If you’ve ever come home from what should have been a normal day and spent the next week in bed, this episode is for you.
Today we’re talking about post-exertional malaise, ME/CFS, long hauler fatigue, and chronic muscle pain from the perspective of someone who both treats these conditions and lives with them. Dr. Alison DiBarto Goggin walks through the full spectrum of fatigue, from normal soreness after overdoing it at the gym to the kind of debilitating exhaustion where chewing food is an effort and getting to the bathroom leaves you breathless.
In this episode you’ll learn what myalgic encephalomyelitis actually means and why it matters, how post-exertional malaise differs from ordinary tiredness, why this is not a deconditioning problem and why pushing harder makes it worse, what NIH-funded research is telling us about the gut microbiome and ME/CFS, what testing can and cannot tell us right now, and what a real functional medicine approach to these conditions looks like, including diet, gut health, mitochondrial support, viral protocols, and pacing strategies.
This episode is for women who are tired of being told they just need more exercise, more sleep, or more willpower. There are biological reasons your body responds the way it does. There are root causes worth investigating. And there is a path forward.
Resources mentioned in this episode are available at https://us.fullscript.com/plans/littleblackbagmedicine-pems and http://www.littleblackbagmedicine.com. To work with Dr. Alison directly, schedule online at the same link.

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Transcript:
SEGMENT 1: Understanding the Spectrum of Fatigue and Pain

Welcome back to Functional Wellness with Dr. Alison. I’m Dr. Alison DiBarto Goggin, and today we’re diving into chronic fatigue and specifically the muscle fatigue, joint pain, and brain fog.
We’re talking about post-exertional malaise, muscle fatigue, joint pain, and the full spectrum of what it means to live in a body that seems to be working against you. Whether you’re dealing with ME/CFS, long COVID, autoimmunity, or something that doesn’t have a clean label yet, this episode is for you.

Let me start by mapping out the spectrum, because not all fatigue is created equal.
On one end, we have what I call normal physiological fatigue. You go back to the gym after a month off. You spend the weekend shoveling snow or moving furniture. You wake up the next day sore, stiff, maybe walking a little funny. Your muscles are talking to you. That is normal. That is expected. Give it two or three days, keep moving gently, hydrate, and it resolves on its own. This is very different from chronic fatigue.
Then there is a middle ground, where the soreness doesn’t fully resolve, or where your recovery time starts to stretch a little longer than it should. Maybe you feel run down for a week after a busy weekend. You notice that your energy just isn’t bouncing back like it used to. This is where we start to pay attention, because this is often the early whisper of something deeper.

And then we have the far end of the spectrum, and this is where I want to spend most of our time today. This is the fatigue where moving through your day feels like moving through water. Where your muscles are so exhausted that chewing food becomes an effort. Where getting from your bed to the bathroom leaves you breathless. Where you wake up in the morning feeling like you didn’t sleep at all, like your body ran a marathon while you were lying still. And then you get up and try to do it again.

This is the fatigue that is accompanied by joint pain, by that deep bone-level aching that doesn’t resolve with rest or Ibuprofen. It’s the spinal stiffness, the neck and shoulder tension that is sometimes called coat hanger pain because of exactly where it sits and how it weighs on you. It’s the brain fog, the cognitive heaviness where you can’t find your words, can’t hold a thought, can’t follow a conversation.

This is what is medically known as malaise, and specifically, post-exertional malaise (PEM). In my house, I just call it the PEMS, not DOMS because it is not just being tired after activity. It is a whole body worsening of symptoms that can begin immediately after exertion, or it can be delayed by hours or even days. And here is the part that makes it so difficult to live with: the activity that triggers it does not have to be exercise. It can be a grocery run. A long conversation or a triggering one. An afternoon at a museum. A full day visiting family. You come home, and then you crash, and you don’t recover in a day or two. Sometimes it takes a week. Sometimes longer.

Now let’s talk about the conditions that live on this end of the spectrum, because understanding the language matters. The ME in ME/CFS stands for myalgic encephalomyelitis. Myalgic means muscle pain, and encephalomyelitis refers to inflammation of the brain and spinal cord. ME/CFS is classified as a neurological disease. It is so important to say that this is not a lifestyle problem, it is not laziness, and it is absolutely not imaginary. What we do know is that it involves measurable disruptions in the nervous system and the immune system. Research published in the National Library of Medicine describes it as a complex, multisystem neurological disease with evidence of neuroinflammation.
And then there is CFS, or chronic fatigue syndrome. These terms are often used interchangeably, but they are technically distinct. CFS is diagnosed primarily around the symptom of profound unexplained fatigue, accompanied by at least four additional symptoms such as unrefreshing sleep, cognitive difficulty, headaches, or sore throat, persisting for six months or more. ME has a narrower definition with muscle weakness and post-exertional malaise as the central, non-negotiable features.

