Gut microbiome

The gut microbiome is a complex community of trillions of microorganisms residing in the intestines.

99% of bacteria in the gut are anaerobes

Dysbiosis or an imbalance in this community is a common finding in CFS patients.

Viral infection
Viral infection can cause shifts in the gut microbiome.

In mice, the influenza virus leads to injury of both the lungs (the primary site of infection) and the intestinal tract, even when there is no evidence of viral replication in the gut, and causes decreases Lactobacillus and Lactococcus species and increases in Enterobacteriaceae

Pregnancy
Gut microbiota change dramatically from the first trimester to the third trimester of pregnancy. During the first trimester, there is an overrepresentation of 18 bacterial groups, mainly Faecalibacterium, a butyrate] producer that has been shown to improve symptoms of [[inflammatory bowel disease.

During the third trimester, populations of pro-inflammatory bacteria species such as proteobacteria and actinobacteria increase and there is a reduction in diversity. Populations of Faecalibacterium decrease. Overall bacterial load increases over the course of pregnancy.

Nervous system
The intestinal microbiota play a major role in the gut-brain axis with consequences for both neurological development and host behavior.

Stress
There is growing evidence that the microbiome plays an important role in the stress response. Animals raised in a germ-free environment show an exaggerated HPA response to psychological stress which normalizes when Bifidobacterium infantis is introduced. Escherichia coli can activate the HPA.

Stress also increases intestinal permeability.