L1 - Microbiome Flashcards by Rawan Alkhateeb

Microbiome

The ecological community that shares our body

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Microbiota

the microbes comprising the microbiome

(i. e., microflora)
- Bacteria
- Bacteriophages
- Viruses
- Fungi/yeasts

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Dysbiosis

alteration of the relative abundance of all or part of the microbiota

number one cause of dysbiosis → antibiotics

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Specialized plant carbohydrates that are thought to be growth substrates for the bacteria in the microbiome

Prebiotics

substances that induce the growth or activity of the bacteria in the microbiome (aka probiotics)

(plant-derived carbohydrates)

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What are the microorganisms called that are believed to have health benefits when consumed?

Probiotics

(bacterial cultures)

live cultures of organisms that can be found in yogurt

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These are the microbes that are permanent residents of a given non-sterile body site (i.e. normal flora, microflora)

Commensal

good microbes
does not cause disease

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a microbe that is capable of causing disease

Pathogen

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What kind of pathogen is a Pseudomonas?

Opportunistic pathogens

An organism that does not cause disease in healthy immunocompetent individuals but can cause disease in immunocompromised individuals

(can be normal flora)

Cause disease under certain circumstances
when relocated it can become a pathogen (ex: UTI)

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What do we call it when the microbiome is established early in life and modified by diet, environment, and infectious diseases?

Signature of Microbiome

developed by age 2

It will affect how:

much a person weighs

how they behave

their development

and health in many different physiological systems

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What’s the difference between Commensal vs Pathogens?

commensals –> recognized and tolerated by IS

virulent pathogens –> attacked by IS

The immune system is shaped by early life exposures to microbial life

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True or False

Early exposure, when babies are born, will shape their Immune response

True

gram (-) of bacteria plays an important role in activating immune response

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What are the Commensal Functions?

Play a role in activating IR
Necessary for basic development and regulation of IR
Bacteria produce key metabolites - (vitamins)
Bacteria produce amino acids (eg; tryptophan) that can affect levels of serotonin and other neurotransmitters
Bacteria have different “metabolic rates”

–> some are more or less efficient

–> can result in obesity

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Contain polysaccharide-digesting enzymes that are not present in the human genome
Dietary polysaccharides are degraded in the gut by bacteria
Colonize GI tract & inhibit growth and penetration of pathogens
Make vitamins
Tolerize the immune system

Commensals

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Name some diseases influenced by the Gut Microbiome

Obesity

Autoimmune disease

Allergy

ASD

Depression

Anxiety

GI disease

Heart disease

Infection

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Where does the microbiome come from?

Intrauterine exposure (the placenta microbiome)

Birth canal (no exposure by C-section)

Shaped by diet - Orally by breast milk

Skin to skin contact

Signature microbiome established by age 2

–> By age 2 >3,000 different taxonomic groups (bacteria)

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True or False

Babies born by C-section have normal microbiome exposure like vaginal birth babies

False

they have no exposure by C-section

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For every cell in your body there are how many bacterial cells?

1,000

10 to 100

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What does your microbiome consist of?

bacteria

eukaryotic cells

endogenous viruses

and bacteriophage

Your microbiome is not inert

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Overall genetic composition, only comes from you

70%

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The microbiome in the GI tract can be disturbed by:

That can result in diseases caused by:

Infection with aggressive rapid growing pathogens

(ex: cholera)

Antibiotic treatment

(kills good and bad bacteria)

Diet changes

–> Dysbiosis

–> Infection with dominant pathogen

What is Clostridium difficile (C Diff)?

Where does it come from?

disruption of normal healthy bacteria in the colon

–> small % of people have Normal flora

C diff can result from

–> antibiotics

C. difficile can also be transmitted from person to person by:

–> Gram + spore-forming bacillus

How can you get it?

Fecal-oral transmission through contaminated environment and hands of healthcare personnel

What can C diff cause?

How are risk factors?

Can cause:

Pseudomembranous colitis

(inflammation to the colon)

toxic megacolon
sepsis
death

Risk factors:

Antimicrobial exposure –> major risk factor for disease Can cause dysbiosis:

Suppression of normal flora of the colon

Acquisition and growth of C. difficile (takes over and grows)

What are the antibiotics that tend to result in dysbiosis that will allow for CDiff?

Clindamycin

Penicillins

Cephalosporins

→ antibiotics increase it not suppress it

Which one of the following is the most effective way to treat antibiotic-associated colitis?

Alternate antibiotics

Fecal transplant

Probiotics

Rehydration

Yogurt

Fecal transplant

What is the relation between obesity and the microbiome?

**Good bacteria** (poor converters) promotes **lean** - Bacteroidetes (Bacteroides) **Bad bacteria** (efficient converters) promotes **obese** - everything you eat gets converted into calories - Firmicutes (Lactobacillus, Bacillus, Mycoplasma, _Clostridium_, Streptococcus)

How does the microbiome affect the energy harvest?

