Root causes of SIBO: Motility Issues

One of the main conditions I treat in my clinical practice is small intestinal bacterial overgrowth or SIBO for short. Clients come to the clinic with bloating, food intolerances, nausea and a change in their bowel movements (either constipation or diarrhoea). But the more I work with SIBO patients the more I have come to see this bacterial overgrowth as more of a symptom than a root cause. 

Some dysfunction has allowed bacteria to overgrow in the small intestine. 

Today we will explore one of the root causes of SIBO, a breakdown in gut motility allowing bacteria to take up residence in the small bowel and cause all these unpleasant symptoms. 

In this article we won’t be covering the basics of SIBO. If you need a refresher check out some of the links to past videos below. 

Gut motility issues & SIBO 

Migrating motor complex…peristalsis…gut motility…all words I use daily in the clinic helping to educate patients on why their case of SIBO occured. 

A breakdown in the natural movement through the digestive tract is one of the main root causes of SIBO I see.

Don’t worry we will cover the handful of other root causes I frequently see in future articles. 

There is a complex interplay between the nervous system and the digestive tract. Complex rhythmic smooth muscle contractions, governed by the enteric nervous system, sweeps through the digestive tract moving the contents down and out. This whole process is turned off (or at least downregulated) by the sympathetic nervous system – think fight or flight – and is turned on by the parasympathetic nervous system – think rest and digest (1).

In the fasted state the migrating motor complex performs the sweeping action. In the fed state peristalsis takes over. 

There are a number of things that can impact your gut motility from nerve damage, to inflammation, gases produced by certain microbial overgrowths, past food poisoning and chronic stress and anxiety. 

Occasionally motility issues are caused by adhesions, poor thyroid function, drug side effects, obstructions and hypermobility conditions. Even neuropathy, a possible consequence of diabetes, can impair motility. Today we will cover some of the more common issues impacting gut motility. 

Most of the time clients will present with constipation and bloating but not always. That is why it is so important to test how fast things are passing through your digestive tract – we call this your gut transit time. 

Let’s dive into each of these factors that can slow down your gut transit time and turn off your gut motility now. 

Inflammation and gut motility leading to SIBO 

There is an interesting line of thinking connecting inflammation and gut motility issues. From there the big question is where is the inflammation coming from? In SIBO patients that is a simple enough question to answer. The bacterial overgrowth in the small bowel is a direct source of inflammatory and immunogenic byproducts.

For most of the classic SIBO cases we can see a shift in the small bowel microbiome towards gram negative bacteria, mainly from the Enterobacteriaceae family. SIBO positive patients showed a trend towards Klebsiella and Escherichia overgrowths compared to non-SIBO patients (2).

These two bugs, and the Enterobacteriaceae family in general, contain a bacterial endotoxin called lipopolysaccharide which is potently pro-inflammatory and immune provoking (3). 

‘The blooming of Enterobacteriaceae, which contain these motifs, leads to a more selective pressure and shift toward an Enterobacteriaceae-dominated community’

In layman’s terms – if a bug from the Enterobacteriaceae family can get a foothold it can lay the groundwork for similar pro-inflammatory bugs to take up residence too. 

So we have inflammation established. How does this slow gut motility in SIBO patients? 

LPS and TNF-a slows gut motility

There are cause and effect patterns in the body. Often this is the body trying to regulate and maintain balance. An overload of the bacterial endotoxin LPS triggers an inflammatory cascade in the body governed by a master inflammation switch called tumor necrosis factor alpha, or TNF-a for short. This knock on effect significantly slowed gastric motility via the dorsal vagal complex (4)

Without even taking into account TNF-a and just focusing on the bacteria that produce LPS we can see a slowing effect on the migrating motor complex.

‘The implication of these studies is that constant exposure to gram negative bacillary derived LPS can lead to a diminished migrating motor complex and stasis of luminal contents during the interdigestive period. This stasis then leads to overgrowth of colonic type flora in the small intestine.’

Pediatric Small Intestinal Bacterial Overgrowth in Low-Income Countries
Summary – Inflammation, triggered by bacterial overgrowths can slow gut motility.

Methane gas and gut motility leading to SIBO

Anyone who has experienced methane SIBO will know that a hallmark symptom is constipation. For a deeper dive into methane dominant SIBO check out an overview of my treatment approach – SIBO: Methane Dominant Treatment Plan.   

I focus a lot of energy and time to understand methane SIBO as it can be very stubborn. I see countless clients that are struggling with constipation and bloating, have failed multiple rounds of treatments and are desperate for some relief. If this sounds like you I have documented advanced methane SIBO treatment options here.

Methane gas, a by-product of methane producing archaea like Methanobrevibacter smithii, is a well documented gut motility inhibitor (6).

