Biomedical Sciences: Microbes and the Microbiome (Lecture 1; Exam 1)

Characteristics of prokaryotes

• Unicellular organisms

• Do not have a membrane-bound nucleus, mitochondria, chloroplasts, or other membane-bound organelles.

What organisms are prokaryotes?

Bacteria and archaea.

Characteristics of Eukaryotes

• Cells have a membrane-bound nucleus.

• May be unicellular or multicellular.

What organisms are eukaryotes?

Protists, fungi, and helminths.

What are acellular infectious agents?

Viruses, viroids, and prions.

Do all microbes cause disease?

No. Some are beneficial, while some have no positive or negative impact

However, some may be pathogenic.

Pathogen

A microbe capable of causing host damage.

Extracellular Pathogen

Causes damage while outside of the cell.

Intracellular Pathogen

Must be inside cells to cause damage.

Subclinical Infection

When pathogens get past our barrier defenses, the immune system eliminates them before they cause disease (most of the time).

Eubacteria

“True bacteria”; Prokaryotes

• Multiply by binary fission

• Cell wall made of cross-linked peptidoglycan

• Variety of shapes

• Variety of arrangements

• Some are medically important

• Many commensal microorganisms are eubacteria

Shapes of Eubacteria

• Cocci = spheres

• Bacilli = rods

Eubacteria variety of arrangements

• Chains (divide in one plane)

• Packets (divide in two or more perpendicular planes)

• Clusters (divide in random planes)

Prokaryotic Bacterial Structure

• Cell Surface

  • Capsule

  • Appendages (Flagella, fimbriae & pili)

  • Peptidoglycan

• Cytoplasmic Membrane (cytoplasm and cyotosol)

• Gram--positive & Gram-negative cell envelope

Capsule

Protects from toxins and desiccation.

• Some bacteria have a polysaccharide capsule outside of their cell envelope.

• Can protect from engulfment by phagocytic cells.

• Allows attachment to host cells.

• Can increase virulence

Appendages

• Flagella

• Fimriae

• Pili

Flagella

Organ of movement.

• Bacteria typically move by chemotaxis towards a stimulis.

Fimbriae and Pili

Thin, hair-like appendages involved in the attachment to surfaces and host cells.

• Pili are also involved in bacterial conjugation.

Peptidoglycan

Unique to bacteria; polymerized network mesh that holds the cell together.

• Target of many antibiotics, including the penicillins.

THIN layer in Gram-negative

THICK layer in Gram-positive

Lysozyme

A component of tears and saliva that can dissolve peptidoglycan.

Gram-Staining

• Gram-negative = PINK or red

• Gram-positive = Purple

Cell wall composition determines how the stain appears.

Bacterial Cytoplasmic Membrane

Regulates the movement if molecules in and out of the cell.

• Lipid bilayer similar to eukaryotic cell membrane.

• Osmotic barrier

• Transport systems

Osmotic Barrier

Charged molecules do not pass freely through the membrane.

Transport Systems

• Permeases: Bring in things required by the cell (nutrients, iron, etc.)

• Secretion Systems: Transport molecules out of cell.

What kind of membrane do Gram-positive bacteria have?

Inner membrane only.

• The inner membrane surrounds the cytoplasm.

Plasma Membrane

• Cytoplasm: Entire contents within the cell membrane.

• Cytosol: Jelly-like fluid portion of the cytoplasm in which cellular contents are suspended.

Bacterial Genome/Chromosome(s)

Large, circular, double-stranded DNA with 3,000-4,000 genes.

• Condensed nucleoid, no nuclear membrane or nucleus.

Plasmids

Small, extrachromosomal DNAs that code for nonessential (but important) information.

Ribosomes

Responsible for protein synthesis.

• (Different structure than eukaryotic ribosomes)

Bacterial Structure: Cytoplasmic Content

• Ribosomes

• Proteins

• Ions

• ATP

• Water

Endospores

Allows survival in harsh conditions such as starvation, extremes in temperature, exposure to drying, UV light, chemicals, enzymes and radiation.

• ***Can be resistant to disinfection methods, including drying, UV light and autoclaving.

• Endospores are formed by a few types of Gram-positive bacteria.

Archaea

Prokaryotes that are similar to, but evolutionarily distinct from bacteria.

• Identified as components of the gut, mouth, and skin microbiomes.

Can survive in extreme environments.

*No known pathogenic archaea have been identified.

Why are eukaryotic pathogens difficult to treat?

Eukaryotic pathogens are often opportunistic and are difficult to treat due to shared characteristics with our cells.

Fungi

Includes yeasts and molds.

