In Part III, I discussed how antibiotic use can lead to a cascade of imbalances within the human body, resulting, in my case, in IBS, cystic acne, depression, and finally, suicidal ideations. 

In the following post I will take a look ‘under the hood’ of my own biology, and demonstrate how a complex web of interactions began undermining my mental and physical wellbeing. 

To do this I’ll be sharing the results of several gut microbiome analyses. The discussion around these becomes fairly jargon-y, but bear with me. I believe it’s vital to understand the effects these gut microbes have on overall human health. At the end, I’ll share the first steps I took toward healing my lifelong dysbiosis.

Chapter 05: Naturopathy, A New Path Forward

Following my last GI appointment, I collected myself and resolved to begin saving, setting aside a portion of each paycheck, so I could seek help outside the health insurance system from a naturopathic doctor. 

This journey led me first to a Canadian naturopath who specializes in IBS and offers telemedicine. This doctor explained to me that most IBS cases, an estimated 70%, are caused by SIBO—small intestine bacterial overgrowth—and recommended a lactulose breath test analysis to diagnose if this was indeed the issue. 

Here are the results of this test:

For those interested, I’ve included some commentary and analysis at the end of this post. But I am primarily sharing this as it elucidates my assertion from Part III, that I had “a thriving colony of dysbiotic bacteria, feasting on and mis-digesting my food intake, themselves belching sulphurous, malodorous gases…”

According to Genova, a SIBO diagnostics laboratory, 

“A peak methane level greater than 10 ppm at any point is indicative of a methane-positive result… peer-reviewed literature suggests an association with certain clinical conditions and methanogen overgrowth at levels as low as 3 ppm… which may indicate the need for clinical intervention in the symptomatic patient.” 

My methane levels were more than 6 times higher than the threshold for “clinical intervention” at baseline, meaning that even in a fasted state, bacteria in my intestines were emitting this noxious gas “due to the ability of methanogenic organisms to ferment in the absence of an ingested carbohydrate substrate.”

After receiving this test result, I was surprised to learn that a methane-dominant result is usually associated with constipation-dominant IBS-C, rather than the IBS-D symptoms I had been experiencing for more than two decades. Realizing this wasn’t going to be a straight-forward, open-and-shut case of SIBO, I knew I needed both deeper analysis and a broader perspective for what was happening inside of me. At the referral of a friend I booked an appointment with a naturopathic doctor, meeting him in his Boulder office in December of 2019.

From his perspective, there are three pathways that can manifest in IBS:

1. Abnormal gut flora and fauna (e.g. microbes, yeasts, and parasites)

2. Food sensitivities and allergies (e.g. gluten, dairy, etc.)

3. Psychological distress and Nervous System idiosyncrasies (like those imparted by emotional trauma)

[Wanderer’s Note: For the purposes of this post, I am going to focus primarily on the first pathway. But I would like to emphasize that all three are not only very important to unlocking gut health, they are inextricably intertwined. The interplay and cross-talk between these systems are so extensive and overlapping, I’ve found that I simply cannot write about them all together without creating an incoherent mess of meandering thoughts and scientific jargon.]

Chapter 06: Finally, Answers

My new naturopathic doctor recommended further microbiome analysis via a stool sample, to determine the species of bacteria that might be producing these gases. 

Below I am sharing the results of this microbiome analysis. It is important to note that the human gut has an estimated 1,000+ species of microbes, and even modern testing cannot possibly capture all of them, so while this test detected an overgrowth of a few commensal and dysbiotic species, the doctor explained there are likely many more “bad actors” in there. 

What do we see here?

An overgrowth of several commensal strains of bacteria, as well as the dysbiotic Enterobacter cloacae:

As my doctor explained, this is a particularly harmful strain of bacteria. Researching this pathogen later, the existence of what I am calling the “Trauma-Dysbiosis cycle” came into view. 

Here’s what I mean by that:

In my post, 04: Trauma, Part I: What is trauma?, I wrote about the demonstrated, lasting changes in hormone levels for individuals with emotional trauma in their past:

“Cortisol, the stress hormone, is interestingly also reduced. This is because cortisol’s role in stress is that it helps to bring down the high levels of adrenaline and norepinephrine that are released during fight or flight. Adrenaline and norepinephrine are responsible for memory formation and arousal, so not having enough cortisol to completely bring down the sympathetic nervous system at the time when it is very important for a person to calm down, may partially explain the formation of traumatic memory or generalized triggers.”

And that this phenomenon has actually been demonstrated in LGBT populations:

“The trauma for gay men is the prolonged nature of it,’ says William Elder, a sexual trauma researcher and psychologist… Growing up gay, it seems, is bad for you in many of the same ways as growing up in extreme poverty. A 2015 study found that gay people produce less cortisol, the hormone that regulates stress. Their systems were so activated, so constantly, in adolescence...”

