my own bowel/faecal incontinence brand that challenged the stigma associated and created genuinely discreet pads that remained reliable, perfect for me and other IBD patients.

The two pads i recommend:

Attends F6 (more severe incontinence): https://www.attends.co.uk/f6-faecal-pad

IB3 (mild to moderate - much more discreet): www.ib3discreet.com

I hope I was able to shed some light on where your biopsies go, how doctors are able to make a diagnosis and some of the blood tests that we use in monitoring health in IBD.

If you have any questions just drop a comment below. If any of this was helpful, please share where possible.

Have a great day,
Chris

References:

[1] Burke KE, D'Amato M, Ng SC, Pardi DS, Ludvigsson JF, Khalili H. Microscopic colitis. Nat Rev Dis Primers. 2021 Jun 10;7(1):39. doi: 10.1038/s41572-021-00273-2. PMID: 34112810.

[2] Grilo Bensusan I1 , Torres Gómez J2 Microscopic colitis.

[3] Lin Yuan, Tsung-Teh Wu, Lizhi Zhang, Microscopic colitis: lymphocytic colitis, collagenous colitis, and beyond, Human Pathology, Volume 132, 2023, Pages 89-101, ISSN 0046-8177.