1037DOH - Oral Microbiology

microbiology for trimester 2

what is a microbiome?

• the collection of genomes from the total culturable and unculturable microorganisms

• includes biomolecules within a defined habitat

what is a microbiota?

• total collection of resident microbes within the microbiome

what are two features of microorganisms you can use classify and categorise them? briefly describe what these are

• phenotype

  • observable characteristics/traits of an organism

• genotype

  • organism’s complete set of heritable genes/genes that can be passed down from parents to offspring

what are the three domains of life?

1. bacteria (prokaryotes)

2. archaea (prokaryotes)

3. eucarya (eukaryotes)

describe the possible shapes and typical size of bacteria (MORPHOLOGY OF BACTERIA)

shapes

• cocci (spherical)

• bacilli (rod shapes)

• spirochaetes (helical)

• pleomorphic (appear as both cocci and bacillary forms)

size

• 0.2 - 5 microns

describe the flagella structure on bacteria

• mono, lopho, peri

• motile - whip like filaments

• made of flagellin (a type of protein)

• monotrichous - single + one ended

• lophotrichous - many + one ended

• peritrichous - all over outer surface

what are fimbriae and pili on bacteria?

• pilin is a protein

• both are fine, hair-like short structure

• they mediate adhesion of bacteria to receptors on host (human) cell surface

what is the glycoalyx? (bacteria)

• polysaccharide coating covering bacteria’s outer surface

• allow adhesion to structures - eg teeth, oral mucosa, heart valves and catheters

• contribute to formation of biofilms

• eg streptococcus mutans - contributes to dental caries

what is the capsule layer around bacteria?

• amorphous gelatinous layer surrounding bacteria

• polysaccharide formed - may also contain protein

• polysaccharides vary between bacteria and within a species (serological type)

what is the cell wall in bacteria?

• multi-layered structure

• allow rigidity

• porous and permeable to substances with a low molecular weight

• inner layer is peptidoglycan (protein + sugar)

• inner layer varies in thickness and chemical composition (depending on gram-staining property of the bacteria)

describe gram positive, gram negative stains and LPS (lipopolysaccharide)

gram positive

• dark blue/purple stain

• indicates thicker peptioglycan layer (inner cell wall)

gram negative

• pink stain

• indicates thinner peptidoglycan layer

• indicates complex outer membrane (including lipopolysaccharide (LPS), lipoprotein, and phospholipids, and porins (transportation of molecules)

LPS

• toxic (endotoxin)

• released when cell lysed

describe the cytoplasmic membrane of bacteria

• phospholipid bilayer

  • similar to eukaryotic cells, but bacterial ones dont normally contain sterols

• allows…

  • active transport + selected diffusion of molecules in and out of the cell

  • secretion of enzymes and toxins

  • electron transport

  • oxidative phosphorylation (in aerobic species)

• has supporting receptors and other proteins of the

  • chemotactic and

  • sensory transduction systems

describe aerobes, facultative aerobes and anaerobes

aerobes

• organism able to live and reproduce only in the presence of free oxygen

facultative aerobes

• grow either with or without free oxygen

anaerobes

• grow in absence of free oxygen

• those that grow only in absence of oxygen are called obligate/strict anaerobes

describe the cytoplasm structure of bacteria

• thick solution (amorphous matrix)

• fills each cell

• enclosed by cytoplasmic membrane

• mainly composed of water, ions, metabolites and proteins

• structures:

  • nuclear material

  • ribosomes

describe the nuclear material (nucleoid) of bacterial DNA

• single, supercoiled and circular chromosome

• 2000 genes

• 1mm long

• undergoes semi-conservative replication bidirectionally from a fixed point

describe the nuclear material (nucleoid) of eukaryotic DNA

• contained within the nucleus

describe function of ribosomes

• in bacterial (prokaryote) ribosomes are in the cytoplasm

• in eukaryotes, ribosomes are attached to the rough endoplasmic reticulum

• facilitate protein synthesis

what is E. coli’s full name?

escherichia coli

what is S. mutan’s full name?

streptococcus mutans

name the 3 anaerobic bacterial species identified in carious coronal dentine (GRAM POSITIVE)

1. peptostreptococcus (COCCI)

   • P. anaerobius

   • P. parvulus

   • P. micros

2. eubacterium (RODS)

   • E. alactolticum

   • E. aerofaciens

   • E. saburreum

3. propionibacterium

   • P. acnes

   • P. avidum

   • P. lymphophilum

name the 3 facultative bacterial species identified in carious coronal dentine (GRAM POSITIVE)

1. streptococcus (COCCI)