But these very hormones also create the conditions for dysbiosis: 

According to a 2018 study published in the journal Brain Research, “the pathogens Enterobacter cloacae, Shigella sonnei, and Staphylococcus aureus were all found to have improved growth in vitro in the presence of norepinephrine” [1].

Chapter 07: My Trauma-Dysbiosis Cycle

While childhood emotional trauma and the chronic stress of hiding my sexuality were kicking my nervous system into fight-or-flight, the norepinephrine that flooded my system (and remained there) as a result, created the very environment for Enterobacter Cloacae to multiply and thrive. 

The flourishing of this dysbiotic bacteria led to frequent gas and diarrhea, and “urge moment” stress (described in 08: Trauma, Part III), which then began jerking my nervous system into “fight-or-flight” on a daily basis, inviting even more stress hormones, more discomfort, more dysbiosis. 

But the analysis revealed even more concerning results:

The utter absence of three genera of beneficial bacteria: Bifidobacterium, Lactobacillus, and Enterococcus. 

What do these bacteria do for healthy human biology? 

Members of the genera Lactobacillus and Bifidobacterium “are among the first microbes to colonize the human gastrointestinal tract and are believed to exert positive health benefits on their host.” Lactobacillus in particular is the most common species found in probiotic supplements today, owing to its wide-ranging proven and purported health benefits. There are typically nine different species of Bifidobacterium, and four or more species of Lactobacillus, commonly found in the healthy human microbiome. [2]

Delving into some peer-reviewed research, I learned that “members of the Bifidobacterium and Lactobacillus genera… have been reported to produce GABA” [1].

GABA—gamma aminobutyric acid—in recent years, has exploded on the supplement scene for its purported stress- and anxiety-busting, as well as cognitive-enhancement benefits. In our biology, GABA is the “chief inhibitory neurotransmitter in the mammalian central nervous system. Its principal role is reducing excitability throughout the nervous system” and is known for “producing a calming effect. This can help with feelings of anxiety, stress, and fear” [3].

The antagonizing role of antibiotics in the Trauma-Dysbiosis cycle now comes into focus. In the onslaught of broad-spectrum pharmaceutical antibiotic abuse, having repeatedly “scorched my intestines” of all bacteria, good and bad, these beneficial strains never made a comeback. And yet, these were the very strains with the ability to produce a “calming effect“ to bring down and regulate my agitated nervous system.

Finally, a possible connection to my skin:
As I looked into the other missing genera of bacteria, Enterococcus, I learned of a possible reason for the regular inflammatory skin outbreaks I’ve experienced my entire adult life.

The Enterococcus genus “comprises over 50 species that live as commensal bacteria in the gastrointestinal (GI) tracts of insects, birds, reptiles, and mammals” [4].

According to a 2018 paper published in the journal Frontiers in Microbiology, certain strains within this genera of bacteria are beginning to be used as a probiotic supplement to treat acne. Enterococcus is “being extensively studied for use in the treatment of acne. For example, lotion prepared with [a strain of Enterococcus] has significantly reduced the inflammatory lesions caused by Propionibacterium acnes, suggesting a potential role in acne treatment as an alternative to antibiotics” [5].

As the skin-gut connection gains acceptance in the medical community, I look forward to a day when individuals suffering from inflammatory skin conditions like cystic acne are no longer treated with broad-spectrum antibiotics like I was, but perhaps instead, with diet, pre-, and probiotics. 

I believe there’s more to the story of my skin issues, for they persist even today. As I write this I am afflicted with painful, inflamed cysts on my chest and scalp. Those who are curious can find photos at the end of this article. I plan to explore the skin-gut-psyche connection in depth once I feel I have found a path to healing it, for good.

As a final note
on this section from my microbiome analysis: Each of these three genera of bacteria are keystone inhabitants of the human microbiome, typically representing more than 60 distinct species in the average person’s gut. Many of these species have a proven beneficial role in human biology, with implications for the immune system, skin health, and even our mood and mental wellbeing. 

Sixty different species. And according to my test results, I had zero. This, despite eating an almost exclusively organic, whole foods diet, with lots of fermented, probiotic-rich foods; and being hyper-aware, almost to the point of paranoia, about toxins and antibiotics entering my system (yes even alcohol); as I strove to ease my gut issues by being (at least I thought) a paragon of healthy living, for two full years prior to this test. 

I cannot recall a time in my life when I have been so humbled. I now believe that pharmaceutical antibiotic abuse is akin to chemical warfare on the very foundation of our human biology. Even years after the initial attack, the terrain remains a hostile, uninhabitable environment, with untold, harmful ripple effects radiating throughout the ecosystem.

How did I begin to rehabilitate my internal environment?

Chapter 08: Treatment. Results.

My treatment plan consisted of solutions tailored to each of the three pathways. 

1. Psychological distress and Nervous System idiosyncrasies

The first prescription the doctor wrote for me was for “Transcendental Meditation” — a well studied modality for calming the nervous system, and specifically the vagus nerve, the primary neural pathway comprising the “Gut-Brain Axis.” 

