Infectious gastroenteritis

Children, teenagers, adults... almost everyone has had gastroenteritis at least once in their life. Although the disease is the world’s second most common cause of death,1 there is no cause for concern, since infectious gastroenteritis can be avoided through hygiene measures and treatment is steadily improving.2 Moreover, restoring the gut microbiota can limit the severity and duration of symptoms.3

Created 03 August 2021
Updated 31 March 2022

About this article

Created 03 August 2021
Updated 31 March 2022

What is infectious gastroenteritis? What link does it have with the gut microbiota?

A diarrheal disease, gastroenteritis frequently involves severe symptoms which disappear rapidly in most cases.4 Patients display an imbalance of the gut microbiota,which may persist after the resolution of the infection, and which has been associated with an increased risk of developing chronic disorders.6

Did you know?

The word “gastroenteritis” comes from the Greek words gastron, meaning “stomach”, and enteron, meaning “small intestine”, in other words, an inflammation of the stomach and small intestine.7

Generally benign in Western countries, infectious gastroenteritis is a leading cause of death in the developing world, particularly among children under 5 years of age.4 It accounts for 10% of all child deaths in developing countries, where it represents a major public health concern.1 The high mortality rates in developing countries8 are often9 linked to the severe dehydration that it causes. The disease is caused by the ingestion of (sidenote: Pathogen A pathogen is a microorganism that causes, or may cause, disease. Pirofski LA, Casadevall A. Q and A: What is a pathogen? A question that begs the point. BMC Biol. 2012 Jan 31;10:6. ) microorganisms, most frequently viruses, in which case it is known as viral gastroenteritis.

Rotavirus is one of the main causes of viral gastroenteritis worldwide and of fatal diarrhea in children in developing countries, despite the availability of a vaccine.10 Other viruses, such as norovirus or adenovirus, may also be to blame.4 Moreover, gastroenteritis can also be caused by bacteria (bacterial gastroenteritis) or parasites, particularly during travel.7 However, the pathogen involved is rarely identified.11

Contamination occurs via contaminated food or water, or directly through physical contact aggravated by poor hygiene.6 Although data on the association between the gut microbiota and gastroenteritis are still very limited, patients display a gut imbalance ( (sidenote: Dysbiosis Generally defined as an alteration in the composition and function of the microbiota caused by a combination of environmental and individual-specific factors. Levy M, Kolodziejczyk AA, Thaiss CA, et al. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219-232.   ) ) during infection, regardless of the cause.5,12,13 Studies show that children with severe or complicated viral gastroenteritis, and particularly those infected with rotavirus, display a lower gut microbiota diversity than healthy children.14 Lastly, other studies suggest that changes in the gut microbiota may persist over the long term and could have adverse effects on health, such as contributing to the development of irritable bowel syndrome.15 However, current data on the gut microbiota’s contribution to the development, complications and outcome of the disease require further investigation.

Symptoms at times severe but not long-lasting

In addition to diarrhea (defined as three or more loose or watery stools in one day)6, symptoms may include nausea, vomiting, abdominal cramps, fever or anorexia.16 Symptoms of viral gastroenteritis typically last less than a week and usually improve within 1-3 days.4 Special attention should be paid to children, the elderly and immunocompromised individuals, who are at greater risk of dehydration.4 In some cases, the doctor may order additional tests (stool analysis, blood tests, etc.) to rule out other conditions.4

Antibiotics often ineffective or even counterproductive 

Regardless of the cause of infectious gastroenteritis, the treatment is symptomatic.4 For diarrhea, rehydration is the main treatment.6 Antibiotic treatment is not essential and is only justified where a bacterial cause has been established for the diarrhea.11 With viral gastroenteritis, antibiotics may even be counterproductive.11 On the other hand, probiotics, which aim to restore the gut microbiota, may limit the severity and duration of symptoms.7,17

This article is based on scientifically approved sources but is not a substitute for medical advice. If you or your child display symptoms, please consult your family doctor or pediatrician.

BMI 21.19

1 Rivera-Dominguez G, Ward R. Pediatric Gastroenteritis. 2021 Apr 9. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan–. 

2 World Health Organization. 2017. Diarrhoeal disease. World Health Organization, Geneva, Switzerland. 

3 Allen SJ, Martinez EG, Gregorio GV, et al. Probiotics for treating acute infectious diarrhoea. Cochrane Database Syst Rev. 2010 Nov 10;2010(11):CD003048. 

4 Stuempfig ND, Seroy J, Labat-Butler JR. Viral Gastroenteritis (Nursing). 2020 Nov 19. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan–. 

5 Castaño-Rodríguez N, Underwood AP, Merif J, et al. Gut Microbiome Analysis Identifies Potential Etiological Factors in Acute Gastroenteritis. Infect Immun. 2018 Jun 21;86(7):e00060-18. 

6 Kamdar K, Khakpour S, Chen J, et al. Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease. Cell Host Microbe. 2016 Jan 13;19(1):21-31. 

7 Sattar SBA, Singh S. Bacterial Gastroenteritis. 2020 Aug 11. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan–.

8 O'Ryan G M, Ashkenazi-Hoffnung L, O'Ryan-Soriano MA, et al. Management of acute infectious diarrhea for children living in resource-limited settings. Expert Rev Anti Infect Ther. 2014 May;12(5):621-32.

9 Pieścik-Lech M, Shamir R, Guarino A, et al. Review article: the management of acute gastroenteritis in children. Aliment Pharmacol Ther. 2013 Feb;37(3):289-303. 

10 World Health Organization. Immunization, Vaccines and Biologicals - Rotavirus 

11 Kim YJ, Park KH, Park DA, et al. Guideline for the Antibiotic Use in Acute Gastroenteritis. Infect Chemother. 2019 Jun;51(2):217-243. 

12 Taco-Masias AA, Fernandez-Aristi AR, Cornejo-Tapia A, et al. Gut microbiota in hospitalized children with acute infective gastroenteritis caused by virus or bacteria in a regional Peruvian hospital. PeerJ. 2020 Nov 3;8:e9964. 

13 Mathew S, Smatti MK, Al Ansari K, et al. Mixed Viral-Bacterial Infections and Their Effects on Gut Microbiota and Clinical Illnesses in Children. Sci Rep. 2019 Jan 29;9(1):865.

14 Chen SY, Tsai CN, Lee YS, et al. Intestinal microbiome in children with severe and complicated acute viral gastroenteritis. Sci Rep. 2017 Apr 11;7:46130. 

15 Beatty JK, Bhargava A, Buret AG. Post-infectious irritable bowel syndrome: mechanistic insights into chronic disturbances following enteric infection. World J Gastroenterol. 2014 Apr 14;20(14):3976-85. 

16 Dalby-Payne JR, Elliott EJ. Gastroenteritis in children. BMJ Clin Evid. 2011 Jul 26;2011:0314.

17 Dinleyici EC, Eren M, Ozen M, et al. Effectiveness and safety of Saccharomyces boulardii for acute infectious diarrhea. Expert Opin Biol Ther. 2012 Apr;12(4):395-410.


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