Gut Dysbiosis/SIBO In Depth

Roughly 100 trillion bacterial cells reside in or outside our bodies. The ratio of these microscopic bugs to human cells is roughly 3:1, and includes populations of fungi, bacteria, viruses, archaea and protists. These harmless microorganisms exist in crucial symbiotic relationships with our cells, performing vital tasks and interactions, without which we could not function and most inhabit the gut. We are more microbe than human! “...you are more ‘them’ than you are ‘you’.” 

These microbes are not just passive hitchhikers - when they are balanced in type and number, the vital metabolic functions they provide keep us healthy. Compelling evidence is now showing that the digestive tract is a central bodily system in keeping us healthy and can be the root cause of illness when dysfunctional. Maintaining gut balance is crucial to health and gut dysbiosis is increasingly being linked to a plethora of disorders and health conditions, some of which include - 

Autism spectrum disorders, schizophrenia, depression, anxiety, ADHD, other behavior and mood disorders, migraine headaches, arthritis, cardiovascular disease, cancer, asthma, allergy, diabetes, diseases of the liver, metabolic syndrome, obesity, the 50 million Americans suffering from fibromyalgia, chronic fatigue syndrome, and other autoimmune disorders, and dozens of intestinal disorders that collectively afflict 60-70 million Americans such as the irritable bowel syndrome (IBS) have all been associated with an imbalanced microbiome(2).

SIBO is largely under-diagnosed. “The number of people with SIBO in the general population remains unknown. Some studies suggest that between 6 to 15% of healthy, asymptomatic people have SIBO, while up to 80% of people with irritable bowel syndrome (IBS) have SIBO (6).”(3)

Thus, the collective prevalence of the above disorders and gut microbial imbalances have been linked to virtually all of the chronic diseases in the Western world and exactly how many suffer as a result is hard to calculate. This Huffpost article discusses this issue and asks the question - ‘How did we get to this state of epidemic gut dysfunction?’ The truth is, although there a few main culprits of the modern world which directly cause gut dysbiosis; antibiotic use, poor diet and the epidemic of stress and anxiety, the cause can be complex and multitudinous(4). 

‘Irritable bowel syndrome or IBS is the name doctors use to describe a collection of otherwise unexplained symptoms relating to a disturbance in the bowels.  These include abdominal pain, bloating, constipation and diarrhoea.  At any one time, IBS affects around 10-20% of people living in the UK.’(5)

Irritable Bowel Syndrome (IBS) is the most common and vague “last-ditch” gastrointestinal diagnosis given to those who suffer from gut dysfunction and those with SIBO are often incorrectly diagnosed with IBS. IBS and SIBO have many correlations, including symptoms which overlap, a micro-organic basis and chronic gut motility dysfunction. Numerous research has discovered IBS patients to have excessive small intestinal bacterial growth(6), (1), (7). Studies have also shown IBS symptoms to improve from SIBO treatments(8). IBS can be broken down into 3 different types; IBS-C (characterised by constipation), IBS-D (characterised by diarrhoea) and IBS-M (mixed). Much mystery still surrounds IBS - as with most chronic gut disorders - but research is finding that one trigger may also be food poisoning - yet another overlap with SIBO. “...we have shown that now you can have this post-infectious IBS, which essentially is SIBO.”(1) 

Small Intestinal Bacterial Overgrowth (SIBO) is a serious, chronic and highly complex condition of the gut. It’s defined as a pathological increase of bacterial populations in the small bowel (SI) exceeding 105–106 organisms/mL(9). In other words, it's dysbiosis of the gut or a chronic gut infection. However, the bacterial overgrowth itself is just the tip of the iceberg and the result of an underlying issue(s). Gut dysbiosis can also be defined as a negative coexistence of host and microflora which occurs within the GI tract.

The SI is normally a relatively clean place. The stomach receives food, mixes it with acid and digestive juices and turns it into a clean slurry that is pushed through the three parts of the small intestine (duodenum, jejunum, ileum) where the nutrients are absorbed into the body. The refuse is dumped into the large intestine, or colon, where water is absorbed and the poop become more solid before being eliminated from the body.

