MICROBIOME AND SUGAR
(PART OF THE CYCLE OF ILLNESS: IMMUNE SYSTEM PART 3 / HOW THE MICROBIOME AFFECTS OTHER SYSTEMS)
THESE ARE THE SLIDES TO THE VIDEOS AND THE NOTES. SEE ALSO ENDOCRINE/BLOOD SUGAR, MICROBIOME AND THYROID AS WELL*


Gut Bacteria Influence Glucose Metabolism
Certain gut microbes:
- Help break down carbohydrates more efficiently.
- Produce short-chain fatty acids (SCFAs) like:
- butyrate,
- acetate
- propionate during fiber fermentation.
- SCFAs improve insulin sensitivity and help regulate blood glucose by:
- Reducing inflammation
- Supporting GLP-1 and PYY (hormones that improve insulin secretion & control appetite)

Dysbiosis Can Drive Blood Sugar Spikes
When the microbiome becomes imbalanced (aka dysbiosis):
- Harmful bacteria may increase gut permeability (“leaky gut”)
- This leads to systemic inflammation, which impairs insulin signaling and drives insulin resistance
- Increased lipopolysaccharide (LPS) levels in the blood from bacterial toxins = more inflammation and poor blood sugar control
Microbiome Affects Insulin Sensitivity
- Healthy microbes improve GLUT-4 glucose transport in cells
- Some bacteria (like Akkermansia muciniphila) are linked to better glucose tolerance
- Others (like Firmicutes in excess) are associated with obesity and higher blood sugar

Microbiome Communicates with Endocrine Hormones
Your gut flora influences:
- GLP-1 and GIP (hormones that stimulate insulin after meals)
- Leptin and ghrelin (hunger/fullness signals)
- Cortisol levels via the HPA axis — and high cortisol can spike blood sugar
Blood Sugar Affects the Microbiome Too
Frequent blood sugar spikes from a high-sugar diet:
- Feed yeast and harmful bacteria
- Starve beneficial microbes that thrive on fiber
- Can cause microbiome diversity to shrink
How to Support Both Systems Together
- Eat high-fiber foods (especially prebiotics like inulin, resistant starch)
-Include fermented foods (like kefir, sauerkraut, kimchi) for healthy bacteria
-Avoid ultra-processed carbs and added sugars
-Manage stress (to lower cortisol)
-Sleep well (poor sleep dysregulates blood sugar and gut health)

Gluconeogenesis literally means “making new glucose.” It’s the body’s backup plan for when you don’t have enough carbs — sugar or starch — coming in from food.
Instead of shutting down, your body says: “No worries, I’ll just build some sugar myself!”
This process happens mainly in the liver, and to a smaller degree in the kidneys. It uses building blocks like amino acids from protein breakdown, lactate from exercise or muscle activity, and glycerol from fat breakdown. By doing this, gluconeogenesis keeps your brain, red blood cells, and vital organs fueled — even if you haven’t eaten carbs.
Think of your body like a city. Carbohydrates are the regular shipments of fuel trucks, delivering sugar to the power stations. But sometimes, the trucks don’t show up — during fasting, illness, or a low-carb diet. The city can’t just shut down, so the liver acts like an emergency factory. It takes scrap materials — protein, fat fragments, lactate — and rebuilds them into brand-new fuel: glucose.
That way, the power stays on, even when the regular deliveries stop.
Now, to tie this back to the microbiome: propionate, a short-chain fatty acid produced during fermentation, can be used as raw material for gluconeogenesis. In this way, the microbiome actually donates ingredients — like protein fragments, lactate, or propionate — to the body’s backup generator. This helps regulate blood sugar and metabolism.
So, gluconeogenesis isn’t just a backup plan. It’s a dynamic process that connects diet, liver metabolism, and the microbiome — and it directly links to blood sugar problems when regulation goes wrong.

