Microbiology is the study of microorganisms. They can be single cellular, multicellular, or acellular. Microbiology incorporates numerous disciplines found within the field of microbiology.
The years from 1857-1914 are called the Golden Age of Microbiology. Some of the famous members found within this field are:
Binomial nomenclature is composed of two italicized words. The first word which is the Genus, is capitalized, and the second word, is the species designation, is in smaller case.
The standard resource for identifying prokaryotes, bacteria, is Bergey’s Manual of Determinative Bateriology.
To be seen without a microscope, it needs to measure about 100 micrometers. Most microorganisms are smaller than that. Microorganisms differ between each other in size, structure, habitat, metabolism as well as other characteristics. Micros are found in Archaea, Bacteria, and Eukarya life domains.
Microbes in the Bacteria & Archaea domains are all prokayotes (lack nucleus). Cyanobacterium is a prokayotic microorganism. Eukaryotes are Eukaya (has nucleus)Viruses although are microorganisms do not fall within any of the domains of life. Virus is acellular. Peptidoglycan is the ones with cell walls.
Bacteria is a prokaryot because their DNA is not within a true nucleus. It is found everywhere. Yeast is a type of fungal microorganism. Alga is photosynthetic.
Otzi te Iceman was discovered frozen in the Alps. Scientists believe that he died of Lyme disease.
Pathogens cause disease. Most are good. They are named for shape. Common shapes are spherical (coccus), rod-shaped (bacillus) or curved (spirillum), spirochete, or vibrio. Bacteria is very versatile.
Archaea unicellular prokaryote. They are different from bacteria in their evolutionary history as well as numerous other differences. Their cell walls are psuedopetidoglycan. None of these have been shown to be a pathogen.
Please refer to your book for addition information.
- Incubation period—Approximately 43 days
- Acute illness with rapid onset of fever (104⁰ – 109⁰ F)
- Sore throat
- Massive vomiting
- Diarrhea (3 gallons/day)
- Poor Kidney Function
- Poor Liver Function
- Internal & External bleeding (bleed out of every body opening)
- Lyses or bursting of Red Blood Cells (RBC)
Hydrate Slow vomiting & diarrhea Antibodies boost the immune system. They do not kill viruses
- 850 -920 nanometers
- Single strand of RNA virus
- Long thread-like linear molecule
- Has an extra protein coat
Ebola is a member of the filovirus family (Marburg virus). Filovirus can cause severe hemorrhagic fever, which symptoms are, fever, vomiting, prostration, petechial hemorrhages, hypotension, and muscle pain. There are only two members of this virus family (Ebola & Marburg virus). Ebola have five strains with one Ebola-Reston not causing severe disease in humans.
The Filovirus was discovered in 1967 in Germany and Yugoslavia. Researchers were analyzing tissue of a green monkey, which had the disease. Researchers contracted the disease. This virus was named after where the outbreak occurred Marburg, Germany. Ebola was first discovered in 1976 in Africa. There is some evidence that it was originally contracted from bats. Once humans are infected, it spreads from person to person.
Death rate is 23 to 90%. To reduce risk of contracting from another human wear PPE, do not have contact with bodily fluids such as blood, and other secretions. Do not expose yourself to animals out of Africa, which may have the disease.
Currently the medical community is working on a vaccine. Researchers at Howard Hughes Medical Institute have developed at blood test (Virscan) which will tell doctors the patient complete viral history.
Ebola was named after the Ebola River where it was first discovered. There were two major outbreaks in the 90’s and one in Northwest Africa in 2014. Death occurs within six days.
In the United States there are only 19 negative pressure beds. The closest to Louisiana is Atlanta which has four.
Ebola is an enveloped virus meaning it has an extra protein coat. It is hard for drugs or immunity virus to attach & destroy.
Glycoproteins live on surface of virus. These glycoproteins are made up of carbohydrate chains called glycans. There are two types:
- GP1-Attachment (which makes it more potent)
- GP2-Fusion of host and viral membranes.
Genus Bacillus – gram positive, aerobic
spore -forming rods
Largely saprophytic & doesn’t cause
Importance in food preservation
Passion is the genius of genius – Galileo
Do or not do. There is no try. – Yoda
Microbes weigh as much as our brain which is 3 lbs. in our body. We have around 65 different microbes in our belly button
Human Perspective on Micro
- Activities of microbe are responsible for all life on earth. We have to have fungus.
- Bacteria fix nitrogen so plants can feed breaks down nitrates or nitrites.
- Microbes replenish our oxygen. Phytoplankton
- Microbes degree organic pollutants & toxic waste.
- Food stuff: Cheese, sauerkraut, yogurt, kimchee, bread (yeast), mushrooms, root beer, beer, moonshine, and wine
- 90% of antibodies are made by microbes.
- Genomics – use fungi for their restriction enzymes
- Medical microbe
- old world disease –plague, TB, yellow fever
- emerging world disease – Ebola, trichomonas, aids, west nile, H1N1 (West Nile)
1/10 the size of a virus
no outer coat
cause plant disease
short strands of RNA
Prions (Protein only infectious particle) Short strand Protein
- Induce other proteins to become prions
- Cause neurogenerative disease
- can last for years after death
- can penetrate surgical gloves
These are all pan resistant which means no antibiotics affect them:
- Stenotrophomonas maltophilia enzyme (S. Malt), New Delhi metallo beta lactamase type enzyme (NDM1),
Watch Hunting the Nightmare Bacteria on Frontline
Quantum Dot Stain-New
Microscope & staining
- atomic force
- Basic dyes- stains negatively-charged part of cells (nucleic acids, proteins) dyes used: crystal violet, safranin, methylene blue, malachite green
- Acidic dyes-stains the background as in a photographic negative, called negative staining, dyes used nigrosine, India ink
- glass slide & place a drop of H2O in the center
- Take your inoculating loop & put it in the burner
- *Take the heated loop & dip it in your culture. Take the loop put it in H2O droplet & spread all over the slide. This is called a smear.