The normal bacterial flora of the SI, perform important functions including helping to digest certain vitamins like folic acid and vitamin K and  protecting the body from external microorganic threats such as bad (pathogenic) bacteria, via its stunning network of lymphoid cells (cells of the immune system that help fight infections and regulate the immune system). These bacteria also help maintain the normal muscular activity of the small bowel (peristalsis), which creates waves that move the intestinal contents, like food, through the gut. When intestinal function is compromised, bacteria from the colon can migrate upwards and an overgrowth in the SI can take hold. This may be the result of a lack of adequate stomach acid, damage to the intestine by toxins like alcohol, or a decrease in the speed at which the small intestine transfers material to the colon. The colon is not as clean as the small intestine and reflux, or backflow, of stool into the small intestine can colonise it with colonic bacteria when the gut malfunctions(10).

There are 2 different types of SIBO infection; SIBO-C or methane-dominant SIBO and SIBO-D or hydrogen-dominant SIBO. They are so named because methane-dominant bacteria causes constipation and hydrogen-dominant causes diarrhoea. It is important to note that SIBO sufferers often have both hydrogen and methane present in the SI, due to the ecosystem created by the bacteria. Apart from the varying symptoms between the two types, I have found very few studies explaining the differences so I assume that SIBO-D is the preliminary stage of SIBO, which left untreated can develop into SIBO-C.

“An estimated 80% of bacterial infections in humans are caused by biofilms, according to the National Institutes of Health”(11).

The Biofilm Life Cycle

We often think of infections being characterised by bacterial bugs floating around inside our systems, causing mischief. But these single celled microorganisms have evolved a clever way to survive and hide from immune detection and being free-floating or “planktonic” is only the first stage of their life cycle - the Biofilm Cycle. To form a biofilm, bacteria first attach to a surface and then generate a polysaccharides, proteins, DNA, minerals, and heavy metals mucus matrix which forms a physical protective barrier(12). 

The vast majority of pathogenic bacteria (and potentially some beneficial bacteria also) within the human body are hidden behind bacterial biofilms within slime-enclosed communities - classy. Within a biofilm, one or more types of bacteria and/or fungi share nutrients and DNA and there, they undergo changes to evade the immune system. The hostile biofilm community are protected by their physical mucus barrier against most antibiotics and immune cell detection. This recent discovery reveals that the current models of healthcare, which assume that acute infections are caused by pathogenic planktonic bacteria, have been treating illnesses ineffectively(13).   

Evading Detection + Testing

The biofilm membrane is highly effective as a physical barrier and explains why chronic infections are hard to test for, diagnose and treat. Swabs and cultures often show up negative and stool samples usually do not contain the biofilm bacteria either. To add to this complication, biofilms may also play a role in healthy gut function, making it difficult to distinguish between pathogenic and healthy communities. While planktonic bacteria can become antibiotic resistant through gene mutations, a biofilm is often antibiotic resistant for multiple reasons—physical, chemical, and genetic(13), (14). 

GI Tract Biofilms 

Biofilms along the epithelial lining (GI tract) are little understood but its huge surface area and constant influx of nutrients makes for an ideal environment for biofilm-forming microorganisms. The GI epithelium is lined with protective viscoelastic mucus, but this can be damaged in those with excessive inflammation, creating an opportunity for the bugs to hook onto the lining and begin biofilm construction(13). 

Breaking Through the Biofilm

There are many Biofilm disruptors and conveniently, many of the antimicrobial treatments are listed on the SIBO-Killing Herbs page and are effective biofilm disruptors themselves, especially when a combination of a few are taken simultaneously. Once the biofilm has been disrupted and the immune cells can deal with the bugs, it’s important to take a toxin binder to help unburden your system from the onslaught. Two natural and money-friendly binders include citrus pectin and chitosan(13).

Root cause (often autoimmune) > Gut dysfunction (mobility disorder) > SIBO > Archaea (methane byproduct produced) > Further gut damage > Further gut dysfunction increases SIBO > Chronic gut damage + inflammation > Secondary conditions (such as leaky gut syndrome and secondary autoimmune diseases [AIDs])

Once the gut is dysfunctional, SIBO can develop and once in the SI, the bacterial overgrowth creates an alternative, unhealthy habitat ideal for other microorganisms such as archaea (discussed in depth below). In those with SIBO, the microbially-rich SI ecosystem feeds on the foods consumed, causing damage to the gut which further contributes to gut immotility, dysfunction and in the process, making the conditions of their new small bowel habitat even more favourable for themselves and other microorganisms. Left untreated, this cycle perpetuates, the bacterial burden increases and consequently, so too do the symptoms and likelihood of secondary conditions such as leaky gut syndrome and autoimmune conditions. As a result, the individual’s health declines.

