In my work with clients managing autoimmune diseases and chronic illnesses, I’ve seen patterns emerge that are often overlooked. One of the most intriguing links I keep coming across is how certain gut bacteria, like alpha-haemolytic Streptococcus, haemolytic Escherichia coli (E. coli), and Enterobacter cloacae, affect red blood cells and contribute to chronic inflammation and fatigue.
These bacteria show up again and again on stool tests, particularly in clients who are struggling with persistent fatigue, low iron levels, or immune flares.
If you are interested in stool testing for yourself, you will find more details of the Gut Health Testing Package offered at The Autoimmunity Nutritionist Clinic here.
Understanding this connection has been a game-changer in helping my clients take back control of their health. In this article, we will explore these three types of gut bacteria and how they contribute to chronic fatigue and low red blood cell count:
Alpha-haemolytic streptococcus and chronic fatigue
Alpha-haemolytic Streptococcus is one of those bacteria that’s supposed to be part of the gut’s natural flora, but when it’s out of balance, it can cause real problems. It partially breaks down haemoglobin in red blood cells, leading to a kind of low-grade anaemia that’s often missed on routine blood work.
I see this a lot in clients with autoimmune conditions like lupus or rheumatoid arthritis. They come in with constant fatigue, pale skin, and that sense of being “worn out” no matter how much they rest.
If you have rheumatoid arthritis and would like to learn more about the root causes and natural therapies that can help, you can listen to this episode of The Autoimmune RESET podcast here.
When we find alpha-haemolytic Streptococcus on a stool test, it often correlates with these symptoms. By addressing this imbalance—through gut restoration using a 5R protocol, reducing inflammation, and supporting red blood cell production with food and lifestyle changes—clients usually notice a significant boost in their energy levels.
Haemolytic escherichia coli and iron dysregulation
Haemolytic E. coli is more commonly associated with acute infections, but in autoimmune disease, its effects can linger and create chronic issues. These strains produce toxins that break down red blood cells and disrupt iron metabolism.
What I’ve noticed in clients with conditions like Crohn’s disease or other inflammatory bowel disorders is this ongoing cycle: they’re exhausted, their iron levels are low despite supplementation, and their inflammation just won’t settle.
When stool testing identifies haemolytic E. coli, it’s like finding a hidden piece of the puzzle. Addressing it can dramatically improve iron absorption and reduce the constant fatigue many clients face. For some, it’s the first time they’ve felt genuinely energised in years.
Enterobacter cloacae and inflammatory flares
Enterobacter cloacae is another bacterium that frequently pops up on stool tests, especially in my clients with autoimmune diseases. It’s part of the normal microbiota, but when it overgrows, it can wreak havoc. It weakens the gut lining, leading to leaky gut, and allows bacterial toxins to enter the bloodstream. This drives systemic inflammation and often makes autoimmune flares worse.
One client with psoriatic arthritis, for example, had been dealing with stubborn brain fog, joint pain, and skin rashes. Her stool test revealed high levels of Enterobacter cloacae. Once we addressed her gut health, her symptoms started to improve—her brain fog lifted, her joints felt less inflamed, and her skin began to clear. It was like lifting a heavy weight off her shoulders.
How these bacteria affect red blood cells
What all these bacteria have in common is their ability to damage red blood cells and disrupt oxygen delivery to the body. This shows up as chronic fatigue, persistent weakness, and in some cases, symptoms like dizziness or shortness of breath. Over time, it also drives systemic inflammation, which is a huge contributor to autoimmune disease progression.
When I look at blood work for these clients, I often see subtle but telling signs. Low haemoglobin or borderline anaemia is common, as is evidence of red blood cell destruction, like elevated bilirubin or LDH levels. For some clients, we even find fragmented red blood cells, which point to ongoing stress on their blood.
My approach to supporting clients
When I see these patterns in my clients, the first step is always to restore balance to the gut. That might mean working on gut-healing protocols to repair the gut lining, introducing targeted antimicrobials or probiotics, and using dietary strategies to reduce inflammation. Foods like stewed apples, rich in pectin to support gut bacteria, and anti-inflammatory nutrients like omega-3s are staples in the plans I create.
If you are experiencing bloating, you can watch my free workshop, Nutrition Essentials to Beat the Bloat, here.
I also focus on improving red blood cell health through iron-rich, nutrient-dense foods and ensuring the gut is able to absorb those nutrients properly. Supporting the gut and red blood cells simultaneously often leads to profound improvements—not just in energy levels but also in reducing autoimmune flares and improving overall resilience.
Also, reducing stimulants like coffee and alcohol can help to restore your gut function. You can learn more about the effects of alcohol on your gut in this article I was featured in for The Telegraph, “What alcohol can do to your midlife gut health.”
This connection between gut bacteria, red blood cells, and autoimmune disease is something I wish more people knew about. It’s not just about addressing the obvious symptoms; it’s about uncovering the underlying imbalances that keep people stuck in cycles of fatigue, inflammation, and illness. When we start to address these imbalances, it’s amazing to see how the body can begin to heal itself.
Ready to take the first step toward better health? Download my free guide, The Autoimmunity Recovery Plan, for a five-step approach to making lasting changes. Get it here.
Want to learn more about what I do? Explore the services offered at The Autoimmunity Nutritionist here.
VJ Hamilton, BSc, RNT
VJ Hamilton is a Registered Nutritionist (BANT) and an expert in autoimmune disease. VJ combines her knowledge from her medical science degree in Biochemistry & Immunology with Nutritional Therapy to offer a thorough and personalised approach to support her clients based on the most current scientific research. VJ runs a virtual and in-person nutritional therapy and functional medicine practice, The Autoimmunity Nutritionist, specialising in gut skin and immune health.