08.1 GI Microbiota and Infections

The entire collection of genes and interactions within the digestive tract's microbial community, including bacteria, viruses, and fungi.

The living microorganisms residing in a specific environment, like the gut. It's primarily made up of bacteria from the Firmicutes and Bacteroidetes phyla.

Beneficial microorganisms that co-exist peacefully with the host and provide advantages like nutrient synthesis and immune regulation. They don't cause harm.

An imbalance in the gut microbiome characterized by reduced diversity, altered species composition, and disruption of normal gut functions.

A condition involving inflammation of the digestive tract, often related to dysbiosis and immune system dysfunction.

The transfer of fecal matter from a healthy donor to a recipient with dysbiosis.

Pathogens are infectious agents that cause diseases like diarrhea or gastroenteritis.

The study of the interactions between the gut microbiota and the host's health, including how the microbiome affects immunity, metabolism, and disease processes.

The use of antibiotics can disrupt the gut microbiome, potentially leading to dysbiosis and increased susceptibility to infections.

Short-chain fatty acids (SCFAs) are produced by the gut bacteria when they break down dietary fiber. They play a vital role in gut health by nourishing colon cells, regulating immune responses, and maintaining the gut barrier.

These are molecules on the surface of pathogens that trigger an immune response. When the gut microbiome is imbalanced (dysbiosis), these molecules contribute to inflammation and gut problems.

This is a condition where the lining of the gut becomes leaky, allowing harmful substances to pass through. It may be caused by imbalances in the gut microbiome, infections, or inflammation.

This is a scientific study of a particular case, often used to illustrate a medical condition or treatment strategy. In the example given, it shows how a Salmonella infection can disrupt the gut.

This refers to techniques used to identify and characterize the specific pathogen causing an infection. It includes methods like stool cultures, PCR, and microscopy.

This refers to the initial steps in treating an infection, primarily aimed at restoring hydration and electrolyte balance lost due to diarrhea or vomiting.

This is a condition that can develop after antibiotic use, disrupting the balance of good bacteria in the gut. It can lead to various symptoms, including diarrhea and other digestive issues.

This is a treatment that involves transferring healthy gut bacteria from a donor to a patient with a severely disturbed microbiome. It is particularly effective in recurring C. difficile infections.

Butyrate is a type of short-chain fatty acid (SCFA) essential for a healthy gut. It helps strengthen the gut barrier, preventing leaky gut.

Pathogens, like Shigella, invade the lining of the colon, forming sores and producing toxins that damage cells. This invasion leads to inflammation and can cause severe diarrhea.

E.coli strains produce toxins that trigger the release of excess chloride ions. This leads to watery diarrhea as the body tries to expel the excess fluid.

Viruses like Norovirus and Rotavirus damage the brush border, the absorptive surface of the intestines. This disruption leads to malabsorption of nutrients and diarrhea due to fluid loss.

Giardia, a protozoan, lives in two stages: a cyst and a trophozoite. When ingested, these cysts hatch and damage the small intestine, causing malabsorption and diarrhea.

Antibiotics like Metronidazole and Vancomycin are used for severe C.difficile infections. They target different mechanisms, but both aim to kill the bacteria.

Broad-spectrum antibiotics eliminate a wide range of bacteria, including good bacteria. This can lead to dysbiosis and opportunistic infections like C.difficile.

Infectious colitis often resolves spontaneously or with treatment. It's caused by pathogens like bacteria or viruses. In comparison, IBD is a chronic condition that requires ongoing management with immunosuppressants.

Viral gastroenteritis, like Norovirus, tends to have a shorter duration (1-3 days) compared to bacterial infections, such as Campylobacter, which can last up to a week and may cause bloody diarrhea.

A stool culture helps identify specific bacterial pathogens like Salmonella or Shigella. This test helps confirm the presence of specific bacteria.

PCR testing is used to detect viral RNA (like Norovirus) or bacterial DNA markers for pathogens like E.coli. It helps determine the type of infection.

Microscopy for Parasites is used to identify protozoa like Giardia or Entamoeba in stool samples. It helps detect parasitic infections that can cause gastrointestinal problems.

Endoscopy with Biopsy is done for persistent infections or unclear diagnoses. It helps differentiate infectious causes from non-infectious conditions like IBD (inflammatory bowel disease).

Proper hydration and electrolyte management are essential for treating GI infections. Antibiotic therapy is used selectively, and FMT (fecal microbiota transplantation) shows promise for dysbiosis-related conditions.

A diverse diet rich in fiber and probiotics supports a healthy gut microbiome. Conversely, high sugar, red meat, and processed foods reduce diversity and increase disease risk.