Fixing an unhappy Small Intestine

SIBO, (small intestinal bacterial overgrowth) is characterized by unexplained weight loss, malnutrition, mental disorders, fatigue, stomach pain, bloating, diarrhea and constitution B12 deficiency, Leaky gut, depressions, joint pain and, inter alia, rashes. In this page, I’ll examine SIBO’s specificity and  symptomatology, then show what some of the root causes are (Section A). Thereafter, I will  look a different detection and diagnostic tests (Section B) and conclude on treatments plans, risks and relapse issues. (Section C)


Gastric acid secretion and intestinal clearance provide the normal qualitative and quantitative partitioning of intestinal bacteria. Small intestinal bacteria overgrowth (SIBO) occurs when these barrier mechanisms fail. Diagnosis of SIBO is challenging due to the low specificity of symptoms, the frequent association with other diseases of the gastrointestinal tract and the absence of optimal objective diagnostic tests. The Conventional Medical approach to SIBO is oriented towards resolving predisposing conditions, and is supported by antibiotic treatment to restore the normal small intestinal microflora and by modifications of dietary habits for symptomatic relief. However, there are major limitations and toxic side effects with this costly approach. On the other hand, Holistic Medicine focuses on other strategies that tend to be more successful, less harmful and not as expensive as the mainstream approach. In the near future, metagenomics and metabolomics will help to overcome the uncertainties of SIBO diagnosis, allowing an even more effective approach based on personalized strategies hinged on the knowledge of the intestinal microbial community’s composition. Meanwhile, holistic medicine can successfully and durably prevail, even without a complete metagenomic testing.

Section A

Nature of the Disease and Symptomatology

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Contrarily to the large intestine, the small intestine is designed to have way fewer bacteria. The upper two thirds of the small intestine usually contains less than 10,000 bacteria/mL.SIBO is a very heterogeneous syndrome characterised by an increased number and/or abnormal type of bacteria in the small bowel. Most authors consider diagnostic of SIBO to be the finding of ≥ 105 bacteria [i.e. colony-forming units (CFU)] per mL of proximal jejunal aspiration. The normal value is ≤ 104 CFU/mL[3,5-7].

Toskes PP, Kumar A. Enteric bacterial flora and bacterial overgrowth syndrome. In: Feldman M, Scharschmidt BF, Sleisenger MH, editors. Sleisenger & Fordtran’s Gastrointestinal and Liver Disease. 6th ed. Philadelphia: WB Saunders; 1998. pp. 1523–1535.
4. Swidsinski A, Loening-Baucke V. Spatial organization of intestinal microbiota in health and disease. UpToDate on line, 18.1. Wellesley, 2010. Available from:
5. Gasbarrini A, Lauritano EC, Gabrielli M, Scarpellini E, Lupascu A, Ojetti V, Gasbarrini G. Small intestinal bacterial overgrowth: diagnosis and treatment. Dig Dis. 2007;25:237–240. [PubMed]
SIBO, (small intestinal bacterial overgrowth) is characterized by unexplained weight loss, malnutrition, mental disorders, fatigue, stomach pain, bloating, diarrhea and constitution B12 deficiency, Leaky gut, depressions, joint pain and Rashes (
SIBO patients are often deficient in vitamins A, D, E, B12, B9 (folate), calcium and iron [R,R].
The bacteria can also steal protein before it is absorbed, leading to protein deficiency.

Nonspecific, these symptoms often make it difficult to diagnose SIBO. Many other conditions like IBS, pancreatis, Crohns Disease, lactose intolerance, autoimmunity, rosacea, fibromyalgia, hypothyroidism rheumatoid arthritis cirrhosis of the liver
The amount of overgrowth is related to the severity of these diseases. (3)

Section B

Pathogenesis (Causation)


Constellation of causes
The etiology of small intestinal bacterial overgrowth (SIBO) is diverse and frequently multi-factorial. SIBO is thought to result from structural changes of the gastrointestinal tract, disordered peristalsis of the stomach and/or small intestine, or a disruption of the normal mucosal defenses of the small intestine. Alcoholics are reported to have higher rates of SIBO, as diagnosed by jejunal aspirate; however, no data are available on the association between moderate alcohol consumption and SIBO.

Three types of constellations can cause SIBO: distinct groups: Disorders of the gut’s antibacterial mechanisms: Structural abnormalities: Disorders that cause slow digestion

1) Disorders of Antibacterial Mechanisms

The digestive system has ways to prevent the overgrowth of bacteria, such as stomach acid, bile, enzymes, and immune cells. A lack of any of these allows bacteria to thrive, leading to SIBO.