How Gluconeogenesis Links to Blood Sugar Problems
In healthy people, gluconeogenesis — the process of making new glucose — only runs when needed, such as during fasting or low-carb intake.
But in diabetes, the liver often gets the wrong signals. It keeps cranking out glucose even when blood sugar is already high. This is like a backup generator running full blast even though the power grid is already restored, flooding the system with extra electricity — in this case, sugar. The result is hyperglycemia, or high blood sugar.
On the other hand, if gluconeogenesis isn’t working well, your body can’t make enough sugar between meals. This causes hypoglycemia, or dangerous blood sugar crashes. Think of it as that backup generator failing to start when the lights go out — your brain and organs suddenly don’t have enough fuel.
Normally, insulin acts like a brake on gluconeogenesis, telling the liver: “Stop making glucose, we already have enough.” But in insulin resistance, the liver ignores that brake pedal and keeps producing sugar. This not only raises blood sugar, it makes insulin resistance worse, because the pancreas has to keep pumping out more insulin.
It’s a vicious cycle: insulin resistance leads to more gluconeogenesis, which drives higher blood sugar, which then triggers even more insulin resistance.
Now, here’s where the microbiome fits in. Propionate and other short-chain fatty acids made from fiber fermentation can help fine-tune gluconeogenesis, keeping blood sugar steady instead of letting it swing out of control.
But when dysbiosis — or bad microbiome balance — takes over, it worsens the cycle by feeding insulin resistance, inflammation, and blood sugar crashes or spikes.
So where does this fit into the Cycle of Illness framework? Too much gluconeogenesis drives hyperglycemia, diabetes, and insulin resistance. Too little gluconeogenesis drives hypoglycemia.
The microbiome acts as a modulator — either keeping the balance, or driving the dysfunction.

Fermentation in the gut can be a double-edged sword.
SCFAs regulate inflammation and histamine, while dysbiosis bacteria produce biogenic amines like histamine, tyramine, putrescine, leading to MCAS flares.
In a healthy microbiome, gut bacteria ferment fibers into short-chain fatty acids like acetate, propionate, and butyrate. These SCFAs calm inflammation, stabilize blood sugar, and actually help regulate histamine release from mast cells. This is good fermentation.
But when the microbiome is imbalanced — what we call dysbiosis — the wrong bacteria take over. Bugs like Morganella, Klebsiella, or even certain Lactobacillus strains can ferment carbs and proteins into biogenic amines: histamine, tyramine, putrescine, cadaverine.
This overload spikes histamine in the body, worsening food reactions, IBS, migraines, flushing, and MCAS symptoms. This is bad fermentation.
Here’s why symptoms get worse with dysbiosis. A weak microbiome doesn’t properly break down histamine because DAO enzyme activity in the gut lining is low. At the same time, fermentation is producing more histamine than the body can clear. It builds up in the colon, leaks into the bloodstream, and the “histamine bucket” overflows. The result is inflammation and mast cell activation throughout the body.
So, it works something like this: a weak microbiome allows the wrong bugs to ferment carbs and proteins, leading to more histamine production, less DAO breakdown, systemic overload, and worsening mast cell activation and inflammation — all of which push the microbiome even further out of balance.
In dysbiosis, colon fermentation can worsen symptoms because it fuels histamine instead of just producing SCFAs. But in a healthy microbiome, fermentation is your friend — it helps calm inflammation and keep histamine balanced.
What does this mean???
Think of your gut like a kitchen. Good chefs cook healthy meals out of fiber, making fuel that calms your system. But when the bad chefs take over, they burn the food and fill the room with smoke — that smoke is histamine. The more smoke, the worse your symptoms.
REFERENCES:
https://academic.oup.com/ajcn/article-abstract/85/5/1436/4633161?redirectedFrom=fulltext&login=false
59934691_Marginal_BH4_Deficiencies_iNOS_and_Self-perpetuating_Oxidative_Stress_in_Post-acute_Sequelae_of_Covid-19
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https://www.sciencedirect.com/science/article/abs/pii/B9780127022901500163#:~:text=It%20(%20Glucose%20metabolism%20)%20establishes%20the,is%20more%20strictly%20regulated%20than%20glucose%20supply.
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