At Home With Nature

My Experience with Gut Dysbiosis

The wind lifts and drops the branches of the box elders outside our kitchen window in front of a dark sky. Rain showers pelt down, and then disappear. The sun appears, seeming to banish the clouds, then rain returns, and the sky darkens again.

The patterns of this moody weather are much like the ups and downs of my gut and its effects on my feelings of well-being. One day I’m so perky and symptom-free that I’m dancing around the house singing James Brown’s signature tune – while the next I’m moping around, miserable, regretting my last meal decisions.

Thus is the life of my gut, and my foundational health problem – gut dysbiosis.

What is Gut Dysbiosis?

Oh, gut dysbiosis. As soon as I heard its name I knew it was my problem.

Since I’m not a medical professional, I’ll let a team of doctors explain this term to you:

“Gut dysbiosis is a broad term that can be defined as the imbalance of gut microbiota associated with an unhealthy outcome. Dysbiosis involves the loss of beneficial microbial input or signal and an expansion of pathogenic microbes (pathobionts). Dysbiosis is thought to trigger pro-inflammatory effects and immune dysregulation.”

– Jason A. Martinez, et al in Frontiers in Endocrinology.

Gut dysbiosis, is, in other words, the lack of a healthy gut microbe eco-system.

My Gut Dysbiosis Symptoms

Throughout my health journey, I’ve learned to treat my symptoms like evidence in a medical mystery, especially when doctors were no help to me.

And when trying to put the pieces of a medical puzzle together, it can help to go back – way back.

I Was a Colicky Baby

I don’t remember this, of course, but my mom tells me I was a colicky baby.

Some research shows links between colic and gut dysbiosis. In fact, probiotics are now being recommended as a remedy for colic.

I Had Gut Pain as a Child

I wouldn’t say that having an upset tummy defines my childhood experience, but I do distinctly remember the day I found a position that helped to alleviate my upset tummies – the position was pretty much the yoga position child’s pose by the way.

This of course is no proof, just anecdote, but it makes me think that since this relief was so memorable to me as a child, it probably means my upset tummies were perhaps more frequent than I remember.

I Have a History of Severe Gut Pain

In 2004 when I lived in Paris, France, I started experiencing really severe gut pain. It would usually start in the afternoon, while I was at work. Once I got home I would spend spend the rest of the day clutching my abdomen in bed and running to the bathroom.

This period of severe pain lasted for about three years. During that time I consulted several generalists, a specialist, and had scopes and other tests to see what was going on. According to them, nothing was wrong with me – but would I like to try some antidepressants, perhaps?

On my own initiative, I ended up eliminating a few foods from my diet, and my pain decreased in severity.

Continued Gut Issues

After the clearing of that really severe pain, I had about a decade of mostly low grade gastrointestinal issues, and then my symptoms branched out.

I started to experience, for the first time in my life, heartburn, and extreme upper GI acidity.

My gut issues were different than they had been while I lived in Paris, definitely not as severe, but they were getting more and more in the way of me feeling good.

Food Chemical Intolerance

After I figured out that my heartburn and other issues were related to histamine intolerance, a very smart functional medicine doctor recommended I get tested for SIBO.

I tested positive for SIBO, and suddenly I was starting to understand what was wrong with my gut, for the first time in over 15 years of searching for answers.

My SIBO journey led me to uncover other food chemical sensitivities in addition to histamine intolerance, notably oxalates.

Oxalate toxicity is strongly associated with gut dysbiosis. Oxalates, a type of compound used by plants for self-defense among other things, aren’t detoxed by the liver, they have to be broken down by gut microbes. But not all types of gut microbes eat oxalates. When you’re missing the right type of microbes, those sharp little plant compounds can cause problems in the body!

Along with triggering histamine intolerance and being largely responsible for the painful periods I used to have, having too much oxalates circulating in my body seems to have triggered other issues for me as well, such as nutritional deficiencies and additional food chemical sensitivities.

Why I Think I Have Gut Dysbiosis

But symptoms are not the only factors bringing me to conclude that I have gut dysbiosis.

My Microbial Inheritance

I started life with a poor microbial foundation in two different ways.

First of all, my mother took prophylactic doses of antibiotics for years while she was growing up. Non-stop antibiotic use undoubtedly changed her own microbiome, leaving it less diverse. We inherit our microbiome from our mothers.

Next, because of the advice of an undoubtedly well-meaning but poorly informed OB-GYN, my mom didn’t breast feed me. That was strike two. Breastmilk is more nourishing to babies’ microbiomes than formula milk in multiple ways.

Let me point out here that I don’t blame my mom for these issues. The medical community was ignorant about the gut microbiome in those days, and most doctors probably would have laughed off the idea of “good bacteria.”

