The Gut Microbiome
Human gut is home to ~100 trillion microbes (collectively referred to as gut microbiome) which play a major role in controlling many aspects of host physiology and pathophysiology. Gut microbiome makes up about 2 kg of total body weight and outnumber our own cells by 10 times. In essence, we are only 10% human! These microbes are differentially distributed in the gastrointestinal tract with 101-103 cells/g in stomach and duodenum, 104-107 cells/g in jejunum and ileum and 1011-1012 cells/g in the colon .
Not only the number, but the composition of the microbes also varies along the gastrointestinal tract. Gut microbes aid in digestion, synthesize vitamins such as Vitamin B and K, keep the pathogens away and help build our mucosal immune system. Changes in the number and composition of gut microbial community due to environmental factors such as repeated antibiotic use, psychological and physical stress, infection, dietary changes, alcohol abuse, smoking or genetics may lead to microbial imbalance (called dysbiosis) in the intestine.
Dysbiosis has been increasingly linked to many conditions such as small intestinal bacterial overgrowth (SIBO), obesity, diabetes, inflammatory bowel disease, irritable bowel syndrome, colitis, neurodegenerative diseases and cancer. Thus, gut microbes play a central role in our well-being.
What is SIBO?
Small intestinal bacterial overgrowth (SIBO) is a clinical condition that occurs when colonic bacteria infiltrate into the small intestine. The most commonly accepted definition of SIBO is the presence of ≥105 colony-forming units per milliliter (CFU/mL) of bacteria in proximal small intestinal aspirates .
Small intestine usually carries much lower bacterial load compared to colon. Some of the host factors responsible for controlling the bacterial density in small intestine include gastric acid secretion, intestinal motility, ileocecal valve, immunoglobulins and antimicrobial proteins such as lysozyme. Malfunction of these mechanisms may predispose an individual to SIBO. Other risk factors for SIBO include conditions such as intestinal fistulas, removal of the ileocecal valve and previous intestinal surgeries. Being at the wrong place, doing the wrong work, these colonic bacteria interfere with the functions of the small bowel which is digestion and absorption of nutrients.
Fermentation of carbohydrates (which normally takes place in the colon) by the colonic bacteria in small bowel in the setting of SIBO produces gas, abdominal pain and bloating, symptoms typical of SIBO , . These bacteria also compete with the host for nutrients generated in the small intestine, leading to malabsorption responsible for nutritional deficiency and weight loss observed in SIBO patients. In addition, by-products and metabolites of colonic bacteria in the small bowel are toxic and may damage the intestinal epithelium, which may cause leaky gut. SIBO has been associated with diseases such as irritable bowel syndrome , obesity ,Crohn’s disease  and celiac disease .
Treatment of SIBO: Can Probiotics Help?
The most prevalent treatment option for management of SIBO is the use of antibiotics. Commonly used antibiotics include rifaximin, ciprofloxacin, norfloxacin, amoxicillin, and metronidazole. Of these, rifaximin, a broad spectrum non-absorbable antibiotic appears to be highly efficacious , , , . Other treatment is correcting the nutritional deficiency caused by SIBO and including modified diet for managing SIBO.
While antibiotics therapy is aimed at reducing the bacteria that are responsible for SIBO, probiotics work by incorporating the good bacteria that are needed for optimum function of the small intestine. First coined by Lilly and Stillwell , the term probiotics is defined as “live microorganisms, which when administered in adequate amounts confer a health benefit on the host by overcrowding pathogenic bacteria” .
Most common probiotics include bacteria belonging to the genera Lactobacilli and Bifidobacteria. Probiotics imparts several benefits such as enhancing immunity, exclusion of pathogens, positive effects on intestinal motility, balancing the pH of the intestine, helping in nutrient absorption, improving digestion and protecting the intestinal mucosa. In addition, they have anti-carcinogenic properties, anti-diarrheal properties Few research studies have demonstrated that administration of probiotics may be helpful in mitigating the symptoms of SIBO. In one study, it was found that the intervention of a probiotic Lactol (containing Bacillus coagulan) in conjunction with the antibiotic therapy caused a decrease in abdominal pain and other GI symptoms. Also, the hydrogen breath test also came out negative in the same group of patients . Another study showed that in patients with chronic liver disease who were given Duolac Gold probiotic (Cell Biotech Co., Ltd, Gimpo, Korea), a cocktail of probiotics Bifidobacterium bifidum, Bifidobacterium lactis, Bifidobacterium longum, Lactobacillus acidophilus, Lactobacillus rhamnosus, and Streptococcus thermophilus,) there was alleviation in symptoms of SIBO . In a report comparing the effect of antibiotic metronidazole vs probiotic consisting of Lactobacillus casei, Lactobacillus plantarum, Streptococcus faecalis and Bifidobacterium brevis, the probiotics showed higher efficacy in improving SIBO compared to antibiotic treatment .
