Hi Friend
I hope you are well, this is part 3 of explaining your chronic symptoms. If you missed it here is a free nervous system assessment and plan builder.
Today I want to talk about something that almost every one of you has experienced…
Stress that feels “in your body.” Not just emotional stress — but physical symptoms, flare-ups, gut issues, brain fog, fatigue, and pain that get worse when life becomes overwhelming.
This isn’t in your head.
There’s a real biological pathway driving it:
The Chronic Stress → HPA Axis → Leaky Gut → Microglial Activation Loop
Once you understand this loop, your symptoms finally start to make sense.
Let’s break it down step by step.
1. Your HPA Axis: The Stress Command Centre
When you’re under chronic pressure — emotionally, physically, or from illness — your HPA axis (Hypothalamic–Pituitary–Adrenal axis) stays switched ON.
In the short term, this saves your life.
In the long term, it quietly damages your body.
Here’s what happens:
Cortisol rises
Adrenal signalling stays activated
Your nervous system shifts into threat mode
Your parasympathetic system (rest-digest-heal) becomes suppressed
Digestion slows
Gut inflammation increases
This is not a psychological issue — it is biochemical.
2. Stress Begins to Break Down Your Gut Barrier
Your gut lining is held together by “tight junctions” — think of them as tiny gates that decide what can pass through.
When the HPA axis stays activated:
Cortisol weakens tight junction proteins
Gut motility slows
Blood flow to the gut reduces
Your gut bacteria change (more inflammatory species grow)
The lining becomes permeable — this is the beginning of leaky gut
This isn’t fringe science anymore.
It’s one of the most research-supported mechanisms in chronic illness, fibromyalgia, ME/CFS, long COVID, MCAS, and neuroinflammatory conditions.
3. Undigested Food + Toxins + Bacterial Fragments “Leak” Into the Bloodstream
Once the gut barrier becomes permeable, molecules that should stay inside the gut escape into the bloodstream. These include:
LPS (lipopolysaccharides) from bacteria
Partially digested food proteins
Histamine and inflammatory compounds
Environmental toxins
Metabolic waste
Your immune system responds as if you’re under attack.
This is often the point where people begin to notice:
Bloating
Food reactions
Histamine sensitivity
Fatigue after eating
Skin flare-ups
Joint pain
Mood swings
Cognitive fog
“Wired but tired” sensation
This isn’t random.
It’s your immune system on high alert.
4. Microglia in the Brain Detect This Inflammation
Microglia are your brain’s immune and surveillance cells.
When inflammatory signals leak from the gut into the bloodstream, they can activate microglia via:
Vagus-nerve signalling
Cytokine receptors
Compromised blood-brain barrier
HPA-axis signalling pathways
Activated microglia shift into a “defensive phenotype,” which leads to:
Increased pain sensitivity
Heightened threat response
Sleep disruption
Cognitive dysfunction
Increased fatigue
Reduced motivation
Emotional overwhelm
Sensory sensitivity
This is why people with chronic gut issues often also have chronic pain, fatigue, anxiety, and brain fog:
Your gut and brain are having the same conversation — and it’s inflammatory.
5. Chronic Stress → Gut Breakdown → Microglial Activation = Symptom Spiral
Once this loop begins, the body gets stuck in it.
Stress inflames the gut.
The gut activates microglia.
Microglia amplify stress signals.
Stress inflames the gut again.
This is the exact biological cycle we help people break inside The Mend Collective.
But here’s what I want you to understand:
❗You cannot “think” your way out of this.
❗You cannot heal just by resting.
❗You cannot fix microglia without fixing the gut.
❗You cannot fix the gut without calming the nervous system.
❗You cannot calm the nervous system if your HPA axis is over-firing.
Healing requires breaking the entire loop — not one piece of it.
6. Why This Matters
If you’ve ever been told your symptoms are “stress-related,” that doesn’t mean they’re psychological.
It means there is a biological explanation for the pain, the fatigue, the gut symptoms, and the brain fog you’re experiencing.
Your body isn’t malfunctioning.
It’s responding to a loop that can be broken.
Tomorrow I will actually give you insights on what you can do to build your gut microbiome, calm your microglia and help reduce cortisol and stress markers in your body.
Regards
Dr Ahmed
