Tonight’s case takes us down into the crime scene nobody wants to talk about – poop. Let’s be adults about this – I’m talking about the gut. But of course, we evaluate the gut by looking at poop – well I don’t, but some hopefully overpaid scientists do this in specialty labs. Gut issues and brain issues are closely linked to one another. Remember? Your gut is your second brain.
And I don’t mean “butterflies in your stomach” before a big exam. I mean the burning dumpster fire of dysbiosis that links directly to the brain. In autism, the evidence is piling up like a stack of unfiled police reports.
The suspects?
- Antibiotics handed out like candy.
- C-section births and formula feeding.
- Glyphosate, food dyes, seed oils, and ultra-processed food.
- And the usual gang of thugs: clostridia, yeast, and low microbiome diversity.
The crime? A disrupted gut-brain axis that sets kids up for neuronal inflammation, mitochondrial sabotage, and behaviors we ultimately label “autism.”
The motive? Well, that depends on whether you think this is accidental… or by design. My tin foil hat is always freshly ironed.
I’m Dr. Kristen Lindgren, and welcome back to The Dysfunction Files. We kicked off this Autism mini series following the HHS presser implicating Tylenol (and maybe vaccines) as causal agents in the etiology of autism and how a B vitamin called Leucovorin or folinic acid might fit into that picture as a therapeutic agent. Last week, we took a 30,000 ft view of autism – a spectrum of similarly appearing diagnoses that, in all likelihood, have many different causal factors. This week, we’re focusing on the trail of evidence from the gut to the brain – and it’s looking less like coincidence and more like conspiracy.
Let’s get into it.
The Crime Scene – The Gut-Brain Axis
The gut isn’t just a digestive tube. It’s a neural hub, often called the “second brain.” It houses over 100 million neurons – more than the spinal cord – and communicates constantly with the brain via the vagus nerve.
Here’s why that matters:
- When the gut is inflamed, the brain doesn’t just notice – it responds.
- When the gut leaks toxins into the bloodstream, the brain mounts a defense.
- And when the wrong microbes dominate the gut, they don’t just upset digestion. They rewrite neurotransmitters and alter brain behavior.
Think of it like a bad open mic night: the helpful microbes – the healthy Bifidobacteria and Lactobacillus species – never get the stage. Instead, the drunk loudmouths – clostridia, candida, and opportunists – hog the mic. And what they’re singing isn’t music.
It’s toxic metabolites like propionic acid, a compound that can mimic autistic behaviors in lab animals.
So when parents say, “My kid’s autism symptoms get worse when his stomach is a mess” – they aren’t imagining it. They’re describing the gut-brain axis in action.
The Suspects – Dysbiosis
Let’s line up the usual suspects:
Clostridia species – The Propionic Acid Factory
Clostridia are normal gut residents… but when they take over, things get ugly. These bacteria pump out something called propionic acid, a short-chain fatty acid that in small amounts is harmless – but in excess becomes a neurotoxin. We see production of propionic acid in over drive in specific patterns of dysbiois – especially when beneficial butyrate producers are depleted (Faecalibacterium prausnitzii… Roseburia… Eubacterium rectale… Anaerobutyricum) and fermentative species take over (Clostridium species, Candida, Enterococcus) – a pattern often seen in kids with autism, chronic inflammation, or high sugar diets. In that terrain, Clostridia shift into overdrive, flooding the system with this propionic acid situation that crosses the gut–brain barrier, disrupts neurotransmitters, and hijacks mitochondrial function like a tiny biochemical arsonist.
And here’s where the plot thickens:
- In animal studies, when scientists inject propionic acid directly into the brains of rats, the animals develop autism-like behaviors: repetitive movements, social withdrawal, even seizures.
- In kids with autism, stool and urine samples often show elevated propionic acid compared to neurotypical peers.
- And to add insult to injury? Food manufacturers actually add propionic acid to bread, dairy, and processed foods as a preservative. So kids already overproducing it in the gut are getting an extra dose in their diet. Nice.
What does PPA do? It rewrites brain chemistry:
- It alters dopamine and serotonin signaling.
- It blocks carnitine transport, strangling mitochondria and leaving neurons starved for energy.
- It ramps up inflammation and oxidative stress.
Think of it as the mob boss of dysbiosis – sending orders from the gut that leave the brain in chaos.