   • S. mutans

   • S sobrinus

   • S. intermedius

2. actinomyces (RODS)

   • A. israelii

   • A. odontolyticus

3. lactobacillus (RODS)

   • L. casei

   • L. plantarum

   • L. minutus

name 4 gram negative anaerobic bacterial species identified in carious coronal dentine

1. fusobacterium nucleatum (RODS)

2. porphyromonas (RODS)

3. prevotella (RODS)

4. veillonella (COCCI)

describe fungi

• eukaryotic, single-celled microorganisms

• genus Candida yeasts are pathogenic

describe viruses

• not living

• can infect all types of life forms

• exist in form of independent particles or virions

• DNA or RNA is their genetic material

• shapes range from simple helical/icosahedral forms to complex structure

• about 1/100th the size of bacteria

when infected with a virus, a ____ cell is forced to rapidly produce thousands of identical copies of the original ______

1. host

2. virus

what is pulpitis?

• inflamed pulp

• pain in A-delta and C-type nerves

• reversible) mild, can heal once treated (like caries), triggered by cold/sweet, brief pain

• irreversible) too damaged, spontaneous, throbbing, lingers after removing stim. usually treated w. root canal/extraction

what is pulp necrosis?

• pulp death

• after-effect of pulpitis/trauma

• partial necrosis may display pulpitis

• total necrosis is symptomless

what is periapical granuloma?

• affects periapical tissues

• usually resulting from long-standing infection or necrotic pulp

• 3 stages

  1. primary acute apical periodontitis

     • new, acute inflammation at the root

  2. chronic apical periodontitis

     • long-term, low-grade inflammation (can lead to granuloma)

  3. secondary acute apical periodontitis

     • chronic lesion that flares up

     • becomes acutely painful again

what is a periapical abscess?

• localised collection of pus at the root tip due to bacterial infection

• two types

  1. primary acute apical abscess

     • occurs at the first sign of infection

     • usually painful

     • swelling may occur

  2. secondary acute apical abscess

     • flare-up of chronic infection

     • becomes acutely infected

     • forms pus

what is ludwig’s angina

• rapidly spreading cellulitis of the floor of the mouth, usually from infected lower molars.

• can block the airway because swelling pushes the tongue up and back.

• firm swelling under the chin/neck, pain, fever, difficulty swallowing, drooling.

• tx) IV antibiotics + sometimes surgical drainage.

what is cerebral abscess?

• pocket of pus in the brain, usually from infection spreading from the ear, sinuses, or teeth

• Key features: headache, fever, neurological deficits, nausea/vomiting, sometimes seizures.

• Treatment: IV antibiotics, sometimes surgical drainage.

what type of infection is oral candidiasis/candidosis?

• opportunistic infection

• i.e occurs in ‘compromised’ patients

where do primary and secondary oral candidiasis/candidosis occur?

• primary

  • only in oral/perioral tissues

• secondary

  • oral/perioral tissues

  • other mucous/cutaneous surfaces

what is pseudomembranous, erythematous (atrophic) and hyperplastic oral candidiasis?

PM

• white creamy patches on soft tissue that wipe off and leave behind red sometimes bleeding tissue underneath

EM

• red, smooth, sometimes painful areas on tongue/palate

• linked to long term antibiotic/denture use

HP

• thick white patches that don’t wipe off

• can be chronic

• associated with immunosuppression 

what is candida associated denture stomatitis?

• fancy for sore mouth from dentures from overgrowth of candida

• very common on maxillary dentures (palate covered, warm and moist)

• treatment is denture hygiene or improving its quality

• medical factors (eg diabetes) contribute to this

• antifungals can also help

pinpoint erythema, confluent erythema and papillary hyperplasia of oral candidiasis

PP

• tiny red spots under denture

CE

• red areas merge into larger patches

PH

• long term inflammation causes small pebble like projections on the palate

what is median rhomboid glossitis?

• papillary atrophy

• can be ellipitcal or rhomboid

• in the midline of the tongue and anterior to the circumvallate papillae

• oral hygiene and antifungals can help this

what is angular stomatitis/cheilitis?

• lesions on the angles of the mouth

• overexposure to saliva, staph aureus infections, perioral infections, poor oral hygiene contribute

• zinc oxide paste, petrolatum lip balms, antifungals can help this

what is otitis media (chronic suppurative otitis media)?

• infection of middle ear

• appears as earache

• can have discharge and pain

what is sinusitis (chronic sinusitis)?

• occurs in frontal and maxillary sinuses

• can occur during common cold

• can appear with headache, pain, nasal obstruction, and can mimic toothache

what are some complications of a streptococcal sore throat?