Originally the thinking was methane production increased as a consequence or independently to slow gut transit. Newer research is pointing to methane as the cause of slow motility. One possible mechanism involves serotonin, an important neurotransmitter for motility. One small study showed lower serotonin after meals in methane producers (7).

From my clinical experience I have come to see methane SIBO as a cause or effect of slow motility depending on the patient. Sometimes it is as simple as methane slowing down the gut. Other times patients may have a preexisting motility issue that favours a methane producing bloom of microbes. 

Summary – Methane gas produced by some overgrowths can slow gut motility by impacting smooth muscle function.

Chronic Stress and gut motility leading to SIBO

Chronic stress, anxiety or being stuck in the fight or flight mode can disrupt healthy digestive function. It is something that you may have heard in passing but not given it much credit. That was definitely my experience. I was always looking for a new and fancy mechanism of action. 

Truth is that autonomic nervous system dysregulation can be the root cause of poor motility leading to an overgrowth of bacteria in the small intestine. 

Don’t forget that chronic stress and anxiety can be the root cause of your digestive symptoms!

The nervous system is complicated. To keep it simple let’s divide it into the sympathetic , parasympathetic and enteric nervous system. 

The sympathetic nervous system can be thought of as the stress or the fight or flight response. While we need this activated nervous system to respond to acute stressors that would threaten our survival (think running from a tiger), many of us are existing in some form of perceived stress most of the time (mortgage repayments, traffic, school assignments, work).  

Compare this to the parasympathetic nervous system which acts best in a rested, calm state also known as rest and digest. Much of our digestive function is activated or functions best when we are calm and relaxed. Definitely not when we are eating breakfast while running to catch the train to work. 

The enteric nervous system is the third arm of the nervous system and mainly governs digestion with input or influence from the other two divisions (1).

To properly outline the nervous system’s impact on digestion we need to discuss the vagus nerve. This single nerve makes up approximately 75% of the parasympathetic nervous system. It provides input to the majority of the thoracic and abdominal organs (1).

Upwards of 80% of the vagus nerves function is sensory. It can be thought of as an early alarm system for invaders and imbalance in the digestive tract (8).

As a mainly sensory nerve highway the vagus nerve relays information back to the brain regulating intestinal permeability and inflammation. In a stressed state the vagus nerve is inhibited and doesn’t function properly (9).

These are all high flying theories with some research still being teased out. Remember the nervous system is complex. The important bit here is that the vagus nerve innervates the digestive tract from the oesophagus down to the large bowel and helps to regulate, among other things, gut motility (10). As this nerve is governed by the rest and digest arm of the nervous system chronic stress can disrupt proper function.  

Another important side note here is that physical damage to the vagus nerve can impact its function. Think whiplash and head trauma patients with digestive symptoms. 

Summary – Chronic stress can impact gut motility by inhibiting important nerve function.

Post Food Poisoning & gut motility leading to SIBO

An acute food poisoning experience can be a major predisposing event that weakens digestive motility. 

This is fairly new research and we are still ironing out the details but since being educated on this possible consequence of certain acute bacterial infections it is on my radar for anyone with difficult to treat or chronically relapsing SIBO.  

I have a few cases where clients travelled the world and could eat anything from anywhere. One client even described his digestion throughout his life as an ‘iron gut.’ Each of these clients experienced some form of acute gastroenteritis, whether from food poisoning, consuming unfiltered or ‘toxic’ tank water, even poorly treated water when camping. From then on they experienced chronic digestive symptoms like bloating and distention, loose stools and diarrhea and abdominal pain after eating. Sounds a bit like SIBO right?

This is new research coming down the pipe. Much of the data is in the early stages of being worked out but there appears to be a connection with a history of a bacterial food poisoning event and irritable bowel syndrome or SIBO (11).

When we look at IBS patients we can see an auto-immune like condition can occur after bacterial food poisoning events. Certain bacterial infections, common in food poisoning, secrete a very specific toxin called cytolethal distending toxin. This bacterial toxin then cross reacts with a protein found in the human digestive tract (hence the auto-immune like reaction = immune system targeting itself). One major function of vinculin is to help regulate gut motility (12).

In human studies we can see a significant increase of anti-vinculin and anti-cytolethal distending toxin antibodies in IBS patients (13).

Image taken from: Study of Antibodies to Cytolethal Distending Toxin B (CdtB) and Antibodies to Vinculin in Patients with Irritable Bowel Syndrome 

A large study found that anti-vinculin and anti-cytolethal distending toxin was higher in mixed and diarrhoea prone IBS but not constipation prone IBS (14). 