Gut microbiota affects - **energy harvest/conversion** **Obese** --\> Gut microbiota is disturbed Transferred through fecal transplants - Effects of diet on the gut microbiome - Gut microbiota regulates host metabolic genes

Which one of the following microbes is likely to predominate in the microbiome from an obese person? Bacterium, good energy harvester Bacterium, poor energy harvester Pathogenic bacterium Yeast

**Bacterium, good energy harvester**

Bacterium, good energy harvester --\> Bacterium, poor energy harvester --\>

- the most efficient energy harvest from substrates by bacteria will lead to weight gain - will not process substrates to yield more calories (pathogens and yeast not linked to obesity)

What roles do microbes have in metabolism?

**Synthesize** essential amino acids and vitamins **Process** indigestible components (e.g. plant polysaccharides) Can **regulate** host metabolic genes

When the microbiota regulates host metabolic genes What is the result of the normal microbiota vs the dysbiosis (altered) microbiota?

Plant polysaccharides → **normal microbiota** → SCFA signal → bind to GPCR 41 and GPCR 43 → results in **energy balance** **Dysbiosis microbiome** → no signal = SCFA not produced → **insulin resistant** **obesity** **metabolic syndrome**

Normal Metabolic process vs Disrupted Metabolic process

**Fermentation →** Signal for protein G3PCR 41 and 43 for normal homeostasis and metabolic function **When it's disrupted →** you don't have homeostasis and that can lead to type 2 diabetes, obesity and metabolic syndrome

What is the “Leaky Gut” Syndrome?

--\> **Result of microbes in the GI tract affecting the integrity of the intestinal barrier in the epithelial cells in the intestinal tract, breaking them apart, loosening the tight junctions so compounds can escape GI tract** Damage to intestinal wall mediated by diet infection and drugs results in escape of: - toxins - microbes - undigested food Thought by some to because of a range of chronic diseases including: - diabetes - lupus - multiple sclerosis - migraines - autism

If dysbiosis, inflammation, and leaky gut can occur resulting in:

→ Toxins, organism, undigested food, medications, metabolites, can leak out IR produces potential widespread effects - can cross the blood-brain barrier and result in neurological effects: diabetes asthma lupus multiple sclerosis depression anxiety, autism

What is the relationship between Autism spectrum disorders and the GI

- ASD patients often have GI sypmtoms Certain bacteria are over-represented in ASD gut microbiome Clinical improvement has been reported in ASD patients who - Developed fever - Given antibiotics - Ingest probiotics

Normal flora is found in all but? Genitourinary Oral Cavity Optic Cavity Nares

**Optic Cavity**

True or False Fungi are not part of our microbiome.

**False** - Bacteria - Bacteriophages - Viruses - Fungi/yeasts Are all part of microbiome

To enhance the growth of the good bacteria in your gut microbiome, what would you eat? Yogurt Fiber Probiotic Pills Poopsicles

**Fiber** Remember: induced growth is by prebiotics

The main cause of dysbiosis is? Diet Change Prebiotics Probiotics Antibiotics

**Antibiotics**

Clostridium species would classify as what? Good bacteria - poor harvest Good bacteria - efficient harvester Bad bacteria - poor harvester Bad bacteria - efficient harvest

**Bad bacteria - efficient harvest**

What are some examples of Commensals?

E. Coli Pseudomonas --\> can cause UTI

How much gut bacteria can an individual have?

Over 1,000 species 160 species/individual \>99% of gut microbiome Makes up: 2-3 lbs of microbes in the human body

Name the good vs bad bacteria in body

_Harmful Bacteria_ Clostridia --\> production of entertoxins _Good Bacteria_ Lactobacillus Bifidobacterium Campylobacteriojejum

**Good** bacteria --\> (**poor** converters) --\> **lean** **Bad** bacteria (**efficient** converters) --\> **obese**

_Good bacteria/poor convertors_ will not break down everything and thus will **not** absorb all the glucose - Bacteroidetes Bacteroides _Bad bacteria/efficient converters_ break down and convert **everything** eaten resulting in obesity Firmicutes•Lactobacillus, Bacillus, Mycoplasma, Clostridium, Streptococcus

How can the Microbiome affect and result in ASD?

women who suffer from a high, prolonged fever during pregnancy are up to **seven times** more likely to have a child **with autism** **40 to 90 %** of all children **with autism** suffer from **gastrointestinal symptoms** - Dysbiosis has been noted in gut - Neuroinflammation

In Autism, we see an increase in we see a decrease in

**Clostridia** **Lactobacillus**

In Type 2 Diabetes, we see an increase in we see a decrease in

Clostridia Lactobacillus

In Alzheimer's, we see an increase in

**Clostridia**