Both can exist together. And both frequently show up in people who have a history of viral infections, autoimmune conditions, or significant environmental exposures like mold. Women are diagnosed with ME/CFS between one and a half to four times more often than men, and research consistently shows that women also tend to experience more severe symptoms and a greater number of co-occurring conditions. That is not a coincidence. That is a pattern worth paying attention to.
SEGMENT 2: How Do You Know If This Is What You Have?
So how do you know if what you’re experiencing falls into this category? First, I want to say something important. You know because you cannot function the way that a healthy person can. Not the way you used to. Not the way the people around you do.

I’ll use myself as an example. Last year I spent a full day out, doing what most people would call a normal, enjoyable day. The zoo, dinner out, time with people I love. I came home and had a low-grade fever. I couldn’t think clearly. I didn’t leave my bed for three days. That is not normal recovery from a good day. That is post-exertional malaise. And I live this too.

I ask my patients a question that I find very revealing: do you wake up in the morning feeling like you had the party of your life the night before, even though you didn’t have a drink? That hangover feeling without the party? If your answer is yes, we need to talk about what is happening in your immune system, your nervous system, and your brain inflammation. That is often the fingerprint of autoimmunity and immune dysregulation.

Testing: What We Have and What We Don’t
Let me be honest with you about testing, because I think it’s one of the most frustrating parts of navigating these conditions. Currently, there is no single confirmatory lab test for ME/CFS, post-exertional malaise, or fibromyalgia. Diagnosis is clinical, meaning it is built from your symptoms, your history, and the process of ruling out other causes.
For ME/CFS specifically, diagnosis requires symptoms to be present for at least six months, including a substantial reduction in your ability to function, post-exertional malaise, and unrefreshing sleep, plus either cognitive impairment or orthostatic intolerance. This is the 2015 IOM criteria that the CDC now uses.

There is no blood test that says, yes, this is ME. We do have genetic testing now that can offer insight into detoxification pathways, methylation, and immune regulation, and that can absolutely be part of the picture. An MRI can sometimes show changes in brain tissue or inflammation. A tilt table test can help diagnose the POTS component that often accompanies these conditions. A sleep study is important because disordered sleep is both a symptom and a driver.
For fibromyalgia, diagnosis involves pressure point sensitivity and meeting specific clinical criteria. Again, no blood test.

For post-exertional malaise on its own, there is currently no standard test. We are hoping that in the future we will see options like muscle biopsy or more targeted metabolic testing, but we are not there yet.
What we can and should test for are the root causes that drive or worsen these conditions: iron, ferritin, thyroid function, complete blood count, inflammatory markers like CRP and cytokines, viral loads including Epstein-Barr and COVID antibodies, autoimmune panels, and hormone levels. These don’t diagnose ME/CFS, but they tell us where the body is struggling and what we can actually support.

SEGMENT 3: What Is Causing This? The Real Root Causes
Now let’s talk about what is actually happening in the body, because I want to be very clear about something before we go any further:
This is not a deconditioning problem. This is not an issue of needing to exercise more, train harder, or push through. This is a serious metabolic and energy crisis happening at the cellular level, and more exertion will not fix it.
I know how much it stings when a doctor suggests that you just need to get moving more. The research does not support that approach for PEM, ME/CFS, or long hauler conditions. In fact, graded exercise therapy has been shown in multiple studies to worsen outcomes for people with these conditions. So let’s set that narrative aside right now and talk about what we do know.

Theories on What Is Happening
Right now, the research is pointing in several directions simultaneously, and the honest answer is that we don’t have a single agreed-upon explanation. Some researchers and clinicians believe this is fundamentally a neurological and nerve function issue. Others are focused on cellular energy and mitochondrial dysfunction, the idea that the cells themselves cannot produce or utilize energy efficiently. Others are looking at genetics, at who is predisposed to these patterns. And then there are those who still argue it is psychological in origin.
For anyone living with this, you already know that explanation falls profoundly short. Yes, the nervous system is involved. Yes, emotions and the stress response affect how the body functions. But this is not a psychological condition with physical symptoms as a side effect. It is a physiological condition that also affects mental function, and that distinction matters enormously for how we treat it.

