When I started Fermentfulness, I called it fermentation and mindfulness for a reason. My own path back to health was never only about what was in the jar. Yes, L. reuteri and SIBO yogurt changed my life, and I'll be grateful to Dr. Davis forever for that. But healing, honestly, turned out to be bigger than nutrition. It was body, mind, and something quieter underneath both—a felt sense of whether I was safe or bracing.
Nothing has helped me understand that quiet layer better than learning about the vagus nerve and polyvagal theory. It gave language to things I'd felt but couldn't name: why stress lingers in the body long after the stressful thing is gone, why chronic illness and chronic tension seem to travel together, why old patterns and cravings grip hardest when we feel unsafe, and why presence—that fresh, awake, the-world-is-alive feeling—comes and goes like weather.
This is a long one, because there's so much to say. Let's take it gently.
This article is for educational purposes only and is not medical advice. Nothing here diagnoses, treats, or cures any condition. Please work with a qualified healthcare provider, especially if you live with chronic illness, trauma, or mental health concerns.
#What Is Polyvagal Theory? (The Short Version)
Polyvagal theory, developed by neuroscientist Dr. Stephen Porges, proposes that the autonomic nervous system has not two states but three, organized by the vagus nerve—the long, wandering nerve connecting the brainstem to the heart, lungs, and gut. Instead of just "stress" (sympathetic) versus "calm" (parasympathetic), it describes a ventral vagal state of safety and connection, a sympathetic state of fight-or-flight, and a dorsal vagal state of shutdown [1].
That third state is the piece most of us were never taught—and it changes everything about how we understand stress and healing.
#Beyond "Fight or Flight vs. Rest and Digest"
Most of us learned a tidy two-part model in school. The sympathetic nervous system revs you up for danger; the parasympathetic nervous system calms you down to rest and digest. Push and brake. Stress and relaxation.
It's a useful model, but it's incomplete—and that incompleteness matters. Because if calm is simply "the brake," then why do so many people who are exhausted, ill, depressed, or numb not feel calm at all? They feel shut down. Foggy. Disconnected. Frozen. If there are only two options, that state doesn't fit anywhere.
Porges' insight was that the parasympathetic "brake" isn't one thing. The vagus nerve has two functionally different branches: an older, unmyelinated branch and a newer, myelinated branch that appears in mammals. He argued these branches produce two very different experiences—one of connection, one of collapse—and that our bodies move between them in a predictable order [1]. Suddenly there was a name for the frozen, numb, checked-out state that "rest and digest" never explained.
#The Three States of Your Nervous System
Think of these less as a ladder you're stuck on and more as three colors your inner weather moves through, often many times a day.
#Ventral Vagal: Safe and Social
This is the state of the newer, myelinated vagus. When your nervous system reads the world as safe, this branch is online. Your heart rate is steady, your breathing is easy, your face is expressive, your voice has warmth and range. You can make eye contact, hear the human frequencies in someone's voice, digest your food, think flexibly, and feel genuine connection.
Porges links this branch to what he calls the social engagement system—the wiring of the face, ears, voice, and heart that lets mammals soothe each other and cooperate [1]. Ventral vagal is where healing happens, where creativity flows, where you feel present. It's the physiological home of the freshness and aliveness I think we're all quietly chasing.
#Sympathetic: Fight or Flight
When your system detects a threat, it mobilizes. Adrenaline and cortisol rise, the heart pounds, muscles tense, attention narrows to the danger. This is fight-or-flight—brilliant for outrunning something dangerous, exhausting when it never switches off.
In modern life, the "threat" is rarely a predator. It's a deadline, an unread message, a difficult memory, a body in pain. The mobilization is the same. Chronic sympathetic activation is the low-grade urgency and irritability so many of us live in without noticing.
#Dorsal Vagal: Shutdown and Freeze
This is the state that reframes so much. When a threat feels inescapable—too big to fight, too fast to flee—the oldest branch of the vagus can pull the system into shutdown. Heart rate and energy drop, digestion slows, and we go numb, foggy, disconnected, or collapsed. In animals it's the "play dead" response. In humans it can look like depression, dissociation, chronic fatigue, hopelessness, or that hollow "I'm here but not really here" feeling.
Understanding dorsal vagal was a turning point for me. So much of what we judge as laziness, apathy, or lack of willpower may be a nervous system that has hit its limit and protected itself the only way it knew how. That reframe—from broken to protective—is where self-compassion begins.
#Neuroception: Why Your Body Decides Before You Do
Here's a word worth keeping: neuroception. Porges coined it to describe how the nervous system detects safety or danger beneath conscious awareness [1]. Before you have a single thought, your body has already scanned the tone of a voice, the tension in a face, the pit in your stomach, the memory in your muscles—and shifted states accordingly.
