Session 1: Microbiota

Microbiota

Community of microorganisms that live in a specific environment (living in and on our bodies)

Microorganisms can commonly be found in what anatomical locations of a human body?

Skin

Gut

Mouth

Lungs

The normal flora or microbiota are microorganisms that are regularly found at anatomical sites in humans and do not cause ___

Infection or disease

What is the microbiome?

Collective genomes of the micro-organisms in a particular environment (collection of all their genetic maternal - RNA/DNA)

What four important beneficial roles does the human microbiota have on health?

1) Digestion

Digesting carbohydrates

Producing vitamins/enzymes needed for digestion

2) Immunity

Microorganisms in gut help regulate immune function and protect against harmful pathogens

3) Mental health

Gut-brain axis = gut microbiota linked to anxiety and depression

4) Weight management

Some gut bacteria help prevent obesity via breaking down dietary fat and increasing energy expenditure

Name the four dominant phyla in the human gut (microbiota)?

FBAP = Firm Bacteria Active Protest

1) Firmicutes

2) Bacteroidetes

3) Actinobacteria

4) Proteobacteria

Most microbiota bacteria belong to which genera?

Fusobacterium

Eubacterium

Two main ways in which microbiota are acquired?

1) Vertical transmission from mother

2) Horizontal transmission from sources OTHER than parents e.g., diet/environment

In vertical transmission of microbiota to baby, what are the two main sources of microbiota for the baby?

1) Mother's vaginal bacteria

Onset of labor leads to rupturing of membranes

GBS bacteria travels up the vagina to amniotic fluid

GBS bacteria can also transfer as baby moves down birth canal during labour.

Aspiration of GBS bacteria into baby's lungs

2) Mother's gut bacteria

Baby exposed to GBS bacteria from contact with maternal fecal matter during birth process.

Would having a C-section rather than a vaginal delivery impact the microbiota of the baby?

Yes

As certain vaginal and gut bacteria from the mother are transferred to the baby via vertical transmission. This occurs during vaginal delivery.

Early-Onset GBS Disease

A common bacterium found in the vagina and rectum of healthy women.

However, an infant infected with this bacteria can develop sepsis, pneumonia, or meningitis in a condition known as...

What type of bacteria is GBS?

Gram positive

Beta-hemolytic bacterium

GBS is a common colonizer of the human ___ and ___ tracts

GBS is a common colonizer of the human gastrointestinal and genitourinary tract

GBS can cause severe disease in what demographics of people?

Young infants

Pregnant women

Older adults

Immunocompromised/immunosuppressed adults

What bacteria is this image showing?

Group B Streptococcus (GBS)

or Streptococcus agalactiae

What is beta hemolysis?

Complete lysis of red blood cells.

Some bacteria produce hemolysin enzymes which break down hemoglobin in RBCs leading to lysis of RBCs.

E.g., GBS is a beta-hemolytic bacteria

Why is beta hemolysis important in microbiology?

Diagnostic tool

Beta hemolytic bacteria (e.g., GBS) will produce clearing on blood agar mediums around the bacterial colonies on samples in the lab. This is due to production of hemolysin enzymes which break down the hemoglobin in RBCs leading to lysis (clearing).

Beta hemolysis is the strongest

Alpha hemolysis is weaker

Gamma hemolysis is weakest

What condition can GBS lead to in minority of newborns?

Early-onset GBS disease

Leading to early-onset sepsis, pneumonia or meningitis

Risk factors for early-onset GBS disease

Obstetric

- Preterm delivery

- Prolonged rupture of membranes

- Infection of placental tissues/amniotic fluid

Maternal

- GBS in mother's urine

- Previous infant with GBS disease

- Low maternal levels of anti-GBS antibodies

Demographic

- African american

- Young maternal age

One of the major factors involved in horizontal transmission of microbiota is...

Diet

What types of microorganisms found in gut microbiome?

1) Symbiotic organisms

2) Opportunistic pathogens

3) Commensal organisms

The microbiota plays a major role in...