• rheumatic fever

• chronic heart valve disease

• acute glomerulonephritis

explain the rheumatic fever complication of a strep throat

• symptoms are fever, pain and swelling in the joints

• pancarditis: inflammation of all parts of the heart

explain the chronic heart valve disease complication of a strep throat

• damage to heart valves over time, esp mitral and aortic valves

• increases risk of bacterial endocarditis (infection of heart valves)

• requires prophylactic antibiotics before dental procedures to prevent infection

explain the acute glomerulonephritis complication of a strep throat

• kidney glomeruli are inflamed

• can cause blood in urine

• swelling

• and high bp

describe bacterial/infective endocarditis

• predominately bacteria-caused

  • streptococci (60%)

  • staphylococci (25%)

  • other bacteria (15%)

• can happen thru periodontal treatment

• identify at-risk patients

• use preventive dental care

what bacteria cause bronchitis?

• H. influenzae

• S. pneumoniae

what is a major effect of cystic fibrosis? (infections of trachea/bronchi)

• compromised natural defence mechanisms

what causes pertussis (whooping cough)? (infections of trachea/bronchi)

• bordetella pertussis

• happens in children

• prevent via vaccinations

what bacteria causes tuberculosis?

• mycobacterium tuberculosis

what is human immunodeficiency virus?

• RNA virus

• leads to acquired immune deficiency syndrome (AIDS)

common oral signs of AIDS (orofacial manifestations)

• fungal infections

  • oral candidiasis (thrush) - white patches in mouth

• viral infections

  • herpes simplex virus

    • herpetic stomatitis (cold sores)

  • human herpesvirus 8

    • kaposi’s sarcoma (purple/red lesions)

  • epstein-barr virus

    • hairy leukoplakia (white hairy patches on the side of the tongue)

• severe, necrotising gingivitis and periodontitis

3 distinct particles of Hepatitis B

• Dane particle

  • 42 nm

  • complete infective virus

• spherical forms

  • 22 nm

  • non-infective

• tubular forms

  • 22 × 100 nm

  • non-infective

describe chronic persistent hepatitis B

• does not develop liver damage but liver inflamed for more than 6 months

• produces viral liver antigen (HBsAg)

• has mild symptoms (fatigue) or no symptoms at all

describe chronic active hepatitis

• extremely infectious

• Dane particles present in blood

• can progress to cirrhosis or liver cancer if untreated

• immune system actively fighting virus = liver damage

describe HCV (hep C)

• affects 3% of the population

• parental route is blood products

• persistent chronic infection - can progress to cirrhosis or liver cancer

dental implications of Hep C

• oral tissues can show lichen planus, cancer or salivary gland disease in chronic cases

• blood is main infectious media - saliva can contain viral RNA but transmission risk lower

• must follow precautions to avoid sharps injuries and cross-contamination

_______ result in cell aggregation, leading to improved clearance of _______ from the oral cavity during swallowing, chewing and speaking

• agglutinins

• bacteria

what do lysozymes do?

• breaks down bacterial cell walls

• part of the defence mechanisms of the oral cavity

name some antimicrobial peptides (defence mechanisms of the oral cavity)

• Histatin 5

• Human beta defensin-1 (and defensin-2)

• Magainin II and Magainin II amide

how do tonsils contribute to the defence mechanism of the oral cavity?

• house B and T lymphocytes and macrophages

• lymphoid tissue

how does epithelium defend the oral cavity?

• inhibits bacterial adhesion

• facilitates shedding of cells

• has a keratin layer

what does connective tissue possess that makes it part of the oral cavity’s defence mechanism?

• highly vascular so has lots of inflammatory response cells

why is gingival crevicular fluid a good oral cavity defence mechanism?

• continuous flow of fluid

• has albumin, transferrin and lysozymes

• has components of the immune system (lymphocytes, plasma cells and macrophages)

describe how a bacterial infection spreads in the tooth and surrounding structures

1. dental plaque (usually supragingival)

2. infected enamel

3. infected dentin

4. dentinal tubule biofilm

5. root canal system infected

6. infected peri radicular/extra radicular tissues (surrounding bone and tissues)

what does dentinal tubule fluid do?

• protect pulpo-dentine complex from bacterial antigens or toxic by-products

• allow pulp healing

• deposits serum in dentinal tubules to inhibit bacterial invasion of dentin by S. gordonii and E. faecalis

describe the colonisation of microbial biofilms

• think: they get there, eat, form a gang, fight, grow

• first bacteria adhere to host tissue

• they utilise available nutrients

• compete and co-operate with other species in the immediate environment

• contend with host defence mechanisms

• cells divide and grow

• host becomes colonised in multiple sites

describe the biofilm benefit to cells

• why are bacteria better in a biofilm than floating around on their own?