Low Stomach Acid and Enzyme Production

Stomach acid destroys bacteria before they reaches the small intestine [R].

A lack of acid production allows bacteria to pass through the stomach into the small intestine where they can multiply. Enzymes released from the pancreas also help destroy bad bacteria in the small intestine [R].
Lack of Bile Flow

Bile acids inhibit bacterial growth in the small intestine [R,R]. When bile production in the liver or flow from the gallbladder decreases, pathogenic bacteria in the small intestine increase

Underactive Immune System in the Gut

Immunoglobulin A (IgA) is a type of antibody that helps fight bad bacteria in the gut. SIBO is common in people with a genetic condition that lack IgA (selective IgA deficiency) [R].
Bacterial overgrowth is also common in AIDS patients due to an underactive immune system [R]

2) Structural Abnormalities

Structural flaws in the small bowel can lead to SIBO. Certain structural abnormalities trap bacteria and allow them to accumulate.

Small Intestinal Inflammation

Diverticula are small pouches in the small intestine that can become inflamed. These pouches can collect bacteria and lead to SIBO.
One study found that 59% of the patients with diverticulitis had SIBO. Treatment with antibiotics decreased the SIBO and the inflammation [R]

Bad Connections Between Intestine and Organs

Intestinal fistulas are unnatural connections between an organ and the intestines. Bacteria can become trapped in these connections [R].

Ileocecal Valve Dysfunction

The ileocecal valve separates the end of the small intestine from the beginning of the large intestine. When this valve is damaged or removed, bacteria can come up from the large intestine and take over [R].
Stomach and Gut Surgeries

Stomach and gut surgeries such as gastric bypass surgery can cause SIBO [R].

Stomach and gut surgeries that bypass parts of the gut can create sections that collect bacteria called blind loops Because SIBO often develops in people who have these blind loops, it is often referred to as Blind Loop Syndrome (BLS).

3) Disorders Causing Slow Digestion (gut flow disorders)

Normally, the muscles lining the stomach and small intestine will contract and relax in waves. This process is known as the migrating motor complex (MMC). The MMC stops bacteria in the colon from coming up into the small bowel [R].
Peristalsis is the movement of food down the gut caused by wavelike contractions of muscles lining the gut. It occurs whether food is present or not.
Any disease or disorder that stops the MMC or slows peristalsis will let bacteria from the large intestine travel into the small intestine.

Diabetic neuropathy

Diabetic neuropathy is damage to the nerves of the gut from diabetes. When the nerves become damaged because blood sugar is too high, gut movement slows down.


Scleroderma is a chronic connective tissue disease. It partially blocks the intestines, slowing down the movement of food. This allows bacteria to accumulate.
Research has found SIBO to be present in 43-56% of scleroderma patients [R,R].

While small amounts of good quality wine benefits the gut and longevity, (Cf ) questionable high dosed alcoholic beverages can damage many organs, including the liver and intestines.

Overconsumption of Refined Carbohydrates

Diets rich in refined sugars tend to increase the growth of bacteria, both good and bad [R]. The body can only absorb so much sugar at once and any extra can be used by opportunistic bacteria [R,R].

Common Risk Factors

The following increase the risk of developing SIBO:
• Use of proton-pump inhibitors (PPIs) and other antacids [R]
• Use of painkillers [R]
• Lack of breastfeeding [R]
• Antibiotic use [R]
• Age [R]
• Celiac Disease [R]
• Crohn’s Disease [R]
• IBS [R]
• Liver diseases [R]
• Kidney Failure [R]
• Inflammation of the pancreas [R]
• Leaky Gut [R]
• Immunodeficiency [R]
• Diabetes Mellitus (type I and type II) [R]
Birth Control Medications
Use of birth control medications have been associated with IBD and IBS [R,R]. Given the strong link between these conditions and SIBO, it is likely that birth control pills are also associated with SIBO.

Section C

There are two popular tests used to diagnose SIBO:
• jejunal aspiration
• hydrogen breath test (HBT).

Hydrogen/Methane Breath Test
The challenges of jejunal aspiration led to the invention of another type of test called the hydrogen breath test. It is the most popular way to diagnose SIBO due to its low risk, simplicity, and noninvasive nature.
The test involves the patient fasting overnight and then eating a sugar that is fermented by the bacteria in the small intestine. The gases from the bacteria are then captured and used to see if there is an overgrowth [R].

HBT has its drawbacks. In about 15-30% of people with SIBO, the bacteria will produce methane instead of hydrogen [R].
It is necessary to also test for methane if the hydrogen breath test is negative. People who test positive for methane tend to have constipation [R,R,R].