The Viral Connection
What has become undeniable, especially since COVID, is the connection between viral infections and these conditions. We are seeing massive numbers of people develop symptoms of ME/CFS, post-exertional malaise, and dysautonomia following COVID infections. And this is not new: Epstein-Barr virus has been linked to ME/CFS for decades. Research has shown abnormally elevated inflammatory markers up to three years after an Epstein-Barr infection, which tells us something important: the immune system does not simply return to baseline after some infections. It stays in a state of activation.
We also see these patterns in people with Ehlers-Danlos syndrome, lupus, and other connective tissue or autoimmune conditions. The common thread is immune dysregulation, where the immune system has lost its ability to regulate itself appropriately.

Oxygen, Iron, and Cellular Energy
We are also seeing important connections to oxygen saturation and delivery. Whether this comes from asthma, changes in lung tissue after an infection, or sleep apnea, reduced oxygen delivery to the muscles and cells can create exactly the kind of metabolic crisis we see in these conditions. This is why iron and ferritin levels matter so much here. Not just whether you are technically anemic, but how efficiently your body is transporting and utilizing oxygen at the cellular level.

The Gut Microbiome Connection
This is where I want to highlight some really significant research. Two studies funded by the NIH, published in Cell Host and Microbe and reported by Science Daily in 2023, found consistent and measurable differences in the gut microbiomes of people with ME/CFS compared to healthy controls. What did they find? People with ME/CFS had abnormally low levels of key bacteria, particularly Faecalibacterium prausnitzii and Eubacterium rectale, which are the bacteria responsible for producing butyrate.

Butyrate is a short-chain fatty acid that is the primary energy source for the cells lining your gut, providing up to 70 percent of their energy. When butyrate production drops, the gut lining suffers, immune regulation suffers, and the ripple effects move through the entire body. Researchers also found that the less Faecalibacterium prausnitzii a person had, the more severe their fatigue tended to be. And while we don’t yet know whether the gut changes are causing the ME/CFS or the ME/CFS is causing the gut changes, the connection is significant enough that it changes how we approach treatment.
This is also where biofilm becomes relevant. Biofilm is the protective layer that harmful bacteria, yeast, and even dormant viruses create to shield themselves in the gut. It can harbor the very microbes that are driving immune dysregulation, and it can block the effectiveness of any protocol you put in place if you don’t address it strategically.
We also need to run PCR testing for active viral infections and an immune panel to understand your history of past infections, because that history shapes what is happening in the body right now.

SEGMENT 4: What Do We Actually Do About It?

The Hardest First Step: Knowing Your Limits
I want to start this section with what is genuinely the hardest part, and I say this as someone who lives this reality myself. The first and most important thing is to stop overtraining, stop overworking, and stop trying to outthink your body’s capacity.

I know this intimately. My mental state and my energy do not match what my body can actually sustain. My mind wants to spend the weekend deep-cleaning the house, getting all the laundry done, going for a five-mile hike, seeing friends, having a great dinner, and then waking up the next morning feeling fantastic. My body has a different vote. Usually just getting the dishes done requires a rest.

I have patients who tell me they washed the floors and then had to nap for the rest of the day. That is real. That is their reality. And it is not weakness. It is the physiology of this condition. We need to know our limits and honor them, not try to outsmart them.

If you are planning a big day, whether that means giving a presentation, going to a second store on your errand run, or attending an event, build in the recovery time after. Your marathon might look nothing like anyone else’s marathon. That does not make it less real or less deserving of recovery.

Foundational Testing
Before anything else, we test. We need to rule out major contributing factors: iron deficiency anemia, hypothyroid, autoimmune conditions, sleep disorders. This is not optional information, this is the foundation of a personalized plan.
In an ideal world, I would run a full viral load panel, a GI Map stool test to look at your gut microbiome directly, an organic acids test to assess how your cells and mitochondria are actually functioning, and a full hormone panel. From there, we build something specific to your body, not a generic protocol from the internet.

Diet: Fuel Your Cells Differently
I recommend a balanced ketogenic-style diet for most people dealing with these conditions. The goal is to shift your body toward burning fat for fuel, which reduces the glucose swings that drive inflammation and supports hormone production. Add in MCT oil for an extra source of easily usable ketones, which can support both brain function and cellular energy. This alone can make a meaningful difference in brain fog and baseline fatigue.

Gut Health: The Butyrate Priority
Based on the research we just discussed, butyrate supplementation is one of the first things I reach for. Supporting the short-chain fatty acid production that is likely depleted is foundational. From there, we layer in multi-strain probiotics, prebiotics, and postbiotics.

