MI01: Microbes and the Microbiome

What are the major catergories of prokaryotic and eukaryotic microbes?

Prokaryotes: bacteria and archaea

Eukaryotes: protists, fungi, and helminths

Compare and contrast prokaryotes and eukaryotes.

• Prokaryotes are unicellular organisms and do not have membrane bound organelles.

• Eukaryotes are unicellular/multicellular organisms that have membrane bound nucleus (also other organelles)

What are the three categories of acellular infectious agents.

Viruses, viroids, and prions

What is a pathogen?

A microbe capable of causing host damage.

What are intracellular pathogens?

Pathogens that must enter cells to cause damage inside.

What are extracellular pathogens?

Pathogens that cause damage while outside of our cells

What can disease result from?

Direct microbial action, host immune response, or both.

Define proper immune response.

Immune response that clears a pathogen in a timely manner with limited collateral damage.

Define weak/insufficient immune response.

Immune response that allows the pathogen to damage the host (results in disease)

Define excessive immune response.

A immune response that is too strong, long, or unnecessary will be damaging and cause disease.

What is the iceberg concept of disease?

…

What is subclinical infection?

When pathogens breach barrier defenses and immune system eliminates them before they cause disease.

What is a capsule?

Outer surface of the bacteria on the cell surface (some are made of polysaccharide)

What are characteristics of eubacteria?

• Binary fission

• Cell wall made of cross-linked peptidoglycan

• Various shapes (cocci/bacilli) and arrangements (chains and packets)

What is the role of a capsule?

• Protect from toxin and desiccation (drying out)

• Attachment to host cells

• Increase virulence

• Protect from engulfment via phagocytic cells

What is a flagella?

Organ used for movement via chemotaxis

What are fimbriae and pili?

Fimbriae: Hair-like appendages involved in attachment to surfaces and host cells. (shorter and more than pilli)

Pilli: Involved in bacterial conjugation

What is peptidoglycan?

A polymerized network mesh that holds the cell together and is found in almost all bacteria that is recognized by the innate immune system.

Compare and contrast the peptidoglycan layer in gram neg and pos cells.

(-) = thin

(+) = thick

What colors do gram pos and neg stain?

Pos: purple

Neg: pink/red

What is gram stain used for?

To examine cell wall composition and used to view cell morphology

What is lipopolysaccharide (LPS, endotoxin)? What are some triggers?

It’s a powerful activator of the immune system that is activated via release of lipid A core during lysis. Triggers fever, diarrhea, and septic shock/organ failure/death.

What is the difference between cytoplasm and cytosol?

Cytosol: contents within the cell membrane

Cytoplasm: fluid and all cellular contents

How are endospores formed?

Formed by gram pos that allows survival in harsh conditions like starvation, extreme temp, exposure to drying, UV light, chemicals, enzymes, and radiation.

Why is it hard to disinfect bacterial spores (like endospores)?

They are resistant to disinfection (drying, UV light, and autoclaving)

What do endospore cores consist of?

• Nucleoid, ribosomes, and cytoplasm (very dehydrated).

• They are wrapped by inner membrane, outer membrane and spore coat which protect from environmental stress.

What is found in the cell wall of fungi?

Chitin

What are helminths?

Multicellular and extracellular worm-like parasites (infects 2 billion people worldwide) including flukes, tapeworms, and roundworms. Hard to get eliminated by immune system.

What are protozoa?

Single celled and motile eukaryotic parasites which can cause deadly human diseases like malaria.

What are some characteristics of prions?

• Misfolded proteins that induce misfolding which lead to cell death.

• Resistant to proteases and disinfection (heat, ionizing radiation, and formaldehyde)

What are viroids?

Infectious pathogens that are single-stranded and circular RNAs.

What are advantages of being in a biofilm?

• Protected mode of growth (e.g. survive harsh enviro, resistant to fluid shear, and colonization by dispersal of microorganisms)

• Resistance to immune defenses and antimicrobials

• Increase virulence

Define microbiota and microbiome.

Microbiota: living organisms found in a environment

Microbiome: collection of genomes from all microorganisms in environment

Define dysbiosis.

Disruptions to the healthy microbiome result in a shift to an abnormal microbiome

What are some characteristics unqiue to archaea?

• Possess genes and metabolic pathways that are more closely related to eukaryotes.

