Microbiology of the Gastro intestinal tract

The gastro intestinal tract (G I Tract) of humans and animals usually harbour a large number of micro organisms which can be saprophytic and pathogenic. A large number of these micro organisms are beneficial to the host, for example Lactobacillus aids in digestion. Certain microbes produce useful vitamins like Vitamin K and Folic acid while others provide resistance against GI infections by producing antimicrobial substances which prevent pathogens from infecting the intestine. The colonization pattern of intestinal flora differs among infants and adults.

Intestinal flora in the Newborn
In case of human beings, 80-90 percent newborn infants have almost sterile intestine but in 10-20 percent a few micro organisms are acquired during labour. In all cases intestinal flora starts establishing within 4-24 hrs of birth. In breast fed infants the microbial population mostly contains Lactobacillus bifidus, Enterococci, and Staphylococci.
In bottle fed infants L.acidophilus and enterococci are predominant.

Intestinal flora in Adults
With a change in diet to adult pattern the flora also changes as diet has a marked influence on the intestinal flora. Their population and pattern of distribution depends on the part of the GI tract where they settle. For instance the number of microbes in the stomach and upper regions of the small intestine is comparatively low (approximately 10,000/ml).The reason being the presence of HCL produced by the stomach and the rapid progression of food through this part of the intestine.

The bacterial population increases progressively beyond the duodenum till the colon with the terminal portion of the colon having the highest number.

Normal flora of the intestine
The normal intestinal flora includes
Obligative anaerobes like Clostridia
Facultative anaerobes like Escherichia coli
Facultative bacteria like Klebsiella pneumoniae, Streptococcus faecalis, Mycoplasma, and Pseudomonas
Yeasts like Candida albicans

Pathogenic flora of the intestine
Enteric pathogens which are of medical significance to man include pathogenic Escherichia coli, Genus Salmonella and Genus Shigella belonging to the family of Enterobacteriaceae, Vibrio cholerae and certain viruses.
The mode of transmission of enteric pathogens is ingestion of contaminated food and water

Escherichia coli
E.coli is a motile gram negative rod and a facultative aerobe. It is the dominant member of the normal flora of the intestine and usually non pathogenic. However four groups of E.coli are found to cause gastroenteritis and diarrhoeal disease particularly in infants and sometimes in older children and adults as well. They are named as enteropathogenic E.coli, enterotoxigenic E.coli , enteroinvasive E.coli , and enterohaemorrhagic E.coli based on their mode of action..


The genus Salmonella are motile gram negative rods which are pathogenic to man and lead to enteric fever(typhoid) gastroenteritis, septicaemia etc. The most important being S.typhi which causes typhoid fever. S.paratyphi causes less severe form of enteric fevers while other Salmonella cause gastroenteritis characterized by diarrhoea, nausea or vomiting.


Four species of the genus Shigella (S.dysentriae, S.fiexneri, S.boydii, S.solmei) cause bacterial dysentery in man. Shigella species produce an endotoxin which is responsible for the disease. They are short gram-negative non motile rods.

Vibrio are gram negative, curved or comma shaped rods which are actively motile. V.cholerae is the causative agent of Cholera which is an acute gastrointestinal tract infection and is usually transmitted through contaminated water. In it's most severe form, cholera is a dramatic and terrifying disease in which profuse watery diarrhoea and vomiting may lead to death in less than 24 hrs. In treated cases the disease takes 4 days to subside.

Enteric viruses
More than 60 species of viruses have been recovered from the intestinal tract of man. They comprise of mainly three groups:
• Polioviruses -the causative agent of Polio, which is a paralytic disease of children. However except for a few developing nations polio has been eradicated.

• Coxsackieviruses which produce a variety of clinical syndromes in man.

• ECHO(Enteric Cytopathogenig Human) viruses.

• Besides these, Hepatitis Virus also causes enteric infection (Hepatitis Type-A).

Isolation, Identification of pathogens causing enteric infections

1. Sample collection and Isolation of the pathogen
In order to identify the causative agents of an enteric infection, the first step is to isolate the pathogens from the other normal flora of the intestine. Stool samples are the best specimen for enteric infections. The stool specimen should be collected early in the course of an enteric disease (i.e. first 3 days) and should be immediately inoculated to the culture media or stored in a transport medium like Buffered Glycerol Saline while transportation.
Selective and differential media are used for isolation of the pathogens from the normal flora. For example Enteric bacteria can be differentiated into Lactose and non lactose fermenters by using a culture medium like Eosin Methylene Blue agar which contains Lactose. E.coli is a lactose fermenter and produces colonies with a green mettalic sheen while Salmonella and Shigella which are non lactose fermenters produce colourless colonies.

2.Further Identification

Once the preliminary identification is done, the isolated pathogen is subjected to a variety of Biochemical assays for further identification

3.Final identification and serotyping
Final identification of the pathogen is confirmed by serological typing using pathogen specific antiserum.

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