• the antimicrobial chemicals get diluted in the biofilm before they even reach the tooth surface or the cells deep in the biofilm

• outer layers of the biofilm act like a shield, stopping antimicrobials from getting inside

• some bacteria go into a ‘sleep mode’ or change how they function (resistant phenotype) so they’re less affected by drugs that normally kill these

clin sig

• makes it harder to kill harmful bacteria in plaque/root canals, meaning treatments like disinfectants, antibiotics or irrigation don’t work as well

list the 5 factors that affect the development and characteristics of biofilms

• fenat

• flora

• ecology

• nutrients

• anatomy

• time

flora factor of characteristics/development of biofilms

• one species may supply essential nutrients for the growth of other species (like vitamin K)

• strong bacterial positive interactions occur (like P. micros and P. anaerobius)

• redox conditions

• co-operate and compete with other species in immediate environment

nutrition factor of characteristics/development of biofilms

The oral cavity, especially in diseased areas, contains decaying tissue, root canal fluids, and serum-like substances rich in nutrients such as carbohydrates, amino acids/peptides (for protein synthesis), and growth factors like vitamin K and hemin (required by certain anaerobes).

In the early phase, sugar-metabolizing bacteria (e.g. Streptococcus) dominate, consuming available carbohydrates.

As carbohydrates are depleted, the second phase begins—bacteria capable of protein breakdown ferment peptides and amino acids, creating conditions that favor anaerobic growth.

In the final phase, protein degradation predominates, supporting the colonization of late, proteolytic species such as Prevotella intermedia, Fusobacterium nucleatum, and Eubacterium.

_______ anaerobes dominate initially and develops with ________ anaerobes

• facultative

• obligate

presence of _____-_______ _________ (eg prevotella) associated with advanced disease

gram-negative anaerobes

explain the community-as-pathogen theory

• spg eoe

• Structure: open architecture with channels → nutrient/waste flow.

• Protection: resist host defenses and antimicrobials.

• Gene activity: coordinated gene expression and cell-cell signaling (quorum sensing).

• Environment: spatial differences allow diverse habitats and efficient nutrient use.

• Outcome: enhanced virulence compared to single bacteria.

• Example: S. gordonii helps P. gingivalis adhere to collagen and invade tissues.

what are macrophages?

• phagocyte

• detect, engulf and destroy pathogens and apoptotic cells

what are dendritic cells?

• think chef

• cells that process antigen material (engulf + chop em up - antigens)

• present it on the cell surface to T-cells

• link innate immune system to adaptive immune system

what do B and T lymphocytes do respectively?

B

• make antibodies

T

• help kill tumor cells and control immune responses

what does the complement system do?

• tap

• enhances the ability of antibodies and phagocytic cells to clear microbes and damaged cells

• Tagging microbes so immune cells can eat them (opsonization)

• Attracting immune cells and causing inflammation (chemotaxis)

• Punching holes in pathogens to kill them (membrane attack complex)

what do cytokines do?

• they are small secreted proteins released by cells

• tell immune cells what to do

• help cells communicate, control inflammation, and coordinate the immune response

types of cytokine (list them)

• lymphocytes

• monocytes

• chemokine

• interleukin

what is PAMP (pathogen associated molecular pattern)?

• small molecular motifs found on microbes (bacteria, viruses, fungi) but not on human cells.

• examples include lipopolysaccharide (LPS) on gram-negative bacteria, peptidoglycan on gram-positive bacteria, flagellin, or viral RNA/DNA.

• immune cells like dendritic cells and macrophages have pattern recognition receptors (PRRs) that detect PAMPs. once detected, the immune system is activated to fight the invader.

what are pattern recognition receptors (PRR)?

• sensors of the innate immune system

• toll-like receptors (TLRs) detect bacteria, viruses, fungi

• proteins or inside immune cells

• once PRR binds its target, it activates immune responses: inflammation, cytokine release, and other immune cells recruitment

Summarise the development of a bacterial biofilm (10 marks)

• Bacteria adhere to surface in aqueous environment

• Excrete a slimy glue like substance to anchor them

• Single bacterial species, but more often biofilms consist of many species of bacteria as well as fungi, algae, protozoa, debris and corrosion products

• Once anchored to a surface, biofilm microorganisms carry out a variety of detrimental or beneficial reactions

• functions like a tissue