Another article showed the effectiveness of Lactobacillus strains in treatment of SIBO related chronic diarrhea . Lactobacillus casei strain Shirota (Yakult) was effective in reducing SIBO in patients with IBS . In contrast, one study showed no significant effect of probiotic Lactobacillus fermentum KLD on improvement of SIBO symtpoms . Overall, the existing data indicates that probiotics maybe useful in alleviating symptoms of SIBO. However, further research needs to be carried out to explore the potential of probiotics in the treatment of SIBO and diseases associated with it.
Fermented Foods as Excellent Source of Probiotics
Fermented foods make up a large part of the diet throughout the world. Incorporation of fermented foods in the diet dates back thousands of years. Elie Metchnikoff, “father of natural immunity” wrote “prolongation of life” in 1907 in which he mentioned that consumption of Lactic Acid Bacteria (LAB) in fermented dairy products was responsible for enhanced health and longevity in many people living in Bulgarian villages. Dairy fermented foods include foods such as yogurt, kefir, buttermilk and cheese and non-dairy fermented foods include kimchi, sauerkraut, pickled cucumbers, kvass, miso and tempeh. Fermented foods are rich in probiotics, with every mouthful you’re consuming billions of different strains of beneficial microbes and most of them contain Lactobacilli , . Bifidobacterium is another common probiotic found in fermented dairy products.
Fermented foods appear to be more beneficial than probiotic supplements as they offer much higher number and variety of viable bacteria compared to the probiotic supplements and are cost effective. Supplements available in the market are proprietary products and may not work for everyone since each individual has a unique signature of gut microbiome. Moreover, fermented foods are highly nutritious and may also provide essential prebiotics important for growth of probiotics. Substantial clinical research is needed to confirm the benefits of fermented foods on SIBO. Nevertheless, it is tempting to believe that the consumption of fermented foods may help with the symptoms of SIBO owing to the presence of good bacteria in these food which may help restore beneficial microbes in the gut. In general, fermented foods should be consumed to maintain a good gut health and as a preventive measure to avoid SIBO and dysbiosis of gut microbiome.
Another promising treatment option is use of prebiotics. Prebiotics are non-digestible dietary compounds that promote the growth of good resident bacteria such as Lactobacillus and Bifidobacterium. Some examples of prebiotics include inulin, fructooligosaccharides and galactooligosaccharides and other oligosaccharides. Studies need to be carried out to determine if prebiotics could be useful in the treatment of SIBO.
Soil Based Organisms:
One of the least highlighted but key to our gut microbiome profile is the inclusion of soil based organisms.
Soil-based probiotics are least discussed alternative to the more traditional lactic acid-based formulations. Research over the years has shown promising results, particularly with respect to IBS and other digestive conditions, and we know that individual strains of soil-based bacteria have antifungal properties. If you are not seeing the results that you want with your current probiotic, a soil-based probiotic might be the solution.
By reintroducing soil-based organisms in our intestines it increases the diversity of beneficial bacteria in our guts this helps in improve digestion, boost immunity, and all this diversity weeds out the pathogenic bacteria by . Soil-based organisms (SBOs) have been linked to reductions in abdominal discomfort, bloating, nausea, flatulence, and constipation. Soil-based organisms have also been shown to activate the immune system, overcome auto immune diseases, stimulate the production of white blood cells and antibodies. There is a lot of anecdotal evidence that these soil based bacteria helps in overcoming constipation in C-IBS.
Many people think that it is our stomach that digests our food for us. This is not completely true. Our stomach produces gastric juices, which is primarily made up of hydrochloric acid.  This helps break down the food, making it easier for us to digest. The actual absorption of nutrients happens in the small intestine.  Your small intestine is divided into three parts, name duodenum, jejunum and ileum.
The duodenum neutralizes the stomach acids and receives additional digestive juices from your pancreas and gall bladder. The jejunum absorbs proteins and simple sugars. The ileum, which also happens to be the longest part of your small intestine, absorbs water, minerals, fats, salts and complex sugars.  The unabsorbed food material is passed from the ileum to the large intestine, which is also known as the colon.
Both the small intestine and the large intestine are a host to a wide variety of bacteria, which play an essential role in the digestive process. The amount of bacteria in the large intestines tends to exceed the amount present in the small intestine. However, if the amount of bacteria in the small intestines exceeds the optimal amount, the patient starts suffering from Small Intestinal Bacterial Overgrowth (SIBO), which is a serious medical condition. People suffering from SIBO show a wide variety of symptoms, which can be summarized into the following: 
- Chronic diarrhea.
- Nutritional deficiencies, which may manifest itself in the form of malnutrition, unintentional weight loss, anemia  and even osteoporosis.
Is SIBO caused by Good Bacteria or Bad Bacteria?
Based upon what we have discussed already, we have established that an “overflow” of bacterial fauna causes SIBO. But is SIBO caused by an increase in the natural bacteria in the small intestine, or is it caused by harmful bacteria? Unfortunately our understanding of SIBO is still in its infancy and what we know so far tends to indicate that the answer is far more complicated than that.
Why not Probiotics Work for all cases?
