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Understanding The Gut Bacteria Escherichia Coli (E-Coli): Testing, Diagnosing, and Treatments

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Understanding The Gut Bacteria Escherichia Coli (E-Coli): Testing, Diagnosing, and Treatments

Escherichia coli (E. coli) is a diverse group of bacteria found in humans' and animals' environments, food, and intestines. Although this group of bacteria is renowned for causing food poisoning and diarrheal diseases, most strains of E. coli are harmless and are commensal bacteria within the human microbiome. Read on to learn about the differences between the beneficial and pathogenic strains of E. coli.


What Is Escherichia coli?

Belonging to the Enterobacteriaceae phylum, E. coli is a Gram-negative facultative anaerobe, meaning that, unlike other types of probiotic bacteria, it can live in environments with or without oxygen. Humans become inoculated with E. coli by maternal transmission during birth, through exposure to the mother's fecal matter and subsequent handling. (1)

Many bacterial strains belong to the E. coli species, most of which are harmless and normal commensal inhabitants of the gastrointestinal tract. There are six pathogenic strains of E. coli that notoriously cause diarrhea, which include (2):

  • Shiga toxin-producing E. coli (STEC)/Enterohemorrhagic E. coli (EHEC): This is the bacteria most commonly known for E. coli food contamination and causing diarrhea. E coli O157 is the strain of STEC that most frequently causes diarrheal illness in North America by producing a toxin called Shiga, which damages the small intestine's lining.
  • Enterotoxigenic E. coli (ETEC): This strain is a common cause of travelers' diarrhea
  • Enteroaggregative E. coli (EAEC)
  • Enteroinvasive E. coli (EIEC)
  • Enteropathogenic E. coli (EPIC)
  • Diffusely adherent E. coli (DAEC)

What Is Escherichia coli's Role in the Gut Microbiome?

Beneficial strains of E. coli produce vitamins B12 and K, consume oligosaccharides and simple sugars, and ferment amino acids. E. coli consumes oxygen, maintaining a safe environment for the beneficial microbes of the gut microflora that are strictly anaerobic (bacteria that cannot grow when oxygen is present). (1, 3)

The presence of beneficial E. coli strains helps to prevent intestinal infections by competitively excluding pathogenic agents from binding to epithelial binding sites. E. coli Nissle 1917 (EcN) is one probiotic strain of E. coli shown to inhibit inflammatory pathways, protect the intestinal barrier, and alleviate gastrointestinal disorders, such as inflammatory bowel disease. (4, 5)

What Are the Health Consequences of Unbalanced Escherichia coli in the Gut Microbiome?

Some E. coli species are pathobionts, opportunistic microbes that can stimulate inflammatory immune responses and contribute to disease states. E. coli is a producer of hydrogen sulfide (H2S) and ethanol and, as such, is a promoter of intestinal permeability when present in large amounts. (3, 6)

Both commensal and pathogenic E. coli strains can produce biofilms, assemblies of microbial cells enclosed in bacterial-produced matrixes of polysaccharides and proteins. Biofilms are associated with increased infection chronicity and severity because they aid pathogen evasion of host immune defenses and resistance to antibiotic intervention. (7, 8)

Human studies have implicated E. coli in the development and severity of inflammatory bowel disease, especially Crohn's disease (9).

What Causes Low Levels of Escherichia coli?

A study on 250 vegetarian and vegan individuals concluded that fecal E. coli levels were lower in groups with lower stool pH, as seen in patients eating higher carbohydrate and fiber diets. (13)

The intake of prebiotics (FOS, GOS, inulin, and lactulose) and probiotics (fermented foods and dietary supplements) has been shown to beneficially modulate the gut microbiome composition so that it favors beneficial Lactobacillus and Bifidobacteria and reduces E. coli. (10, 11)

What Causes High Levels of Escherichia coli?

Dietary choices can promote the growth of E. coli within the intestines, as shown by studies that found higher fecal E. coli levels in patients eating more animal protein and gluten-free diets. (13, 14)

E. coli infection is caused by eating contaminated food, drinking contaminated water, or personal contact (fecal-oral transmission). The most common contaminated food sources of E. coli include ground beef, unpasteurized milk, and fresh produce. (2, 12)

Symptoms of Escherichia coli Infection

Ingestion of pathogenic E. coli strains, even in small amounts, causes infection, characterized by the following symptoms (2, 12):

  • Diarrhea, ranging in severity from mild to severe and bloody
  • Stomach pain and cramping
  • Nausea and vomiting
  • Loss of appetite
  • Fever
  • Fatigue

Hemolytic uremic syndrome (HUS) is a potential complication of STEC that develops on average seven days after the first symptoms of E. coli infection. HUS occurs when Shiga toxin enters the bloodstream, destroys red blood cells and platelets, and causes kidney damage. HUS can be life-threatening and develops in 5-10% of patients infected with STEC. Children five years and younger are at the highest risk of this health complication. Symptoms of HUS include (2):

  • Bloody diarrhea
  • Fever
  • Abdominal pain
  • Vomiting
  • Decreased urination, blood in the urine
  • Pale skin with easy bruising
  • Increased heart rate
  • Fatigue
  • Lightheadedness, confusion, seizures
  • Kidney failure

How to Test Escherichia coli Levels

Functional labs allow you to measure commensal E. coli of the gut microbiome and diagnose pathogenic E. coli infection.