This is why you can't simply think your way calm. You can know, logically, that you're safe and still feel your chest brace. Neuroception is faster than thought and often shaped by the past. Which means the work of regulation isn't about arguing with yourself—it's about sending your body new signals of safety it can actually feel. We'll get to how.
#What This Reframes: Stress, Chronic Illness, Addiction, and Presence
For me, the power of this lens is how much it explains once you're holding it.
#Chronic Illness and Inflammation
The vagus nerve isn't only about mood—it's a physical regulator of the body. One of its best-established roles is calming inflammation. Neurosurgeon Dr. Kevin Tracey mapped what he called the inflammatory reflex: the vagus nerve senses inflammatory signals and, through a "cholinergic anti-inflammatory pathway," tells the immune system to dial down the release of inflammatory molecules like TNF [2]. This is real, well-replicated physiology, and it's part of why vagus nerve stimulation is being studied for inflammatory conditions.
Alongside it, researchers use heart rate variability (HRV)—the subtle beat-to-beat variation in your pulse—as a window into vagal activity. Higher HRV generally reflects a more flexible, resilient nervous system; chronically low HRV has been associated with higher inflammatory markers and poorer stress recovery [3]. None of this means low vagal tone causes any specific disease, or that "toning your vagus" cures illness. But it offers a plausible thread tying together something many of us with chronic conditions have sensed: that unrelenting stress and physical illness are not separate stories.
#Addiction and Patterns
Polyvagal theory reframes cravings and compulsions as, in part, attempts to regulate state. When we're stuck in sympathetic urgency or dorsal collapse, the pull toward anything that promises quick relief—food, screens, substances, distraction—makes painful sense. The behavior isn't the disease so much as a strategy for a nervous system that doesn't feel safe. This doesn't excuse harm or replace real recovery support, but it can soften the shame that keeps patterns locked in place. You're not weak; you're dysregulated and reaching for relief. That reframe opens the door to gentler, more effective ways in.
#Presence, Freshness, and the "Magic" of Being Alive
This is the part I find most beautiful. That quality of presence—when colors seem brighter, food tastes fuller, conversation flows, and life feels fresh—maps closely onto the ventral vagal state. When we feel safe, the nervous system stops guarding and starts receiving. Awareness opens. Curiosity returns. The same walk, the same meal, the same person can feel dull in shutdown and luminous in safety.
So a huge part of what we might call mindfulness or spiritual practice can be understood, in nervous-system terms, as cultivating access to ventral vagal safety—and building the awareness to notice which state you're in. You can't force presence. But you can learn the conditions that invite it.
#An Honest Word About the Science
Because Fermentfulness is built on trust, I won't oversell this. Polyvagal theory is a compelling framework, and it has been genuinely helpful to millions of people and clinicians. It's also scientifically debated, and honesty means saying so.
Several researchers have challenged some of Porges' specific anatomical and evolutionary claims—for example, whether the myelinated "smart vagus" is truly unique to mammals, and whether respiratory sinus arrhythmia cleanly measures vagal tone [4]. Some critics argue the theory's core premises are untenable; Porges and others counter that the critiques misread the theory. That debate is ongoing and worth respecting.
Here's how I hold it: the underlying science—that the vagus nerve regulates the heart, gut, and immune system; that HRV reflects autonomic flexibility; that safety and connection change our physiology—is well supported [2][3]. Some of the interpretive framework built on top is contested. You can find the polyvagal map useful for navigating your inner states without treating every detail as settled fact. A map doesn't have to be perfect to help you find your way home. I use it as a lens, not a law.
#The Gut Connection: Your Microbiome Talks to Your Vagus
Now for the part that ties this back to the jars on my counter.
The vagus nerve is the main physical highway of the gut-brain axis—the two-way conversation between your digestive tract and your brain [5]. Roughly 80% of vagal fibers are afferent, meaning they carry information up from the gut to the brain far more than the other way around. In a real sense, your gut is constantly briefing your brain on how things are going down there, and that briefing helps set your nervous system's tone.
Your gut microbes are part of that conversation. In a now-classic study, mice fed a specific Lactobacillus rhamnosus strain showed calmer behavior and changes in brain receptors for GABA (a calming neurotransmitter)—but when the vagus nerve was cut, those effects disappeared [6]. The message traveled along the vagus. It's mouse research, so we shouldn't overstate it for humans, but it's striking evidence that the bacteria in your gut can speak to your brain through this nerve. This is the science behind the emerging idea of "psychobiotics"—microbes that may influence mood.
There's an even sweeter thread. Certain L. reuteri strains—the same species behind the yogurt so many in the Dr. Davis community make—have been shown in animal studies to raise levels of oxytocin, the connection-and-bonding hormone [7], and oxytocin signaling is itself closely tied to vagal pathways. Oxytocin, bonding, ventral vagal safety, a warm bowl of homemade yogurt: I don't think that overlap is a coincidence, even if the human science is still young and these are early findings, mostly in mice.
