Gut on fire: Chapter 1

Dr. Laura Roxann Alexander
11 min readJan 17, 2024


A true story about my stomach, my life, and my autoimmune disease

Chapter 1: Birth and Beginnings

My stomach has hurt for as long as I can remember. Even when I was incredibly young, although I didn’t have the words to express the hurt, I still remember there being something wrong. It seems like the “burn” has always been a part of me and it should have been a sign that something had gone awry in my gastrointestinal symptom. Unfortunately, even today, the first sign that something is wrong in children and adults is often the symptom that is dismissed, downplayed, and swept under the rug with a shrug of the shoulders and unhelpful statements like, “Your body just produces more acid than normal,” or “Your labs look great.” And the best statement of all, “We can’t find any reason why your stomach would hurt, everything is fine.”

As a child and a young adult, I believed that it was just me. The stomach pain and acid reflux had been there so long that I didn’t question that there could be an alternative path that could keep my stomach from hurting. I assumed I would have to take medication to stop my stomach from producing extra acid for the rest of my life because that is what the specialists told me to do. All that changed when I began to question the diagnosis of too much stomach acid.

The lightbulb moment may not have ever happened if it wasn’t for a family friend suggesting that I listen to a functional medicine podcast by author and co-founder of the Cleveland Clinic, Dr. Mark Hyman. He is my hero. His words, telling me that I had the power to heal my body, hit me right in the gut. Maybe I didn’t have to live with acid reflux? Maybe there was something I could do to heal my stomach and live without acid reflux and pain. Maybe it wasn’t just my stomach being dumb or dysfunctional like all the specialists kept telling me? Maybe it was something I was eating or drinking everyday that impacted how my stomach felt?

These questions lead me to even more questions. I began to question to the whole medical system and the use of prescription drugs long term. I read about the “safe” medications that I had been taking for 20 years and realized that the particular class of acid reducers called proton pump inhibitors cause a multitude of nutrient deficiencies and long term side effects. No wonder I was anemic, had leg cramps, developed IBS, and had low energy. The medication that was suppose to be helping me was ultimately part of the problem. Dr. Mark Hyman spoke about proton pump inhibitors many times on his podcast. They are powerful. They reduce stomach acid production by as much as 80%. I had unwittingly been breaking my digestion for years. I also read that these medications increase the risk for dementia as well as cancer. It was those two words, cancer and dementia, that led me on a path to discover the real reasons I had stomach pain and acid reflux. If I found the reasons, then I could stop it from happening.

To understand why I have gut dysfunction, I have to explain my past. It’s the past, my birth and habits as a child, the stressors of college, and a marriage that left many scars, that led to the dysfunction of my gut and ultimately, many parts of my body. I can look back now and see the webs of connection, but that took many years of study. I might complain about it here in the words to come, but I don’t for one second regret any of it. I have learned to be grateful for the struggles. It is the struggles that put my mind and body to the test and I didn’t fall apart. I’m a little bit cracked and rough around the edges and pretty dysfunctional at times, but never fully broken beyond repair. Those challenges have made me into the person I am today and I wouldn’t change that for anything.


The trauma to my gut started right from the beginning with my birth. I was born via caesarean section. There wasn’t any other choice. My mom’s uterus was shaped in a way that made vaginal delivery impossible and her doctor suspected there would be difficulty with the labor process. It was 1983 and I was way overdue, by 2 weeks. The doctor tried to induce me when it was apparent that I wasn’t coming out on my own. They tried for 2 days but each time the epidural wore off my mom was in extreme pain, right at her hip. They gave her a drug called Pitocin, a synthetic form of oxytocin, which is a hormone that is released during labor to help the uterus contract. Unlike oxytocin, which is released in waves and gives the body a break, Pitocin pushes the body to have more frequent, stronger contractions than usual, which can end up hurting both the mother and baby.