Comprehensive Stool Test

Comprehensive stool tests use various technologies, such as stool culture and polymerase chain reaction (PCR), to identify the growth of beneficial E. coli. Genova Diagnostic's GI Effects Profile is an example of a comprehensive stool test frequently ordered by functional medicine providers. Genova offers an add-on enterohemorrhagic E. coli test to screen for pathogenic STEC infection as warranted by patient symptoms.

The GI-MAP test by Diagnostic Solutions is another popular comprehensive stool panel that extensively screens for the various pathogenic E. coli strains and Shiga toxin.

E. coli Shiga Toxins

Diagnosis of E. coli infection can be made by measuring the presence of Shiga toxin in stool. Generally, a positive Shiga toxin test is confirmed by follow-up fecal testing for E. coli O157.

How to Treat Escherichia coli Infection

Treatment of E. coli infection largely depends on bacterial strain and severity of illness. Symptomatic management is a mainstay of both conventional and functional medicine, with oral and/or IV rehydration and antidiarrheals, like bismuth subsalicylate or loperamide. Antibiotics are recommended for severe illness, but due to the increased risk of HUS, they are not indicated for patients with suspected or confirmed EHEC/STEC. (15)

Herbal antimicrobials can be an effective alternative to prescription antibiotics when indicated. Hydrastis canadensis or Berberis aquifolium are highly indicated as potent antimicrobials and intestinal tonics. One clinical trial showed that a single oral dose of 400 mg of berberine significantly reduced stool volume in patients with ETEC infections and that 42% of patients were asymptomatic (compared to only 20% of controls) within 24 hours.

Activated charcoal is an effective adsorber of E. coli toxins, reducing small intestinal damage and gastrointestinal symptoms caused by the infection.



E. coli is a bacteria found naturally in the human gastrointestinal tract. While many strains of E. coli benefit human health, an overgrowth can be associated with bowel inflammation, and infection with specific strains can cause severe diarrhea and health complications. Functional medicine testing can help analyze intestinal E. coli growth and diagnose E. coli infection. An integrative medicine approach to gut health can prevent and treat pathogenic E. coli infection and commensal E. coli overgrowth.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

1. Blount, Z. D. (2015). The unexhausted potential of E. coli. eLife, 4.

2. E. coli: What is It, How Does it Cause Infection, Symptoms & Causes. (2020, September 21). Cleveland Clinic.

3. Rey, F.E., Gonzalez, M.H., Cheng, J., et al. (2013). Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proceedings of the National Academy of Sciences of the United States of America, 110(33), 13582–13587.

4. Guo, S., Chen, S., Ma, J., et al. (2019). Escherichia coli Nissle 1917 Protects Intestinal Barrier Function by Inhibiting NF-κB-Mediated Activation of the MLCK-P-MLC Signaling Pathway. Mediators of Inflammation, 2019, 1–13.

5. Jia, K., Tong, X., Wang, R., et al. (2018). The clinical effects of probiotics for inflammatory bowel disease. Medicine, 97(51), e13792.

6. Miura, K., & Ohnishi, H. (2014). Role of gut microbiota and Toll-like receptors in nonalcoholic fatty liver disease. World Journal of Gastroenterology, 20(23), 7381.

7. Høiby, N., Ciofu, O., Johansen, H.K., et al. (2011). The clinical impact of bacterial biofilms. International Journal of Oral Science, 3(2), 55–65.

8. Rossi, E., Cimdins, A., Lüthje, P., et al. (2018). "It's a gut feeling" –Escherichia coli biofilm formation in the gastrointestinal tract environment. Critical Reviews in Microbiology, 44(1), 1–30.

9. Martinez-Medina, M., & Garcia-Gil, J. (2014). Escherichia coli in chronic inflammatory bowel diseases: An update on adherent invasive Escherichia coli pathogenicity. World Journal of Gastrointestinal Pathophysiology, 5(3), 213.

10. O'Callaghan, A., & Van Sinderen, D. (2016). Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Frontiers in Microbiology, 7.

11. Singh, R., Chang, H., Yan, D., et al. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15(1).

12. E. coli - Symptoms and causes. (2022, October 1). Mayo Clinic.

13. Zimmer, J.M., Lange, B., Frick, J., et al. (2012). A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European Journal of Clinical Nutrition, 66(1), 53–60.

14. Bonder, M.J., Tigchelaar, E.F., Cai, X., et al. (2016). The influence of a short-term gluten-free diet on the human gut microbiome. Genome Medicine, 8(1).

15. Mueller, M., Tainter, C.R. (2023). Escherichia Coli. StatPearls Publishing.

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