The HBT also has a high false negative rate. This means that the test turns up a negative result when in fact the person does have SIBO [R].

Lastly, there is no consensus as to what determines a positive result. The only way of being confident in the results is to treat SIBO and see if symptoms disappear [R].

Despite these drawbacks, most doctors still prefer the use of the HBT [R].

Sampling The Small Intestine
The gold standard for SIBO testing is jejunal aspiration. This involves taking a sample from the small intestine and counting the number of bacteria per mL.
It is a costly and invasive procedure that requires a tube to be inserted into the small bowel. Another issue is the risk of contamination of the tube as it is passed through the stomach [R].

Section D

Treatment Plans


Many different antibiotics, diets, and supplements are effective in eradicating SIBO. Most conventional doctors will treat the condition using antibiotics. However, SIBO often returns.

Conventional Medicine





1) Pharmaceutical Antibiotics

The standard therapy for SIBO is antibiotics such as tetracycline, vancomycin, metronidazole, neomycin, and rifaximin (mainly individually) [R].

This is counterintuitive, as antibiotics can cause SIBO. However, certain antibiotics like rifaximin actually reduce bacterial overgrowth.
Rifaximin’s effectiveness has been thoroughly studied. It is also poorly absorbed so it stays in the gut and doesn’t lead to bacterial resistance [R].

Conventional Medicine’s SIBO Standard of Care is Outdated

Rifaximin is the most commonly studied antibiotic treatment for SIBO, with an overall breath test resolution rate of 49.5% (95% confidence interval, CI 44.0-55.1) in 8 clinical trials.18 A recent meta-analysis reported that the therapeutic efficacy of rifaximin to treat SIBO in the setting of IBS showed benefit; however, the therapeutic gain was only 9.8%, and the number needed to treat is 10.2 with mild heterogeneity (P=.25, I(2)=26%).39 Additionally, rifaximin is currently not approved by the US Food and Drug Administration (FDA) for the treatment of SIBO and is only labeled for hepatic encephalopathy. Furthermore, a month’s supply of rifaximin retails for $1247.39, and according to Medicare part D, a patient’s copay in 2014 will be $638.09 for preferred ($703.70, non-preferred) pharmacy or mail-in.40 Antibiotics may also produce a wide range of toxicity (Clostridium difficle colitis, antibiotic induced diarrhea, anaphylaxis, Steven’s Johnson reactions, hemolytic-uremic syndrome, etc).41 Antibiotics have also been postulated to have pervasive adverse effects on the gut microbiome and protective biofilm layer.42 In fact, a 7-day course of clindamycin has been shown to reduce commensal flora and gut microbial diversity and select antibiotic-resistant genes for over 2 years.43 Thus, research into more effective and safer therapeutic options for SIBO are ongoing



Holistic Medicine should be the New Standard of Care

Glob Adv Health Med. 2014 May; 3(3): 16–24.

Published online 2014 May 1. doi:  10.7453/gahmj.2014.019

PMCID: PMC4030608

Herbal Therapy Is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth

Victor Chedid, MD, Sameer Dhalla, MD, John O. Clarke, MD, Bani Chander Roland, MD, Kerry B. Dunbar, MD, Joyce Koh, MD, Edmundo Justino, MD, Eric Tomakin, RN, and Gerard E. Mullin, MDpastedGraphic.png

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Patients with small intestine bacterial overgrowth (SIBO) have chronic intestinal and extraintestinal symptomatology which adversely affects their quality of life. Present treatment of SIBO is limited to oral antibiotics with variable success. A growing number of patients are interested in using complementary and alternative therapies for their gastrointestinal health. The objective was to determine the remission rate of SIBO using either the antibiotic rifaximin or herbals in a tertiary care referral gastroenterology practice.


One hundred and four patients who tested positive for newly diagnosed SIBO by lactulose breath testing (LBT) were offered either rifaximin 1200 mg daily vs herbal therapy for 4 weeks with repeat LBT post-treatment.