Candida/yeast overgrowth
Candida ferments sugar into acetaldehyde, a toxic alcohol byproduct. Imagine your toddler’s brain getting micro-dosed with alcohol all day, every day. That fogs attention, slows speech, and destabilizes mood.
Low diversity microbiome
Multiple studies show kids with autism have less microbial diversity. A healthy microbiome is like a rainforest – dense, balanced, resilient. Autism kids’ guts look more like a strip-mined desert. Weeds, thorns, and not much else.
The Accomplices – Modern Lifestyle
Dysbiosis doesn’t just appear out of nowhere. It’s manufactured by modern living:
- Antibiotics: A single course can wipe out years of microbial diversity, leaving resistant bad actors to move in.
- C-section birth: Babies born by C-section miss the maternal vaginal microbiome “starter kit” and instead pick up microbes from the hospital environment.
- Formula feeding: Breast milk contains unique sugars (HMOs) that specifically feed protective gut bacteria. Formula replaces them with cow’s milk proteins and processed sugars.
- Glyphosate: This weed killer, sprayed on much of our food, doubles as an antibiotic. It preferentially kills the good bacteria, letting clostridia thrive.
Together, these accomplices create the perfect breeding ground for gut dysfunction – and by extension, brain dysfunction.
Leaky Gut, Leaky Brain
Now the plot thickens.
The cells that line your gut are called enterocytes and they are literally cemented together like a brick wall. Nothing gets in or out of that lining unless it’s intentional – you need receptors and transports because everything your body doesn’t need is headed for your toilet. There’s no willy nilly criss-crossing through the gut wall lining. Unless it’s leaky, of course. When the intestinal barrier weakens, you get leaky gut. Tight junction proteins loosen, and bacterial toxins like lipopolysaccharides (LPS) seep into the bloodstream.
The immune system reacts like a SWAT team crashing through the door – cytokines, inflammation, and collateral damage.
And here’s the kicker: kids with autism often have a compromised blood-brain barrier too. So those same inflammatory molecules march straight into the brain. The result? Chronic brain inflammation, neurodevelopmental disruption, and behaviors we can see – but conventional medicine often shrugs at.
The Evidence Trail – Propionic Acid, Mitochondria & Stool Testing
This is where the evidence really piles up.
Let’s go back to our prime suspect – clostridia. Remember, they pump out propionic acid (PPA), and in small amounts it’s harmless. But in excess? It’s a neurotoxin with a rap sheet a mile long.
Here’s what PPA does:
- Mitochondrial sabotage → PPA blocks the transport of carnitine, the shuttle system that ferries fatty acids into the mitochondria. Without carnitine, neurons can’t burn fat for energy. They stall, misfire, and run on fumes.
- Neurotransmitter chaos → PPA alters dopamine and serotonin signaling, changing how kids process reward, focus, and mood.
- Neuroinflammation → PPA ramps up oxidative stress and cytokines, leaving the brain inflamed and irritable.
- Behavioral proof → In lab animals, injections of propionic acid trigger autistic-like behaviors: repetitive movements, social withdrawal, even seizures. That’s not coincidence – that’s a smoking gun.
And again, propionic acid isn’t just made in the gut. It’s also added to food as a preservative. Bread, cheese, processed snacks – all stamped “safe,” while quietly dosing kids with the very same compound linked to autistic behaviors.
So how do we catch it in the act? Enter comprehensive stool testing.
- Tests like the GI-MAP or an Organic Acids Test (OAT) don’t just list who’s living in the gut – they measure the damage.
- They can flag clostridia overgrowth, show markers of PPA metabolites like HPHPA, and reveal leaky gut indicators like zonulin.
- It’s basically a crime lab report on the microbiome, complete with fingerprints and a list of accomplices.
And once you know who’s running the show, you can actually intervene — lower PPA production, support mitochondria with carnitine and antioxidants, and restore balance to the gut ecosystem.
The Experimental Frontier — Fecal Transplants & The Microbiome Reset
Now – if you thought the story couldn’t get any weirder – hold on to your hazmat suit.
Because the next twist in this case involves a treatment so literal it almost sounds like a punchline: fecal microbiota transplantation, or FMT.
Yes, you heard that right. A poop transplant.
I told you this episode might get messy.
The idea is shockingly simple: if a child’s gut ecosystem is a crime scene dominated by bad actors like clostridia and yeast, then maybe the fastest way to restore order is to replace the whole microbial population with one from a healthy donor. It’s a total microbiome reboot.
