The science of
the small intestine
and causes of SIBO

FixSIBO OP Dr James Freeman profile photo

The science of the small intestine
and causes of SIBO

Medically reviewed by:
Dr James Freeman

The small intestine is about 20 feet long and folds many times to fit inside the abdomen. The small intestine consists of three parts; the duodenum, jejunum, and ileum.[1]

Small intestinal bacterial overgrowth (SIBO) is a condition that occurs when an excessive number of bacteria colonise the small intestine. A healthy small intestine is usually home to very few bacteria, about ten thousand per ml, and a person with SIBO has around one million bacteria per ml. The bacteria are often “supposed” to be in the digestive tract but in the large intestine, making stool testing ineffective for diagnosis. It can cause bloating, diarrhea, or constipation (sometimes both).

The large intestine contains most of a person’s gut microbiome; the small intestine was only designed to house a very small portion of bacteria. As a result, the small intestine cannot handle the number of bacteria present in SIBO.

Compared to healthy subjects, the small intestine of people with SIBO contains bacteria from the large intestine such as E.coli, Enterococcus, Klebsiella pneumonia, and Proteus mirabilis.[2]

When a person eats, these bacteria begin to ferment the food and consume nutrients which causes pain and stretching of the small intestine, and that can cause a host of symptoms.

A study on small intestine biopsies in patients with SIBO revealed thinning of the mucosa and crypts and increased inflammation.[3]

Causes of SIBO

• Low motility: Usually, the intestines push food and bacteria through the digestive tract, preventing too many bacteria from accumulating in the small intestine. However, if someone has low motility, this mechanism slows down, allowing food to ferment in the small intestine.[4] That can occur for a variety of reasons.

• Dysbiosis: Dysbiosis is when a person’s microbiome becomes imbalanced, containing too many harmful microbes or not enough beneficial species. The ratio of good to bad bacteria has become imbalanced. Research into how different microorganisms influence the gut is still growing. Still, studies suggest that people with IBS often have fewer beneficial species, less diversity, and higher amounts of methane-producing species in their microbiome, which can slow motility.[5]

• Low stomach acid (medically known as Hypochlorhydria): Hypochlorhydria refers to low levels of stomach acid, also known as hydrochloric acid. When there is insufficient stomach acid, bacteria can travel further down the digestive tract than usual, as a highly acidic environment is required to kill them. Researchers believe that people who take proton pump inhibitors (PPIs), have autoimmune gastritis, or have undergone gastrectomy have an increased risk of hypochlorhydria and SIBO.[6] However, there is a lack of conclusive evidence on this, and low motility is a more significant risk factor.

• Structural differences: Sometimes, SIBO occurs because a person has structural differences in the digestive tract. Examples include small bowel diverticulosis, fistulas, and a shortened colon. A study in 2018 found people who have had a colectomy are more at risk of developing SIBO for this reason.[7]

• Alcohol abuse: Excessive alcohol consumption can damage the microbiome, leading to a disruption in the balance of bacteria that can damage to the intestinal walls.[8] and result in inflammation.[9]

2 Sachdev and Pimentel, 2013
3 Dukowicz, Lacy and Levine, 2007
4 Sorathia and Rivas, 2020
5 Wei et al., 2021
6 Pimentel et al., 2020
7 Rao et al., 2018
8 Gabbard et al., 2013

Conditions that predispose toward the development of Small Intestine Bacterial Overgrowth

      • Food poisoning -even if it was a long time ago
      • Systemic diseases (celiac disease, cirrhosis, pancreatic exocrine insufficiency, non-alcoholic fatty liver disease)
      • Stress- both physical and mental can alter the way your bowel’s function
      • Chronic constipation – because you’re not clearing out your intestines as you should, leading to a backup of bacteria into the small intestine
      • Autoimmune disease -hypothyroidism/endomitosis
      • Surgery
      • PCOS
      • Endometriosis
      • History of eating disorders
      • Hypochlorhydria
      • Prilosec diabetes
      • Severely restrictive diets – this can affect the guts motility and stop the small intestine from moving things along, creating an opportunity for SIBO to develop
      • Achlorhydria (surgical, iatrogenic, autoimmune)
      • Scleroderma
      • Intestinal pseudo-obstruction
      • Diabetic enteropathy
      • Vagotomy
      • Fistulas between colon and small bowel
      • Resection of ileocecal valve
      • Surgical loops (Billroth II, entero-entero anastomosis, Rou-en-Y)
      • Duodenal or jejunal diverticula
      • Partial obstructions of the small bowel (stricture, adhesions, tumors)