So while I'd never claim that fermented food "fixes" your nervous system, tending your gut is a genuine, tangible way to support the whole gut-brain-vagus loop. If you want the deeper microbiome science, Dr. Davis's Super Gut is where I'd start, and our guide to the best L. reuteri starter cultures will get you making it. A daily bowl of L. reuteri or SIBO yogurt or a glass of kefir is, to me, one more signal of care I send my body every morning.
This post contains some affiliate links. If you buy through them, I may earn a small commission at no extra cost to you—it helps keep Fermentfulness free. I only point to things I genuinely use and trust.
#Toning the Vagus: Gentle Ways Back to Safety
You can't command your nervous system into ventral vagal. But you can offer it cues of safety, consistently, until the path back gets easier to find. Think of these as practices, not fixes—and go gently, especially if you carry trauma, where some techniques can feel activating rather than calming. Results vary, and slower is usually kinder.
Slow, extended-exhale breathing. This is the most evidence-backed of all. Breathing slowly—around five to six breaths per minute, with the exhale longer than the inhale—reliably increases heart rate variability and vagal activity [8]. Try inhaling for a count of four and exhaling for six or eight. A few minutes is enough to feel a shift.
Humming, singing, chanting, gargling. The vagus is connected to the muscles of the voice box and throat. Humming a tune, chanting, singing in the car, or even vigorously gargling water gently stimulates it. There's a reason humming feels soothing and communal singing feels like belonging.
Cool water. Splashing cold water on your face, or a cool end to a shower, activates the "dive reflex" and can nudge the system toward calm. Start mild; this is meant to be a gentle signal, not a shock.
Connection and co-regulation. This is the big one, and the most overlooked. Our nervous systems regulate each other. A warm face, a kind voice, a safe hug, time with a trusted friend or animal—these are ventral vagal cues from the outside in. We are wired to find safety in each other. You don't have to do this alone.
Gentle movement and time in nature. Walking, stretching, yoga, dancing, and unhurried time outdoors all help discharge sympathetic activation and coax the system toward safety.
Mindful, unhurried eating. Digestion itself is a ventral vagal activity—you literally cannot digest well in fight-or-flight. Slowing down at meals, savoring, feeling gratitude for the food (that morning bowl of yogurt included) is nervous-system practice disguised as breakfast.
The real skill underneath all of these is awareness: learning to notice, without judgment, which state you're in right now. Am I mobilized? Shut down? Safe and open? That noticing is itself a ventral vagal act—and the first step home.
#The Bottom Line
Learning about the vagus nerve didn't replace anything in my healing—it wove the pieces together. It gave me a way to understand that the yogurt on my spoon and the breath in my chest and the people at my table are all speaking to the same nervous system, all sending the same essential message: you're safe now, you can soften.
Polyvagal theory is a lens, not a doctrine, and I hold its debated parts lightly. But the deeper truth it points to feels solid to me: healing happens in safety. Not in pushing harder, but in helping the body feel safe enough to open, digest, connect, and come fully into the present. That's the whole heart of Fermentfulness—gut-rooted, heart-guided, soul-nourished. Fermentation feeds one end of that conversation. Presence tends the other.
Be gentle with yourself as you explore this. Your nervous system has been protecting you all along.
Individual results vary, and this article is educational, not medical advice. If you're struggling with trauma, chronic illness, mental health, or addiction, please reach out to a qualified professional—nervous-system work is most powerful alongside real support, not instead of it.
#References and Further Reading
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Polyvagal theory overview: Porges SW. "The polyvagal theory: New insights into adaptive reactions of the autonomic nervous system." Cleveland Clinic Journal of Medicine. 2009. PubMed
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The vagus nerve and inflammation: Tracey KJ. "The inflammatory reflex." Nature. 2002. PubMed
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Vagal tone, HRV, and inflammation: Haensel A, et al. "The relationship between heart rate variability and inflammatory markers in cardiovascular diseases." Psychoneuroendocrinology. 2008. PubMed
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Scientific critique of polyvagal theory: Grossman P. "Fundamental challenges and likely refutations of the five basic premises of the polyvagal theory." Biological Psychology. 2023. ScienceDirect
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The vagus and the gut-brain axis: Breit S, et al. "Vagus Nerve as Modulator of the Brain–Gut Axis in Psychiatric and Inflammatory Disorders." Frontiers in Psychiatry. 2018. Frontiers
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Gut bacteria signaling via the vagus: Bravo JA, et al. "Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve." PNAS. 2011. PNAS
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L. reuteri and oxytocin (animal study): Poutahidis T, et al. "Microbial Symbionts Accelerate Wound Healing via the Neuropeptide Hormone Oxytocin." PLoS One. 2013. PubMed
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Slow breathing and vagal activity: Laborde S, et al. "Effects of voluntary slow breathing on heart rate and heart rate variability: A systematic review and meta-analysis." Neuroscience & Biobehavioral Reviews. 2022. ScienceDirect