Three hundred ninety-six patients underwent LBT for suspected SIBO, of which 251 (63.4%) were positive 165 underwent treatment and 104 had a follow-up LBT. Of the 37 patients who received herbal therapy, 17 (46%) had a negative follow-up LBT compared to 23/67 (34%) of rifaximin users (P=.24). The odds ratio of having a negative LBT after taking herbal therapy as compared to rifaximin was 1.85 (CI=0.77-4.41, P=.17) once adjusted for age, gender, SIBO risk factors and IBS status. Fourteen of the 44 (31.8%) rifaximin non-responders were offered herbal rescue therapy, with 8 of the 14 (57.1%) having a negative LBT after completing the rescue herbal therapy, while 10 non-responders were offered triple antibiotics with 6 responding (60%, P=.89). Adverse effects were reported among the rifaximin treated arm including 1 case of anaphylaxis, 2 cases of hives, 2 cases of diarrhea and 1 case of Clostridium difficile. Only one case of diarrhea was reported in the herbal therapy arm, which did not reach statistical significance (P=.22).


SIBO is widely prevalent in a tertiary referral gastroenterology practice. Herbal therapies are at least as effective as rifaximin for resolution of SIBO by LBT. Herbals also appear to be as effective as triple antibiotic therapy for SIBO rescue therapy for rifaximin non-responders. Further, prospective studies are needed to validate these findings and explore additional alternative therapies in patients with refractory SIBO.

Key Words: Irritable bowel syndrome (IBS), rifaximin, Antibiotics, Small Intestine Bacterial Overgrowth (SIBO), Dysbiosis, Complementary and Alternative Medicine (CAM), Herbal Therapies



Which Herbs are best for SIBO




2) Probiotics for SIBO

Probiotics are helpful in managing and even eliminating SIBO, even more so than antibiotics like rifaximin. Probiotics help with gut disorders such as bacterial overgrowth by [R,R,R,R]:

• competing for nutrients with bad bacteria
• producing compounds that fight against bad bacteria
• preventing leaky gut
• reducing inflammation
• boosting the immune system

Combination of:
• B. bifidum
• B. lactis
• B. longum
• L. acidophilus
• L. rhamnosus
• S. thermophilus
Three of the six probiotic species, B. lactis, L. rhamnosus, and L. acidophilus, increased in the feces of the probiotic therapy group (P<0.001), whereas there was no change in fecal microbiota in the placebo group. SIBO disappeared in many individuals of the probiotic therapy group, but none in the placebo (24 vs. 0%, P<0.05). General gastrointestinal symptoms also improved more in the probiotic group

3) Herbal Antimicrobials for SIBO

Herbal antibiotics may be cheaper and have less side effects than drugs [R].

Herbal formulas FC Cidal and Dysbiocide, or Candibactin-AR and Candibactin-BR were more effective (46% vs 34% eradication rate at 4 weeks) than 1200 mg daily rifaximin [R].
The formulas contained extracts of well-studied antibacterial herbs such as thyme, wormwood, olive leaf, ginger, and oregano, in addition to other less-studied ones [R,R,R,R,R].

A combination of nine different herbs called Iberogast® has been studied for its treatment in gut disorders such as IBS. One trial (DB-RCT) found that Iberogast improved IBS symptoms compared to placebo [R]. It is believed to work by improving gut flow and killing bad bacteria [R].

A number of herbs exist that have known antimicrobial activity.4853 In the current study, we chose a combination of herbal preparations to provide broad-spectrum coverage against enteric coliforms.54,55 Oil of oregano (Origanum vulgare) is a well-documented botanical that directly kills or strongly inhibits the growth of intestinal microbes.56,57 Oil of oregano has other beneficial properties such as inducing apoptosis in human colon cancer caco2 cells.58 Berberine extracts and thymus vulgaris are also well known for their broad antibacterial activities.56,5961 Wormwood (Artemisia absinthium) has substantial antimicrobial and anti-inflammatory properties that may be important to the pathogenesis of SIBO and has been used to successfully induce remission of Crohn’s Disease.37,62 

There are other herbals used in our study that have noteworthy properties. Lemon balm offers anti-anxiety and antidepressant effects that may benefit patients with IBS, while coptis root has growth-inhibitory effects on human bacteria.63–65 Red thyme essential oil inhibits the growth of Escherichia coli O157: H7 and Staphylococcus aureus.66 Indian Barbarry root extract (Berberis aristata) contains berberine and has antimicrobial, anti-inflammatory, and antidiarrheal proper-ties.67 Equisetum arvense L. was shown to possesses a broad spectrum of a very strong antimicrobial activity against a variety of enteric microorganisms including Staphylococcus aureus (S aureus), Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella enteritidis and the fungi Aspergillus nigerand Candida albicans.68 Thymus vulgaris has potent antimicrobial and anti-inflammatory actions.69–72 Olea europaea inhibits the growth of a number of staphylococcal species including S aureus.73

4) Elemental Diets

An elemental diet is a liquid diet that consists of the individual nutritional parts of food such as:
• amino acids
• fats
• sugars
• vitamins
• minerals.
It’s given to patients with inflammatory bowel diseases because the nutrients don’t need to be digested and are absorbed easily.