Image taken from: Assessment of Anti-vinculin and Anti-cytolethal Distending Toxin B Antibodies in Subtypes of Irritable Bowel Syndrome

As vinculin plays a role in gut motility, immune mediated reduction in this particular protein can result in small intestinal bacterial overgrowth.

Summary – Certain food borne bacterial infections can slow gut motility through immune mediated cross-reactivity.

Improving gut motility to prevent SIBO recurrence

In this article we have covered 4 common causes of poor gut motility leading to SIBO but there are other issues that can lead to dysmotility and SIBO. 

This is why I look at SIBO as a symptom of deeper dysregulation. 

Often it isn’t as simple as killing the bacteria and patients feel 100% better. Even if they do, taking this approach patients often relapse quite quickly. 

Assessing for and treating the root cause while simultaneously reducing the bacterial overgrowth is key to successful treatment of SIBO. 

In the Byron Herbalist clinic I look at each case individually. There are similarities in treatments from patient to patient but there are always specific changes to each treatment plan. This is why I prefer to custom formulate each and every herbal blend so that I can tailor it to the patient and address their root cause.

Now over to you. Have you experienced gut motility issues? What has helped? Share your thoughts in the comment section below. 

References & Resources

  1. Anatomy, Autonomic Nervous System
  2. The First Advanced Network Analysis of the Small Bowel Microbiome in Small Intestinal Bacterial Overgrowth (SIBO) Reveals That Escherichia and Klebsiella Are Disruptive to Network Integrity: Data From the REIMAGINE Study 
  3. The blooming of Enterobacteriaceae, which contain these motifs, leads to a more selective pressure and shift toward an Enterobacteriaceae-dominated community
  4. Induction of endogenous tumor necrosis factor-α:  suppression of centrally stimulated gastric motility
  5. Pediatric Small Intestinal Bacterial Overgrowth in Low-Income Countries
  6. Elevated methane levels in small intestinal bacterial overgrowth suggests delayed small bowel and colonic transit
  7. Methanogens, Methane and Gastrointestinal Motility
  8. Neural aspects of immunomodulation: Focus on the vagus nerve 
  9. The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis 
  10. Vagal tone: effects on sensitivity, motility, and inflammation
  11. Post-infectious IBS, tropical sprue and small intestinal bacterial overgrowth: the missing link 
  12. Study of Antibodies to Cytolethal Distending Toxin B (CdtB) and Antibodies to Vinculin in Patients with Irritable Bowel Syndrome  
  13. Study of Antibodies to Cytolethal Distending Toxin B (CdtB) and Antibodies to Vinculin in Patients with Irritable Bowel Syndrome
  14. Assessment of Anti-vinculin and Anti-cytolethal Distending Toxin B Antibodies in Subtypes of Irritable Bowel Syndrome

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  1. Hi, I live in Canada and am looking for the probiotic L. Reuteri DSM 17983… I can only find the brand Biogaia, do you know if this is a good one because I’m not stoked about the added ingredients ( xylitol,citric acid,palm oil..) or can you recommend one?🙏

  2. Hi Todd, thanks for the article. I’m curious about the post-infectious IBS piece; it seems to be predominantly affect people with IBS-D or M, so it’s somewhat counter-intuitive that this is a motility issue. Stuff is going too fast, you would think.

    From what I can gather the lack of vinculin disrupts the MMC, which is then unable to clear the small intestines effectively, resulting in SIBO. Is that right?

    Would addressing the motility in these patients with something like ginger or Iberogast work—would this not promote more diarrhea—or would you recommend something else, if not at a particular stage of treatment?

    1. Hi Tim, great comments!
      This is a common misunderstanding (if I am understanding your comment). You can have poor gut motility (peristalsis and MMC function) and still have chronic diarrhoea too. There is some overlap between prokinetics (gut motility agents) and laxatives (moving your bowels) on the herbal front but things like iberogast and ginger are not contraindicated in diarrhoea.

  3. Hi Todd, I have histamine intolerance aka:SIBO. I also have IBS-C, again SIBO. I am getting a lot of information from your articles, however, what do you recommend to get rid of SIBO? What kills it? I’m 99% positive I have the Methane producing microbes.

  4. My 4 year old daughter has post infectious SIBO, and my question is whether her mmc will eventually go back to normal or is she going to struggle with this for life? I have struggled with SIBO for years and I really hope she isn’t destined to struggle for life. What herbs are suitable for a 4 year old to eradicate her SIBO and restore her motility? Do you treat patients virtually in Canada?

  5. Hi Todd. Thank you for this and your other fantastic articles. Noticed an typo in this article while reading it.

    “Compare this to the sympathetic nervous system which acts best in a rested, calm state also known as rest and digest”

    Meant to be parasympathetic right?

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