Severe Health Issues after Antibiotics

While I certainly was treated with antibiotics at least a dozen times (or perhaps two dozen) throughout my life, a single dose of antibiotics in November 2017 seemed to change my health trajectory dramatically.

Shortly after this, I developed heartburn, and worsening GI symptoms. I also started experiencing allergy-like symptoms, which I would later discover were part of a condition called histamine intolerance.

Meanwhile, I couldn’t sleep – sometimes for weeks at a time. My lack of sleep made me feel terrible, I was extremely moody, and constantly felt like I was going to crash.

I felt like my health was in extreme danger and didn’t know what to do.

Microbiome Test Results

Luckily, I learned about histamine intolerance, and starting peeling back the layers of my own personal health “onion” – discovering layer after layer of problems.

I began working with different health practitioners, each of which helped add to my understanding and forward progress.

Finally, under the supervision of a naturopath, I took a stool microbiome test.

My results revealed that I did indeed show signs of a dysbiotic gut.

My Plan for Treating My Gut Dysbiosis

Ok, so I have dysbiosis, but now what do I do? I have a plan.

Avoiding Antibiotics

First thing is first – I am avoiding antibiotics as much as possible.

In cases where they are absolutely necessary, as they were recently when I had the interesting experience of an infected cat bite, I negotiated with the prescribing general practitioner to use an antibiotic that wasn’t quite as detrimental as some other broad-spectrum antibiotics.

Antibiotics will kill off some of my gut bacteria – potentially leaving behind resistant pathogens, so I will only take them if my life is at risk and there are no other options.

For most conditions treated by antibiotics, there are alternatives.


Since there are some important microbial populations missing in my intestines, I’m taking probiotics.

Not just any probiotics, however. I take specific probiotics with research showing they can help my gut issues. I use the website Probiotic Advisor, created by Dr. Jason Hawrelak, as a resource.

While probiotics alone won’t “re-seed” my gut microbiome, they help as they are traveling through.

And since bacteria can borrow DNA from each other, perhaps the probiotics will help my existing populations build back stronger.

Fermented Foods

Fermenting is one of my passions, and it’s another way to introduce bacteria and bacterial materials into the gut.

While fermented foods aren’t really on my menu while histamine intolerance is still a problem, they are part of my long term plan.

Feeding my Microbes

In the meantime, my microbiome-focused naturopath is guiding me in feeding my microbes.

Apparently different types of bacteria like different types of foods. So I’m trying to implement my naturopath’s plan for feeding these bacteria, even though doing so is difficult for me due to salicylate sensitivities.

I’m going low and slow with doses, and have actually improved my diet from a microbe-supporting point of view.

My ultimate goal is to eat 5-7 servings of fruits and 5-7 servings of vegetables per day, with 40 different plant foods per week.

I could have easily met that goal (and probably did) before my health plummeted post-antibiotics. I used a diverse assortment of grains, beans, veggies, and fruits in my cooking, foraging wild foods from both our farm and from our hikes.

Now, my food chemical intolerances have obliged me to eat a very restricted diet where I am nowhere near reaching the goal of 40 different plant foods per week – or even five servings of veggies and fruits each per day. It makes me sad to acknowledge that, but I’m also extremely motivated to keep working towards this goal.

My Future Gut

For now, I don’t have a happy ending to this tale of gut dysbiosis. I’m still smack dab in the middle of the process, working away at doing the hard work I have to do to get better.

But one day – hopefully not too far in the future – I will come back to this post and write my happy ending, the story of my healed gut, a story through food hell and back again.

I look forward to nourishing my future gut with mostly plant-based meals loaded with color, spices, flavor, and variety. This is how I’ll keep my microbiome healthy, resilient, and happy – and it will do the same thing for me in return.

When that day comes, I hope to feel so good, that I’ll have James Brown’s voice on a loop in my head.

Do you have gut dysbiosis too – or think you do? I’d love to hear from you on how you are coping with this condition. Here are a few other posts that may be of interest to you as well:

How I Use a Food Journal for Gut Health

How SIBO Has Changed Me

An Experience with Histamine Intolerance


This article does not intend to diagnose any health conditions or offer treatment advice. Please consult with your health practitioner before trying any supplements or making any dietary changes.

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2 thoughts on “My Experience with Gut Dysbiosis”

  1. I am having the exact same problems. Trying to juggle AIP, low FODMAP and low oxalates with a very well-respected nutritional therapist. My SIBO scores are extremely high. I’m following your story with interest!

    1. Hi Carolyne, Thanks for taking time to leave a comment! I’m sorry you’re suffering with these issues too. It’s so hard dealing with overlapping, restrictive diets, even with the help of great professionals. It’s a great hope, though, that those of us trying to figure out these issues might be able to help each other with our trials and errors – and I think it’s helpful to just acknowledge each others’ pain. Hang in there!

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