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 anecdolat evidence that these soil based bacteria helps in overcoming constipation in C-IBS.
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