Contain chitin in their cell walls.

More than 300 are known to be human pathogens.

Helminths

Worm-like parasites that infect nearly 2 billion people worldwide.

• Include flukes, tapeworms, and roundworms

• Multicellular, extracellular nature makes elimination by the immune system difficult.

Protozoa

Single-celled, motile, eukaryotic parasites.

• Cause some deadly human disease, including malaria.

Viruses

Obligate, intracellular parasites.

• Have DNA or RNA genome inside a protein coating.

• May be enveloped or non-enveloped.

Can viruses replicate on their own?

NO. Viruses cannot replicate on their own, they use host cell ribosomes to make proteins.

Viroids

Small, single-stranded, circular RNAs that are infectious pathogens.

(Differ from viruses in that they are NOT protein-coated and do NOT encode proteins.)

Prions

Misfolded proteins that induce misfolding in normal variants of the same protein, leading to cellular death.

• Resistant to proteases and disinfection by heat, ionizing radiation, and formaldehyde.

Biofilms

Are clusters of microorganisms that stick to surfaces.

• Develop on both biotic (living) and abiotic (non-living) surfaces.

• Often encased in an outer polymer layer (matrix) that is produced by the microorganism or by defensive mechanisms of the colonized host.

What surfaces/locations are most ideal for biofilm formation?

• Positively charged surfaces (cell walls contain negatively charged compounds)

• Rough surfaces (rough surface = more surface area)

• Wet locations with less fluid shear (prevents drying/desiccation)

• Nutrient supply

Biofilm: Stages

1. Stage 1 - Attachment

2. Stage 2 - Microcolony and EPS Formation

3. Stage 3 - Secondary Colonization & Maturation

Advantages of being in a biofilm:

• Protected mode of growth (allows cells to survive in hostile environments)

  • Resistance to fluid shear

  • Allows colonization of new niches by dispersal or microorganisms from the clusters.

• Resistance to immune defenses and antimicrobials

• Increased virulence

Antibiotic Resistance: Four primary mechanisms

• Efflux pumps

• Enzymatic inactivation

• Target modification

• Reduced permeability

Resistance genes may be intrinsic or acquired through mutation or horizontal gene transfer (plasmids, transformation, transduction, conjugation).

Do biofilms cause more antimicrobial resistance?

YES.

Bacteria living in a biofilm can exhibit a 10-1,000-fold increase in antibiotic resistance when compared to similar bacteria living in a planktonic state.

Biofilms and Antimicrobial Resistance: Mechanisms

1. Resistance at biofilm surface and within biofilm microenvironment

2. Resistance of persister cells

3. Polymicrobial nature

Can biofilms cause chronic infections?

YES. They typically persist despite innate and adaptive immune responses and/or adequate antibiotic therapy.

What is a prime surface for biofilms to form in clinic?

Contact lenses.

• Pseudomonas aeruginosa

• Staphylococcus species

Microbiota

Living organisms found in defined environment.

Microbiome

Collection of genomes from all the microorganisms in the environment.

Operational Taxonomic Units (OTUs)

Count of microbial species (or predicted species) based on 16S rRNA sequencing.

Normal Microbiota

Population of microorganisms that routinely grow on the body surfaces (skin, gut, mucous membranes, ocular surface) of healthy humans.

• Blocks pathogens from binding to host cells

• Compete with pathogens for nutrients

• Some members of the microbiota produce compounds toxic to other bacteria.

Provides nutrients such as Vitamin K and short-chain fatty acids.

Dysbiosis

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

• (Associated with disease)

Sterile womb hypothesis

• Placenta/amniotic fluid has long been thought to be a sterile environment.

• Microbial colonization does not begin until after birth.

In utero colonization hypothesis:

Some studies argue establishment of the human microbiome begins before birth.

• (Others believe that these findings are purely due to laboratory contamination.)

Key Influences on the Development of the Early Microbiome

• Vertical transmission from the mother

• Gestational age and birth weight

• Contact with parents, caregivers, siblings

• Breastfeeding

• Antibiotic usage

• Introduction of solid foods

Ocular Surface Microbiome

The ocular surface includes the cornea, conjunctiva, eyelids, and the lacrimal and meibomian glands.

Lacrimal Functional Unit

Controls tear secretion and regulation of the ocular surface microbiome (OSM)

• Lacrimal gland

• Meibomian glands

• Tear film

• Conjunctiva with goblet cells

• Cornea

• Neurointegration of these structures

OSM Dysbiosis is associated with:

• Drye eye disease

• Ocular graft vs host disease

• Meibomian gland disease

• Allergic conjunctivitis

• Bacterial keratitis