“The gut-brain axis (GBA) consists of bidirectional communication between the central and the enteric nervous system, linking emotional and cognitive centers of the brain with peripheral intestinal functions. Recent advances in research have described the importance of gut microbiota in influencing these interactions” [6]. I plan to cover the GBA in depth, in an upcoming post.

2. Abnormal gut flora and fauna

My doctor also provided strain-specific antibiotic herbs for the dysbiotic flora—my microbiome analysis showed Uva Ursi in particular to be effective against the Enterobacter Cloacae. I also received a litany of other natural supplements to bring my gut back into balance. 

3. Food sensitivities and allergies

Lastly, the doctor suggested dietary changes to remove foods I knew were problematic, and recommended a food allergy test to see if there might be other foods causing problems. At this point, I was out of money, and deferred the allergy test for almost a year. 

Results

Within three weeks of implementing this treatment plan, I began to notice a shift. By the sixth week, the progress was remarkable. My bowel movement regularity improved, decreasing to just once per day typically, and usually at approximately the same time each day. Gas, bloating, and cramping were significantly decreased. At my follow-up appointment, my doctor asked me to estimate the progress made, which I pegged at 70-80%. A marked improvement, but still a ways to go. 

• • •

There is no triumphant conclusion to this story. No, on this journey of healing from IBS, I have learned that unwinding nearly 30 years of trauma, antibiotic abuse, and dysbiosis isn’t going to happen overnight. My patience, resolve, and will to continue, have all been tested in this journey—and all have expanded greatly. I suppose this is the biggest lesson I can impart from this story. When we heal, I believe, we are not merely returning ourselves to a baseline level of health. We are growing stronger, more resilient than we were before ‘dis-ease’ ever entered our bodies or our minds. 

My encouragement again to those struggling, is to just keep putting one foot in front of the other. The journey may be difficult, it may be painful, it may even push you, like it did me, to the point of breaking. But when you look back at the road you’ve traveled, at the ways you’ve grown, it will be beautiful.

Notes: 

The SIBO breath test shows a few things:

• I most likely had SIBO. According to Genova, a SIBO diagnostics laboratory, elevated hydrogen (H2) indicates the presence of bacteria in the small intestine

  • “A rise of H2 of ≥20 ppm over baseline in the first 90 minutes of testing is positive for SIBO.” While my test did not meet that threshold, “A rise of H2 of ≥20 ppm over baseline in those samples collected after 90 minutes maybe positive for SIBO in patients with slower transit time.” 

    • My transit time may have been slower due to trauma and my activated nervous system, and the resulting disruptions in my Migrating Motor Complex (MMC) — the mechanism by which the brain sends signals to activate the smooth muscle of the gut lining to move waste through the system. 

• The presence of methanogenic bacteria. 

  • “A peak methane level > 10 ppm at any point is indicative of a methane-positive result. The peer-reviewed literature suggests an association with certain clinical conditions and methanogen overgrowth at levels as low as 3 ppm, CH4 values between 3 and 9 may indicate the need for clinical intervention in the symptomatic patient.” 

  • “ELEVATED BASELINE - An elevated baseline may be a more common pattern with CH4 positive tests primarily due to the ability of methanogenic organisms to ferment in the absence of an ingested carbohydrate substrate.”

• One thing a breath test cannot capture is the presence of hydrogen sulfide (H2S), the gas known for creating the “rotten egg” smell. A naturopathic health coach, reviewing my results, indicated a strong likelihood there were bacteria emitting this gas as well.

References: 

1. Strandwitz P. (2018). Neurotransmitter modulation by the gut microbiota. Brain research, 1693(Pt B), 128–133. https://doi.org/10.1016/j.brainres.2018.03.015

2. O'Callaghan, A., & van Sinderen, D. (2016). Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Frontiers in microbiology, 7, 925. https://doi.org/10.3389/fmicb.2016.00925

3. “What Does Gamma Aminobutyric Acid (GABA) Do?” Healthline. https://www.healthline.com/health/gamma-aminobutyric-acid

4. Hanchi, H., Mottawea, W., Sebei, K., & Hammami, R. (2018). The Genus Enterococcus: Between Probiotic Potential and Safety Concerns-An Update. Frontiers in microbiology, 9, 1791. https://doi.org/10.3389/fmicb.2018.01791

5. Dubin, K., & Pamer, E. G. (2014). Enterococci and Their Interactions with the Intestinal Microbiome. Microbiology spectrum, 5(6), 10.1128/microbiolspec.BAD-0014-2016. https://doi.org/10.1128/microbiolspec.BAD-0014-2016

6. Carabotti, Marilia et al. “The gut-brain axis: interactions between enteric microbiota, central and enteric nervous systems.” Annals of gastroenterology vol. 28,2 (2015): 203-209. https://pubmed.ncbi.nlm.nih.gov/25830558/