• They can be found in the gut, mouth, and skin microbiomes.

• Survive in extreme environments (e.g. salt lakes and volcanic hot springs)

What is the makeup of the bacterial genome?

• Circular and double stranded DNA

• Transcription and translation are regulated

• Condensed nucleoid (no nuclear mem or nucleus)

What is the process of the gram stain?

1. Crystal violet stain (primary stain)

2. Iodine

3. Alcohol

4. Safranin (counterstain)

What are characteristics of the cytoplasmic (plasma) membrane?

• Lipid bilayer similar to eukaryotic cell membrane

• Regulate the movement of molecules in and out of the cell.

• Osmotic barrier

• Transport systems (e.g. permeases transport nutrients into cell and secretion systems transport molecues out of cell)

Why are eukaryotic pathogens difficult to treat?

They are hard to treat due to sharing characteristics with our cells and also are opportunistic.

What are some characteristics of viruses?

• Obligate intracellular parasites that utilize host cell ribosomes to make proteins.

• Have DNA or RNA genomes (inside protein coating)

What are plasmids?

• Small and extrachromosal DNAs that code for nonessential information.

• Replicates separately from chromosome

• Possibly multiple copies in a single cell

• Can be transferred between bacteria

What is the function of ribosomes?

Protein synthesis

What is the significance of lysozyme?

It is a component of tears and saliva that can dissolve peptidoglycan.

What is an example of an antibiotic that target peptidoglycan?

Penicillins (inhibit peptidoglycan cross-linking)

Define biofilm.

Clusters of microorganisms that stick to surfaces (both biotic and abiotic surfaces).

What are surfaces conducive to the development of biofilms?

• Positively charged

• Rough

• Wet and less fluid shear

• Nutrient supply

Describe the biofilm lifecycle.

1. Attachment: Planktonic microbes sense a surface and adhere. Switch “from swim to stick” to attach securely.

2. Microcolony and EPS formation: Colonizers grow in microcolonies (hours to days) and EPS matrix solidify the structure into an organized community. Channeled EPS delivers nutrients and removes waste while protecting bacteria from external environment,

3. Secondary colonization & maturation: sec. colonizers attach to primary colonizers (while community matures). Microbes may join another biofilm.

What are the advantages that being in a biofilm provides to microbes?

• Protected mode of growth (allows survival in hostile environments, fluid shear resistance, colonization of new niches by dispersal of microorganisms)

• Resistance to immune defenses and antimicrobials

• Increased virulence

What are the main reasons biofilms are harder to treat when compared to planktonic microbes?

• Increase in antibiotic resistance when living in biofilms than planktonic

• 3 mechanisms: Resistance at biofilm surface/microenvironment, persister cells, polymicrobial nature

What kind of infections do biofilms usually cause?

Chronic infections

What is clinically important about biofilms and contact lenses?

• CL and lens cases are prime surfaces for biofilm formation

• Lens wear can shift ocular surface microbiome toward dysbiosis and independent of overt infection.

What are OTUs?

Count of microbial species based on 16S rRNA sequencing

What are the characteristics of normal microbiota?

Population of microorganisms that routinely grow on the body surfaces in healthy humans. They also provide nutrients like vitamin K and short-chain fatty acids.

How do normal microbiota contribute to barrier defenses?

• Block pathogens from binding to host cells

• Compete with pathogens for nutrients

• Some produce compounds toxic to other bacteria

What do disruptions to the healthy microbiome result?

Shift to an abnormal microbiome (dysbiosis)

What are two hypothesis relating to the development of the microbiome?

• Sterile womb hypothesis: Microbial colonization is after birth. Also thought the placenta is sterile.

• In utero colonization hypothesis: Establishment of the human microbiome is before birth.

What are the key components that influence the development of the early microbiome?

• Vertical transmission from mother (via vaginal microbes during natural birth/skin microbes during C-section)

• Maternal health (breast feeding)

• Contact with parents, caregivers, siblings

• Intro to solid foods

• Age and birth weight

What are some major challenges in studying the ocular surface microbiome?

• Low-biomass

• Swabbing of the eye (requires anesthetic)

• Determination of live vs dead microbes

What is the development of the microbiome like during and after birth?

• Newborns are exposed to a massive amount of microorganisms

• Colonization follows a temporal and spatial sequence