I use a pulsing approach: seven days of probiotics followed by seven days of an antimicrobial. This helps break down biofilm incrementally, releasing trapped viruses, yeast, bacteria, and mold without creating a massive detox reaction. Then we rebuild with the probiotics. The goal is to chip away at the protective fortress that harmful microbes have built, while simultaneously supporting the beneficial bacteria your gut needs.

Cellular Metabolism and Mitochondrial Support
This is where people often get stuck trying to take everything and seeing results from nothing. There is no single supplement that fixes mitochondrial dysfunction, but there are combinations that make a real difference when you commit to them consistently. I focus on NAD support, glutathione, B-complex vitamins, targeted iron support, and DHEA. I’ll link my Fullscript protocol so you can see exactly what I use and start from a place of quality and specificity rather than guessing at the supplement aisle.
I also strongly recommend beef organ supplements as a nutrient-dense multivitamin foundation. I use Heart and Soil and start with their liver capsules. This is concentrated nutrition in a form your body recognizes and can actually absorb.

Movement: Small, Consistent, Non-Negotiable
I know that movement feels impossible on bad days. But I want to ask you: can you do five minutes? Arm swings. Gentle stretching. Breathwork on the floor. This is not about building fitness right now. It is about keeping your lymphatic system moving, keeping your joints lubricated, keeping your muscles from becoming completely frozen from non-use.
Most of my patients have done physical therapy, and it helps when done appropriately. But it can also feel like running a marathon if you try to do too much. Can you break it into ten minutes in the morning and ten minutes in the afternoon? The goal is to find movement that does not push you into a crash, but keeps the body gently awake.

Viral Support
This gets very individualized, and I want to be thoughtful here. I typically start with nicotine patches for ten days as an anti-inflammatory and neuroregulatory support, which has some interesting emerging research in long COVID cases. I find good results with homeopathic programs, particularly from companies like Desbio that are designed around specific viral loads. And then nutritional antivirals like lysine, monolaurin, and elderberry can be layered in.
One important caution: if you have a known autoimmune condition, many immune-stimulating herbs can actually worsen your symptoms by pushing the immune system further into overdrive through the TH1 or TH2 pathways. This is an area where working with a practitioner who understands your specific immune picture is really important.

The Most Important Principle: Build, Don’t Sprint
Low and slow. Make a few changes at a time. Build on them. If you change your diet for a week, then quit before ever adding gut support or cellular nutrition, you are not going to see the results that are possible.
Start with the change that feels most accessible. Most sustainable. And then add to it. Think of it like building a house: you have to pour the foundation before you can put up the walls.
This is overwhelming. I know it is. And that is exactly why working with someone who can hold the complexity of your case, run the right tests, and build you a personalized plan is so valuable. If you are ready to start that process, you can schedule with me online at http://www.littleblackbagmedicine.com. I work virtually, and I would love to support you in finding your next step.

Thank you so much for being here today. If this episode resonated with you, please share it with someone who needs to hear it. And if you have been struggling to find answers, please know that functional medicine is not giving up on you. The answers exist. The support exists. Sometimes we just have to look in the right places with the right lens.
Until next time, take care of yourself, honor your body’s pace, and remember: healing is not linear, but it is possible.
End of episode script.

RESEARCH REFERENCES FOR SHOW NOTES
Microbiome and ME/CFS: Two NIH-funded studies published in Cell Host and Microbe (2023) identified consistent gut microbiome differences in ME/CFS patients, including reduced butyrate-producing bacteria and altered metabolic pathways. Science Daily summary: http://www.sciencedaily.com/releases/2023/02/230208124337.htm
ME/CFS Diagnostic Criteria: The 2015 IOM/NAM criteria require substantial reduction in pre-illness function, post-exertional malaise, and unrefreshing sleep plus cognitive impairment or orthostatic intolerance for at least 6 months. CDC: http://www.cdc.gov/me-cfs
ME/CFS as Neurological Disease: The WHO has classified ME/CFS as a neurological condition since 1969. StatPearls, NCBI: http://www.ncbi.nlm.nih.gov/books/NBK557676/
Women and ME/CFS: Women are diagnosed 1.5 to 4 times more often than men and tend to experience more severe symptoms and greater comorbidity burden. (ScienceDaily, August 2023)
Post-Exertional Malaise Research: PMC/PubMed: Twisk FN. Accurate diagnosis of myalgic encephalomyelitis and chronic fatigue syndrome based upon objective test methods. PMC4482824
Supplements via Fullscript: https://us.fullscript.com/welcome/littleblackbagmedicine
Beef Organ Multivitamin: http://www.heartandsoil.co