BIOSCI 108: Lecture 9 - A Real Gutsful: Intestinal Microbiota & Human Health

Microbiota

The members of the microbial community inhabiting a specific environment or space.

Microbiome

The collective genomic content of a micriobiota, all the genes of all the organisms present.

Typically, it starts low and matures by 3-4 years old with around 400-1000 bacterial "species" in the gut.

Our microbiomes can also different greatly amongst each other. It is affected by antiobiotics, diet, age, pets, occupation, hygiene, birth mode, and many more.

Microbiome Function

It has roles in our nutrition,

• "Non-digestible" foods (large proteins, fibre, etc) require microbial activity to be broken down
  immune system development,
• Gut bacteria help to fill in all the available ecological niches, making it so that harmful bacteria have no space to invade.
  as well as protection.
• Microbes help prime the developing immune system to recognise and later respond to bacteria invasions

Microbiome Distribution

It is found all throughout our body but most of it is in our bowels.

The distribution differs from parts to parts. In the bowel, it differs accross the gut due to the different conditions (pH, oxygen, nutrition, etc) present.

The main phyla in the human gut are Firmicutes and Bateroidetes.
The main archaeon is Methanobrevibacter/

Studying the Microbiome

Typically, we'd use faecal samples as a proxy for the microbial community in our intenstines.

This way is a cheap and non-invasive way to study our microbiome.

Dysbiosis

A condition in which the normal microbial community structure is disturbed. This is often through external pressures such as disease states or medications.

Dysbiosis is also associated with many other diseases however it's sometimes unclear whether dybiosis causes the disease of the other way around.

ASD & Microbiome

Autism Spectrum Disorder is a complex neurodevelopmental disorder. Gut problems commonly occur with people with ASD.

Some studeis have suggested that people with and without ASD have different gut microbiomes.

In mouse models, the addition of a probiotic bacterium (Bateroides fragilis) to pregnant mice led to lessening ASD-like symptoms in offspring.

• Pregnant mice were given three samples, a control, a virus, and a virus + probiotic. The were no significant differences between the control and the virus + probiotic, suggesting that the microbiome has a role in ASD.

IBD & Micrbiome

Inflammatory Bowel Disease, refers to the many disorders that involve chronic inflammation of the digestive tract. It is most prevalent in developed countries, suggesting a linkage to diet or lifestyle.

Clinical and experimental data suggests that microbial dysbiosis may play a major role in IBD pathogenesis (development & progression).

There is also evidence of differences in microbial and metabolites between IBD and healthy controls. IBD patients showed decreased taxonic diversity relative to healthy controls (common to see in many diseases)

Modifying our Microbiome:
Diet

Nutrient inputs, the diets we have, are an easy way to alter gult microbiota.

There was a study that compared the beta-diversity between individuals with a plant-based and animal-based diet. They found that the animal-based diet was associated with higher beta-diversity as well as seeing more prevalence of bacterial genus Biolphila in them.

Prebiotics are food ingredients that confer specific changes in the microbiomes, typically beneficial effects. Probiotic are living microbes thought to confer a benefit to the host.

Modifying our Microbiome:
FMT

When entire microbial communities are trasnferred between indivduals with a faecal matter transplant, either through a colonscopy or oral capsule. It is a way to restore dysbiotic microbiota and is suggested for many conditions.

The most compelling evidence for it is with Clostridiodes difficile infection (CDI. CDI is an opportunistic bacteria that infects when competing bacteria are removed by antiobiotics. It releases toxins that causes bloaitng, diarrhoea, severe colon inflamation, and death.

However, FMT is extremely successful (~90%) in treatment of recurrent CDI.

Modifying our Microbiome:
Phage Therapy

Targetting a specific, undesired member/s of the micrbiota. But this is typically not in widespread use yet as there are risks of unintentionalyl affecting beneficial bacteria, overthrowing the balance of the microbiome.