Related is a hazda tribe study for the gut microbiome. It pointed to the fact these hunter gatherers have totally different microbiome then what we modern men/women have. The bacterial strains in these people are far more diverse and they even harbour bacterial species which we label as pathogenic for eg c difficile.
Now the take home point is that some people go into remission with probitoics while some don’t and the hazda tribe has bacteria far more diverse than what comes in probotic pills. What this means is that it seems the gut bacteria works in a complex ecological balance. When one species goes extinct or missing the gut microbiome takes a hit. And when a species is reintroduces (like with proboitics) it helps in symptoms remission given that it is the bacterial species that will help in what gene expression is required to curb the symptoms.
Probiotics are mixtures of several different bacterial species, have been used for treating SIBO and IBS, but their effectiveness is not known.
One more point to be noted is that people undergoing colon cleanse which removes all types of bacteria good or bad also feel significantly relieved from the symptoms like nausea, cramps, diarrhea or constipation. This underlines the fact that having no bacteria at all also works.
So how does the good bacteria spill over from the large intestine to the small intestine? It is caused by a backflow of stool from the colon into the small intestine. This can be triggered by the following:
- The ileocecal valve acts as a doorway between the small intestine and the large intestine. It stays closed most of the time and opens shortly to allow the residue from the small intestine to move into the large intestine.  If there is any weakness in the ileocecal valve, then the fecal matter may move into the small intestine, causing it to be colonized by the bacterial fauna that belongs in the colon. 
- If you suffer from severe constipation, it will put a lot of pressure on the ileocecal valve and may damage it in the process, leading to SIBO. Chronic sufferers of constipation should look at investigating the causes of constipation and try resolving it naturally. If you are not responding to any of the usual remedies for constipation, chances are that you may be suffering from hypothyroidism. Research has shown a strong link between SIBO and hypothyroidism. 
Where to Get Good Bacteria without spending Dollars?
Sibo is the problem of compromised gut diversity and bad bacteria outnumbering the good and at the wrong place. One of the most common questions asked by people suffering from SIBO is to where to gut good bacteria to help overcome this imbalance. To answer this question, one needs to understand where the good bacteria come from to re-establish the diverse composition of gut flora. Studying the behaviour of certain African tribes may throw some light into the matter. Please note that their practices are yet to be certified and accepted by western medical authorities. However, the following tips the scales significantly in their favour.
- They are free from modern diseases that plague the people of industrialized world.
- They have a diverse bacterial fauna in their gut.
- Their habits are inexpensive and really easy to implement.
They simply eat home grown and wild organic fruits and vegetables without washing them. They eat them after picking them from the trees or uprooting them from the soil. The dirt, soil clinging to these fruits and vegetables has dozens or perhaps hundreds of different species of good bacteria that are diverse and healthy for the human gut. These tribes also do not cook these food items for extended amounts of time either which kills all types of bacteria good or bad.
Hence, besides providing nutrition, these food items expose the gut to innumerable species of good bacteria that are great for the digestive system. Someone suffering from SIBO should perhaps follow the example of these African tribes and eat a diverse amount of organic fruits and vegetables without washing them. Doing this regularly can possibly re-establish a healthy composition of gut flora but don’t expect things to happen instantly, persistence is the key. It is to be noted that no cases of SIBO or even auto-immune disorders have been noticed in the said tribes.
Due to cooking and rigorous hygiene practices of the current industrialized community we go to great length to wash off every bit of soil and earth from these fruits, vegetables, grains and other eatables and in the process remove all the bacteria we should be getting from them. This results in missing species of gut bacteria that further leads to vulnerable immunity and people often getting ill.
Taking probiotics may be a less cringe-worthy alternative to eating unwashed fruits and vegetables. However please note that most probiotics tend to have only one or few types of gut bacteria. To re-populate your intestinal fauna, you may have to consume several different brands of probiotics daily to cover the hundreds of different species needed, which for some may prove to be prohibitively expensive.
Moreover, not all types of gut bacteria are available in neatly packaged bottles. Hence, unless you are looking to undergo a fecal transplant, eating unwashed fruits and vegetables may be the ideal solution for you!
SIBO and Fecal Transplant
Does fecal microbiota transplant help cure SIBO? The answer is not as simple. It provides reliefs from certain symptoms such as insomnia, constipation, depression, and weight gain. However, on the other hand, there is no evidence that it actually cures the disease apart from some anecdotal evidence.
So how should one proceed? Cautiously, of course! There has been a documented case where a patient was prescribed fecal pills to cure a c difficile infection, although c difficile was cured but he developed SIBO. He is now on herbal antibacterial medication to keep the symptoms in check. This shows that although a fecal pill may help develop bacterial fauna in the large intestine, it may in turn cause an overgrowth in the small intestine as well. So before treating with fecal pills one needs to get rid of the overgrowth from the small intestines. Once the MMC waves are at optimal levels, your body can stop large intestinal bacteria from colonizing the small intestine and you can then start taking the fecal pills. This is also known as a top down approach.
Another way is a bottom-up approach. In this method, one can transfer fecal microbiota via enemas or through colonoscopy.
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