Studies show that Pitocin can cause a decrease in the baby’s heart rate and that it may also impact the nervous system causing an activation in the sympathetic nervous system. In other words, this birth was traumatic for both my mom and me. That was on a Tuesday. By Thursday, the doctor made the call to perform a cesarean section. So, rather than receiving a mouthful of intestinal and vaginal flora that could educate my newborn immune system on the ways of the microscopic world, I received bacteria from the environment in the delivery room and neonatal unit. What I missed was a process called “seeding” which is the transfer of microbes from the mother to the newborn during vaginal delivery.

Several studies have shown that this inoculation process has several implications for the health outcomes of the newborn and as they age, even up to age 7. There are distinct differences in the microbiomes of newborns born vaginally compared to c-section. In those cases, and my own, non-maternally derived environmental bacteria influenced intestinal colonization which results in altered immune development. Even though I missed the key species that are critical for immune education, I did at least get breast-fed as an infant for a few months and so I able to receive some immunity from my mom.

The year I was born, the in utero environment was thought to be sterile. Within the last 20 years, studies have shown that the placenta is not sterile and neither is the amniotic fluid. Bacteria have been found in fetal membranes and even umbilical cord blood, the same bacteria that colonize an adult’s small intestines. As the human microbiome project continues, I believe we will learn even more about the interplay between the intestinal flora and in utero colonization. In 1983, however, bacteria were believed to be bad and there was no understanding of how bacteria might influence a child’s immune system development.

Missing Old Friends

Babies born vaginally are colonized predominantly by Lactobacillus, a Firmicute, while c-section babies are colonized by a mixture of potentially pathogenic bacteria found on the skin and in hospitals such as Staphylococcus. So c-section babies are essentially, colonized by skin flora instead of the vaginal and intestinal bacteria.

Not only do the intestinal and vaginal bacteria play a role in maintaining and balancing the gut microbiome, they also are key in promoting the early development of the gut’s mucosal immune system. This dynamic continues to play a role later in life. The bacteria stimulate the gut associated lymphoid tissue or GALT that resides directly under the intestinal lining, which is one cell layer thick. I think of the GALT as a police station, ready to activate if it senses stranger/danger antigens. The first inoculation teaches the police to leave helpful species alone and to recognize and fight harmful bacteria. This tolerance is also part of the “old friends” hypothesis. The “old friends” hypothesis emphasizes the role of exposures to microorganisms with which humans co-evolved as essential drivers of the regulatory and anti-inflammatory arm of the immune system. Instead of old friends, I most likely received a mixture of bacteria that create an inflammatory response.

Microorganisms perform several useful functions such as fermenting unused energy substrates, training the immune system, preventing growth of harmful, pathogenic bacteria (a major driver of chronic inflammation), regulating the development of the gut, and producing vitamins for the host (such as biotin and vitamin K). Several microorganisms also produce a fatty acid called butyrate which can be used as food source by the coloncytes in the small and large intestine. Butyrate is also thought to be a primary protective factor against colon cancer. Recent insights into microbiome imbalances suggest that coloncyte metabolism might act as a control switch, shifting the gut bacteria community between homeostatic conditions and dysbiosis (an imbalance in a person’s natural microflora). The majority of butyrate producing species are Firmicutes.

Cry Baby

I had colic, almost right from the start. Looking back, that makes total sense. My mom said I cried and cried and cried. The pediatrician even put me on Zantac, a acid reducer. There it was, my first experience with acid reduction, barely a few months old. The interplay between missing microbiota, a reduction in hydrochloric acid, and a stressful birthing process, may very well have been the ultimate set up for long term gut dysfunction.

I think my mom tries to forget the stress that it must have caused to have a baby that cries and seems to be in distress. I was missing out on friends to help me digest my food, like B. infantis, which is the foundational species for building out a healthy gut microbiome in infants and which digest milk sugars. It is probably way more complicated than missing one species. Just like it is incredibly complicated as an adult to figure out what foods or stressors might be causing a flare of autoimmune symptoms.