SIBO doesn’t come about by chance - functional gastrointestinal disorders (FGID), chronic gut motility dysfunction, disturbances of gut immune function or anatomical abnormalities of the GI tract all increase the likelihood of the pathology developing(9). 

• Structural/Anatomic - Small intestine diverticula, small intestine strictures (radiation, medications, Crohn's disease, surgically created blind loops, resection of ileocecal valve, fistulas between proximal and distal bowel, gastric resection.
• Motility disorders - Gastroparesis, small bowel dysmotility, celiac disease, chronic intestinal pseudo-obstruction.
• Low gastric acid (HCL) - low stomach acid levels
• Irritable Bowel Syndrome (IBS) - this may be caused by and perpetuated by SIBO(9) but more research is needed before this is concluded.
• Metabolic disorders -  Diabetes, hypochlorhydria.
• Old age - digestive function decreases as we age. Until recently SIBO was seen primarily in the elderly.
• Organ System dysfunction -  Cirrhosis, renal failure, pancreatitis, immunodeficiency states, crohn's disease, celiac disease, malnutrition.
• Medications - Recurrent antibiotic use, gastric acid suppression(9).
• Compromised, decreased immune function - this includes those who have - Human Immunodeficiency Virus (HIV), immunoglobulin A deficiency, combined variable immunodeficiency(11).

• Weight loss
• Steatorrhea
• Vitamin/mineral deficiencies - Fat-soluble vitamins (A, D, E, K), Vitamin B12, Iron
• Vitamin excess - Folate
• Hypoproteinemia/hypoalbuminemia
• Decreased xylose absorption

When bacteria digest carbohydrates and fibres in the SI, they produce hydrogen as a byproduct. This excess gas can accumulate in the 20 feet long SI, giving rise to abdominal bloating, distension and consequently pain and cramps. This initial bacterial overgrowth creates an environment ideal for other microorganisms; the hydrogen byproduct can in turn feed single-celled organisms in your small intestine called archaea, which produce methane as a byproduct. SIBO sufferers have excess levels or hydrogen, methane, or both in the GI tract, and as a result, a harmful microbial ecosystem which forms the below cycle - 

Carbohydrates (high FODMAP foods + sugars) feed SIBO > SIBO produces hydrogen > archaea feed on the hydrogen > archaea produce methane > methane further contributes to gut damage, leaky gut syndrome etc.

“...recent evidence actually has linked methane production to various disease states.  But we do know from studies that methane-producing archaea are present in 45 percent of people with SIBO.  In other words, a substantial percentage of people with SIBO have methane-producing archaea.”(12)

As stated above, the single-celled organisms with no cell nucleus and no membrane-bound organelles archaea, are present in the majority of SIBO cases. Archaea are fascinating ancient extremophile microorganisms found in almost every environment and habitat on Earth - anywhere organic compounds are found in decomposition - including inside the guts of animals and humans. They lie in a kingdom of their own, having a completely separate genetic make-up to that of bacteria, fungi and eukaryotes.(13) They are now believed to also play an important role, along with bacteria, in human gut health. 

Archaea are methanogens (they produce methane as a byproduct) which along with methanogenic bacteria, feed off and metabolise the excess hydrogen which gut bacteria produce as a byproduct. So as the bacterial overgrowth in the SI increases, so too does the hydrogen they produce and thus the food source for the methanogens increases also. Excess methane presence in the intestines contributes to SIBO by slowing intestinal transit time, allowing the SIBO extended feeding opportunities and has been linked to numerous gut pathologies(14).

Methane + SIBO

Methane (CH4) is a colourless, odourless, inert gas which we begin to produce around the age of 3, suggesting that methane production and archaea are key in how the gut is initially colonised(12). Though little understood, it is now emerging that a range of intestinal gases exert a huge influence on gut motility, function and health and can be altered by many varying factors. 

Several recent studies have focused on CH4 metabolism at the intestinal level and on the association between this gas and the role it plays in the development of organic and functional bowel disorders and intestinal disease. There are numerous methanogenic bacteria within the colon and in the increased presence of hydrogen-producing microbes (among those with SIBO and IBS-C) and CH4 production can be seen to be linked to constipation(14) and altered small intestinal motor function.