Microbiota of the Stomach and Small Intestine

The human stomach maintains a highly acidic pH of 1 to 3, creating a hostile environment for most microbes.

Despite this, acid-tolerant species, such as Helicobacter pylori, can colonize the gastric mucosa, particularly in the antrum.

Although microbial density is low in the stomach, gastric fluids can still contain members of the Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota phyla.

As the stomach transitions into the duodenum, the environment becomes less acidic.

A low-biomass community, often enriched in members of the Bacillota, Pseudomonadota, and Actinomycetota, is present in the duodenum.

This microbiota is shaped by rapid flow from the stomach, the detergent effect of bile acids, and digestive enzymes in pancreatic secretions.

Microbial populations increase in the jejunum as the environment becomes more favorable for bacterial colonization.

In the ileum, the final part of the small intestine, the pH becomes slightly alkaline.

This region hosts facultative and obligate anaerobes, including genera such as Bacteroides and Clostridium, and members of the Enterobacteriaceae family.