Eighteen Months Later

I might have had a better chance of recovering some of those beneficial species if it wasn’t for the fact that at eighteen months of age I got chicken pox. This was before the vaccine, back when parents took their kids to chicken pox parties. I am fairly certain I got it from one of my many cousins. It wasn’t the chicken pox that broke me, but the staph infection that came from scratching the pox sores. I went to the hospital where I was given broad spectrum antibiotics. The antibiotics probably saved my life, but the aftermath of a course of antibiotics was even more gut dysfunction. Antibiotic exposure alters the microbial profile. There are studies that show this alteration can last for many months and there is evidence that multiple antibiotic courses alter the profile for good, meaning it never returns to its original state. This was my first course, it wouldn’t be my last.

There is accumulating evidence that intestinal bacteria play an important role in a newborn’s immune system development. If intestinal flora develops differently depending on delivery and an infant is exposed to antibiotics within the first year of life, then the logical outcome is that the immune system of that infant maybe forever compromised. I know that to be the case for me and an increasing amount of epidemiological data shows that atopic disease and immune dysregulation like asthma, allergies, and various childhood illnesses correlate with a weaker immune system. The diversity and composition of the microbiome in the early days of life is a critical factor for achieving and maintaining good health as we age. The data is becoming increasingly clear on this point, our microbiome may very well be the key to our overall health and wellness.

More than a stomach problem

After reading about my birth and the history of my intestinal development, you might think this story is just about the gut, from stomach to butt. The story doesn’t end there, I wish it were just as simple as tummy troubles. When it comes to our health and the function of our body, it is way more complicated and complex. I know that now, but it took many years for me to put all the puzzle pieces together. Years, that I felt like individual pieces of me were falling apart. I had no idea that the connection was an overwrought and dysregulated immune system. I didn’t know much about the microbiome or why it mattered how I was born, or even that multiple rounds of antibiotics could negatively impact my health in the long run.

As a young adult, if you would had asked me about my immune system, I probably would have said it’s strong. I never get sick. I am as healthy as horse. That was so far from the truth then and, in some ways, even now that it is laughable. It wasn’t until I turned 35 that the connections started to form as I began to research gut health. I looked back over my life and could finally see the threads binding all my seemingly unrelated symptoms to one root cause; immune dysregulation. How I came to this conclusion took years of studying, reading, and a plethora of new and cutting edge scientific testing; which ultimately led me to pursue a functional medicine certification through the School of Applied Functional Medicine.

Over the last 6 years, some my chronic health issues have gotten so much better that it seems like a miracle. But like with any autoimmune disease, there are ups and downs, what the medical world calls flares, that sometimes leaves me feeling exhausted and mentally drained. Even though there are days I struggle to have the energy to lead a fulfilling life, I have so many good days that the bad days are few and far between.

My story

So this is my story. You might think it’s just about a stomach. It’s also a story about growing up, finding love, dealing with loss and heartache, suffering, joy, and a struggle to find my place in the world. It’s a story about being human. It’s about my journey. My stomach was, is, and might always be a little bit broken. Although my stomach takes center stage, it isn’t the only key player impacting my quality of life. Dysfunction started there but doesn’t end there. My ovaries are broken too. My thyroid is under attack and my small intestine used to be a hot mess (depending on what I eat, it still is). I’m 40 years old. I’m still on a journey of healing.

Follow me as I write my story and explain the correlation between all my broken body parts and the poorly regulated system behind it all, my immune system. I will delve into my mental health, my infertility, my thyroid struggles, and my quest to heal physically and emotionally. I hope this story resonates with you and I hope it encourages you to find the reason you are struggling and not get swept away with treating symptoms, your body’s cry for help.

This journey is hard, but it is worth it. No matter how much I have struggled, there has been an equal amount of growth and thriving and I am grateful for all the challenges .



Dr. Laura Roxann Alexander

Pharmacist.Personal Trainer.Lift heavy, skip the run.Let food by thy medicine and medicine be thy food.