1) Digesting food

2) Absorbing/synthesizing some nutrients

3) Delivering variety of growth-promoting and growth-inhibiting factors that influence health

Babies that are breast-fed can have different microbiota than babies that are bottle-fed.

True or false?

True

What is a biofilm

Small community of microbes (microbial community) enclosed by extracellular material such as mineral crystals, blood and other substances.

Where do biofilms typically form?

1) Medical devices

2) Surfaces

What do biofilms secrete?

Biofilms secrete slimy substance called extracellular polymeric substance (EPS)

This acts like a glue which allows them to irreversibly attach to a surface.

Why are biofilms important in infectious disease?

Bacteria in biofilms are often protected from antibiotics

Bacteria within biofilms have increased resistance to antimicrobial drugs (antibiotic resistance)

Biofilms encompass over ___% of microbial infections

>80%

Where are biofilms found in body?

- Dental plaques

- Gastrointestinal tract

- Airways (CF)

- Medical implants e.g., on pacemaker in heart

What is dysbiosis?

Disturbance to microbiota homeostasis

Causes of dysbiosis

Imbalance in flora

Change in functional composition of flora

Change in metabolic activities of flora

Change in local distribution of flora

Dysbiosis leads to three harmful effects. What are they?

1) Loss of beneficial organisms

2) Excess growth of potentially harmful organisms

3) Loss of overall microbial diversity

Dysbiosis has been linked to some diseases...

Give some examples of these diseases

- IBD

- Obesity

- Allergy disorders

- Type 1 diabetes

- Autism

- Colorectal cancer

What is the effect of the microbiota on adiposity?

The microbiota can influence weight, diet, cravings and metabolism.

Microbiota can help prevent obesity via...

1) Breaking down dietary fat

2) Increasing energy expenditure

Healthy mice with microbiota transplant from obese mice have ___ adiposity

Increased

List three types of symbiotic interventions

1) Probiotics

2) Fecal transplantation

3) Environmental change

Describe probiotics and prebiotics and how they are useful symbiotic interventions

Probiotics are live microorganisms that intend to have health benefits when consumed.

Prebiotics are nondigestible food components which selectively stimulate activity or growth of certain desirable microorganisms.

Synbiotics are products that combine both probiotics and prebiotics.

Pros and cons of probiotic and prebiotic symbiotic interventions

PROS

- Oral application

- Restoration of good bacteria and gut barrier

CONS

- Oral dose that reaches gut varies

- Potential loss of adaptation of culture-derived probiotics in the gut

Describe fecal transplants and how they are useful symbiotic interventions

Fecal microbiota transplants (FMT) or bacteriotherapy is the transfer of stool from healthy donors into the gastrointestinal tract of a patient for the purpose of treating.

Pros and cons of fecal microbiota transplants (FMT) symbiotic interventions

PROS

- Safe application

- Simple procedure

- 90% success rate to treat Clostridium difficile

CONS

- Variable impact

- Not very effective in IBD

- Quality of donor stool is important in efficacy of treatment

Success rate of 90% for fecal microbiota transplants (FMT) in what infection?

Clostridium difficile

Describe environmental change as a symbiotic intervention

This is an extreme symbiotic intervention.

Changing the environment microbial status can either promote disease or confer protection.

Pros and cons of environmental change as a symbiotic intervention

PROS

- Early-life exposure to microbes is important for improving later life immunity

CONS

- Not qualitative/quantitative

- Mechanisms of effect unknown

Antibiotics alter the population structure of the ___

Microbiome

While the overall structure of the gut microbiome is recovered after some time (when using antibiotics), the genomic structure of the microbiome is...

Not fully recovered

In the picture of a Clostridium difficile cells here, imaged under phase contrast microscopy, what is the bright feature highlighted with the arrow?

A spore

3 multiple choice options

Upon studying bacteria under the light microscope, you will observe that cells will be arranged in a particular way. This can be useful in identification. Which genus of bacteria will be arranged in a cluster, which could be describe as a bunch of grapes?

Staphylococcus

3 multiple choice options

If you observe a chain of coccus shaped bacteria under the light microscope, which Genera would you be looking at?

Streptococcus

3 multiple choice options