Elemental diets starve bacteria because they are low in carbohydrates that the bacteria in the small intestine eat.
In IBS patients with SIBO, 15 days of an elemental diet resulted in normal breath tests for 80% of the patients [R].
5) Low FODMAPs, Specific Carbohydrate Diet, and GAPS Diets for SIBO

A diet called the low-FODMAP (Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet has shown to be treat symptoms of irritable bowel syndrome [R,R,R]. The diet limits carbohydrates that are poorly absorbed by humans but easily eaten by bacteria.

Given the link between SIBO and IBS, it is likely that the effectiveness of the low-FODMAP diet is due to its ability to starve bacteria.

Another diet called the Specific Carbohydrate Diet (SCD) restricts all carbohydrates besides glucose and fructose, as they do not need to be broken down to be digestive. The diet is based on the fact that many people with gut disorders don’t have the enzymes necessary to break down carbohydrates and therefore can only tolerate simple sugars.
The Gut and Psychology Syndrome (GAPS) diet is another diet that resembles the low FODMAP and SCD diets. It restricts complex carbohydrates like those found in grains, and starchy vegetables and potatoes. The GAPS diet incorporates lots of fermented foods and bone broth. Bone broth helps heal the gut due to its gelatin content and provides minerals that are often deficient in SIBO patients.

Note: Some people may respond negatively to bone broth as it contains certain carbohydrates that can feed bacteria in the small intestine, potentially making SIBO worse. If this is the case, it is recommended to eat meat broth instead, which contains less of these carbohydrates but still helps heal the gut with gelatin and minerals.

How to Prevent SIBO Relapse

A difficult aspect of treating SIBO is that it often comes back after treatment has stopped [R]. This is because there is usually an underlying disorder or disease causing it.

If there are other disorders, those should also be treated to prevent the overgrowth from coming back. Otherwise it may be necessary to continually treat SIBO.
In patients who tested negative for SIBO after taking rifaximin, 44% of them tested positive for it nine months later. Symptoms also returned during this time [R].
Prokinetic Drugs
Prokinetic drugs are drugs that stimulate gut movement (peristalsis). These include:
• Octreotide
• Low-dose naltrexone
• Tegaserod
• Low-dose erythromycin.
Tegaserod is a prokinetic drug that activates serotonin (5-HT) receptors in the gut, increasing gut movement [R].
Researchers tested tegaserod or low doses of the antibiotic erythromycin (also a prokinetic) in preventing SIBO from returning in 64 IBS patients. These patients had eliminated SIBO with antibiotics and were symptom-free.
The time until SIBO returned was 60 days in those who didn’t take a prokinetic. Erythromycin extended this time to 139 days and tegaserod extended it to 242 days [R].

Vagus Nerve Stimulation

Improving the function of the vagus nerve (vagal tone) may also help prevent SIBO from coming back. The vagus nerve plays a key role in digestion by causing the release of stomach acid and digestive enzymes [R].

The vagus nerve also plays a role in the wavelike movements of the bowels that pushes food along the gut (peristalsis). Peristalsis helps prevent the buildup of bacteria [R].
Stress Management
Stress is likely to play a role in SIBO [R].
A review of 15 randomized controlled trials showed that psychological therapies aimed at reducing stress improved IBS symptoms and quality of life in IBS patients [R].

User Experiences with Antibiotics, Supplements, and Diets
Discussion and HM Institute Consult

Although rifaximin is safe and effective, it is very expensive. A month’s supply retails for ~$1,300 and is not usually covered by commercial health plans in the U.S. [R].


Rifaximin refractory…..recurrence, bac tolerance… 2 years bad gut effects….

oregano also colon cancer etc


Holistic rout
Why SIBO or IBS Patients React Poorly to Probiotics
In many SIBO patients gut movement is slowed down. Normally, the movement of the gut sweeps bacteria and food down, preventing them from collecting in the small intestine. Decreased gut movement allows bacteria to grow in the small intestine [R].

In addition, giving more bacteria to someone that already has too much may make the issue the worse.
Many probiotic products also contain prebiotics, which can be fermented by the bacteria in the small intestine. This can worsen SIBO symptoms.

The effectiveness of SCD in treating SIBO is questionable. One study found that the low FODMAP diet, but not the SCD improved symptoms of IBS after three months. A potentially worrying results was that patients on the SCD saw their vitamin D drop by 42% and their folic acid levels drop by 67%.



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