Dr. David Perlmutter has written extensively on this. He calls it a “reset button for the gut”-and while it’s still experimental, the data are starting to look… promising.
Here’s what researchers have found so far:
- In early open-label studies of kids with autism and severe GI issues, FMT and its cousin, Microbiota Transfer Therapy (MTT), not only improved constipation and diarrhea, they cut behavioral symptom scores almost in half – and some of those gains persisted two years later.
- Follow-up work from Arizona State University’s research team showed sustained microbial diversity and reduced levels of the very toxins – like propionic acid – that we just talked about.
- Animal studies back it up: when scientists transfer gut microbes from neurotypical mice into autistic mouse models, social interaction improves and inflammation drops.
But before anyone starts ordering black-market donor samples on eBay, let’s talk reality.
This therapy isn’t FDA-approved for autism – or for anything beyond recurrent C. difficile infection in the U.S. The trials we have are small, open-label, and tightly controlled. Donor stool must be screened like it’s auditioning for NASA: parasites, viruses, antibiotic resistance genes – all have to be ruled out. Because along with friendly bacteria, you could also transfer something far worse.
And results aren’t always permanent. Some kids lose benefits after a few months; others need maintenance dosing or follow-up probiotic protocols to hold the gains.
Still, FMT is proof of concept that the microbiome itself can be therapeutically engineered. That’s a huge paradigm shift. Instead of targeting one microbe or one pathway, we restore an entire ecosystem.
So yes – it’s gross. It’s controversial. But it’s also the boldest evidence yet that the gut and brain are inseparably linked… and that when you fix the terrain, the brain starts to heal.
Now let’s talk about the tools you can actually use today to start cleaning up the crime scene.
The Roadmap – How To Clean Up The Crime Scene
Parents often ask: “Okay, but what do we do?”
Here’s the roadmap I use in practice:
1. Test, Not guess – you don’t know what on God’s green earth you’re dealing with until you test it. Just because we see ‘patterns’ of dysbiosis in autistic populations doesn’t mean it’s universal. Everyone is different. Poop in the box and find out.
2. Elimination diets – Ideally you test here too for food sensitivities. But regardless of what that test shows, gluten and dairy are big offenders. Refined sugar, fake sugar or sugar alcohols, food dyes, and seed oils. Get ‘em outta there. Some kids also react to soy and corn. Pulling these foods reduces inflammation and improves behavior almost universally. Is this easy? No. It’s not. I’m not promoting the gluten free chicken nugget but hey – at least it doesn’t contain any gluten. Remember, every positive change helps. This isn’t all or nothing.
3. Probiotics & prebiotics
- Targeted probiotics help reintroduce missing species.
- Prebiotic fibers feed the good guys, restoring balance.
4. Gut lining repair
- Nutrients like L-glutamine, zinc carnosine, omega-3s strengthen the intestinal barrier.
- Collagen and bone broth can also be supportive.
5. Antifungals/antimicrobials
- Herbal protocols (oregano oil, berberine, caprylic acid) or prescriptions if necessary.
- These knock back yeast and clostridia overgrowths.
6. Diet upgrade
- Whole-food, organic, low-glyphosate diets.
- Less sugar, less processed food, more diversity.
I can’t emphasize this enough: Heal the gut, calm the brain.
Case Study: Sophia
Sophia was developing perfectly – until she wasn’t.
Around her first birthday, her parents watched the light dim. Eye contact faded, words disappeared, and climbing became her new language. After months of ‘wait and see,’ a Zoom-era psychiatrist labeled her Level 3 autism.
But her mom wasn’t ready to accept that as the end of the story.
In 2025, she brought Sophia to us. We started in the gut – because that’s where inflammation whispers before it screams. Two rounds of Nystatin, gentle silver for H. pylori, diet cleanup, and later spore-based probiotics. Within months, words returned. Sleep improved. The light came back.
Today, Sophia counts to twelve, sings her ABCs, and tells you her favorite color. Her brain is catching up because her gut has finally calmed down
Closing
So what have we uncovered?
The gut isn’t an innocent bystander in autism. It’s a co-conspirator – maybe even the mastermind. Dysbiosis poisons the brain. Leaky gut fuels inflammation. Mitochondria are strangled. And kids pay the price.
But here’s the hopeful part: when you heal the gut, you give the brain a fighting chance.
