The Microbiome in Health & Disease

Microbiome

genomes of microorganisms

biome = genes

Microbiota

live in and on human body

biota = creatures

Largest contributor of microbiome

Large intestine (colon)

Skin and oral cavity also have high []

pH influences composition in _________ more than other regions

duodenum

oxygen-tolerant of firmicutes and proteobacteria found? VS anerobic of firmicutes found?

small intestine

colon

High degree of interindividual variation. Colon microbiome influenced by (3)

Genetics, environmental components, especially diet

Do you want to have a more diverse microbiome? How do you get that?

YES

eat different types of foods

Microbiome seeded when

very early in life during birth, possible earlier.

Develops and changes over time

Critical 1000-day window to develop

diversity, especially in the first year of life, that influences risk of NCDs (e.g., allergy)

Children with nondiverse microbiome early on have more allergies

Do adults or children have less diverse microbiome

Children have a less diverse microbiome than adults; typically stabilizes at ~5 years of age

Vaginal VS c section delivery on microbiome

Children born through vaginal delivery > gut microbiome matches vagina

Children through c section > gut microbiome more similar to skin microbiome

Is there an initial difference in microbiomes due to delivery method? does this change over time?

Yes

Yes- over time microboimes become more similar to each other (effect is detectable in infants)

Other factor on microbiome of infants

Feeding

bottle vs breast fead

Formula feeding > more diverse microbiome (compared to breast feeding) due to higher sugars

For how long can you detect these infant microbiome differences

4-5 months later: mode of delivery and how they were fed differences still detectable

Why is microbiota in our gut

Gut microbiome like internal skin to protect from pathogens > help avoid food poisoning for example

Non-redundant gene

humans can not make themselves

for example: one that codes for prokaryotic subunits

Which do we have more of gut microbiota or genes

Genes greatly outnumbered by gut microbiota

Vitamin B12 is synthesized exclusively by (2)

archaea and bacteria

What’s special about vitamin B12

We get a lot of it from bacteria (i.e. from animals with bacteria or from bacteria themselves) – it is too complex for us to make ourselves we must consume it

Most common metabolites produced by bacteria

acetate

butyrate

propionate

Dysbiosis

dysfunction in the microbiome - implicated in several chronic diseases

Inflammatory bowel disease

altered microbiome composition and dysbiosis relative to healthy individuals

Reduces gut bacteria diversity and reduces in pathways associated with SCFAs and vitamin synthesis

In IBD more __________, less (2) compared to healthy

more Shigella species

less Eubacterium rectale and Faecalibacterium prausnitzii

Crohn’s VS Ulcerative colitis

Crohn’s – whole intestine inflamed

Ulcerative colitis – parts intestine inflamed (more similar to healthy gut)

Hprt4-18 looks like what which causes…

insulin > trigger immune response > T1DM (more likely)

3 major “gut healthy” food types

• Plant-based foods for intake of fibre, vitamins and minerals, and polyphenols

• Limiting consumption of ultra-processed foods and foods with high (added) sugars, saturated fat, salt

• Unsaturated fatty acids and ω-3 PUFAs over saturated fat

Following Canada’s Food Guide tends to promote microbiome diversity

Probiotics vs prebiotics

Probiotic – living organism you consume, taken with target in mind (lactose intolerant take to help digest lactose)

Prebiotic – no specific target in mind, increase general abundance and diversity of microbiota

Probiotics: transient VS targeted

Transient: do not colonize the gut over the long-term

Targeted: selected for specific functions (e.g., metabolites, conditions, etc.)

Prebiotic usually

indigestible material (fibre) that is converted into SCFAs (fuel) by commensal bacteria in the colon

Do probiotics work for GI diseases

in general yes

NOT for traveler’s diarrhea or necrotizing enterocolitis

Do “gut healthy” foods work for chronic diseases?

Evidence gut healthy food is supportive or supplemental intervention (doesn’t cure it) (ie less red meat)

Can probiotics prevent UTIs, vaginal infections, resp infections? Antibiotic use?

Generally no