- *Heat “fix” the slide over the hot plate
- Place a drop of methylene blue or crystal violet on the slide. Let it stand for one minute. Rinse with water, blot dry & observe
- Prepare smear & fix
- Flood the smear with primary smear-crystal violet let it stand 1 minute & rinse with H2O.
- Flood smear with Gram’s iodine. Let it stand one minute. Rinse with H2O. Iodine acts as a mordant. Mordant increased the likelihood of a structure to take up stain.
- Take 95% ethanol and drop by drop rinse the smear. Rinse with H2O. E + OH (ethanol) decolorizes gram negative bacteria.
- Flood the smear with your counter stain which is safranin. Let it stand 30 seconds. Rinse with H2O blot dry & observe. Crystal violet will stain gram + purplish to blueish
Safranin stain gram negatives pink – reddish color.
1. Spherical or round – coccus
2. Rod or cylinder – bacillus
3. Spiral – spirillum
4. Short, curved rod – vibrio
5. Star shaped – prosthecae
Some prokaryotic (bacterial structures)
1. Ribosome – make protein
2. Plasmids – small, circular strand of DNA
3. Nucleoid – twisted DNA strand
4. Glycocalyx – layer of polysaccharide lying inside bacterial cell wall
b. Flagella- consists of a hook for rotation, basal body for anchoring, filament tail for movement
Types of flagella
1. Monotrichous – single flagella–has tail as one end see example ﺻ
2. Amphitrichous- flagella at both ends—has tail at both ends see example ﺻ~
3. Lophotrichous-tuft of flagella—has tufted tails on bottom see example Ꙛ
4. Perithrichous-flagella all over—has tufted tails all over see example ꙰
Communities or group of microorganisms that attach to the surfaces of animate objects, heart valves, bone tissues, etc and inanimate structures prosthetic in plants, catheters, etc. only effective treatment K removal of infected tissues
1. Form shape
2. Elevation- cross section
3. Margin-magnified edge of colony
5. Opacity-clear, opaque, translucent
Rudolph Virchow (1821-1902)
1. Father of modern day public health
2. Shaped modern day public health
3. Discovered correlation between cancerous & normal cells, modern day autopsy procedures, hair analysis
4. Names: leukemia, chordoma, embolism, thrombosis, agenesis, parenchyma, osteoid, spina bifida
Anton von Leeuwenhoek
1. Father of microbiology
2. Discovered protists & bacteria
3. Distilling H2O to kill contaminants
4. Described bacterial motility
5. Single-celled (ocular) microscope
6. Most published author in the Royal Society of Great Britain
2. Lived near Stirling
3. Interest was in eradication of small pox through variolation & family & neighbors using variolation
4. After 1796, he inoculated 500 nearby families, 2 families chose no inoculation
5. President of Royal Society gave him equipment to do much more inoculation.
6. Set up shop in his cottage (1808), travelled throughout Scotland inoculating people. Took neither payment nor a meal.
1. Dormant form of a bacterium that is formed by reorganized the cytoplasm.
2. Spore has great resistance to outside influences heat, radiation, dessication, chemicals
3. Can remain dormant for years 50-100 years
4. Will germinate if conditions become favorable
5. Size, shape, & position of an endospore is constant within a species & has taxonomic value
Types of Endospores
1. Central-middle of cell
2. Terminal-end of cell
3. Subterminal-between middle & end
EMB agar (eosin methylene blue)
1. Selective & differential
2. Used to isolate gram (-)
3. Methylene dye in small amounts
4. Eosin dye responds to changes in pH – colorless to black under acidic conditions
5. EMB contains lactose & sucrose, but no glucose for energy
Lactose fermenting bacteria (usually enteric) acidify EMB & colonies appear black with green sheen (E. coli, Klebsiella, Enterobacter)
Lactose non-fermenters are translucent to pink (salmonella, shigella, and pseudomonas
The EMB selects for growth of gram (-) bacteria & differentiates between genera of gram (-)
We must be willing to get rid of the life we have planned so as to have the life that is waiting for us. Joseph Campbell
Dynamics of Prokaryotic (Bacterial) Growth
Only 1% of all prokaryotes can be cultured as a pure culture. You need a good growth medium to grow which is agar. It was developed by Robert Koch. Agar is:
- specific nutrient solution
- degraded by bacteria
- destroyed at high temperatures
Environmental factors that influence microbial growth are temperature, oxygen, pH, water.
Temperatures: psychrophiles, phychrotrophs, and mesophiles
Oxygen: obligate aerobes obligate anaerobes facultative anaerobes microaerophiles, aero tolement anaerobes
pH: neutrophiles, acidophiles, alkalophiles
Water: halophiles-love salty water
- complex media
- chemically defined media
- selective media- adds ingredients that inhibit the growth of orgs other than the one bring sought
- differential-contains an ingredient that can be changed by bacteria in a recognizable way.
The zone hemolysis is the area where blood is breaking down. The above are examples. Please refer to professor notes for the example he/she gives.
Detecting and Meaning
- direct cell count
- direct microscopic count
- coulter counter
- flow cytometer
- viable (alive) cell count
- most probable #
- plate count
- pour plate
- spread plate
- membrane filtration
- direct cell count
- direct microscopic count
- coulter counter
- flow cytometer
- viable (alive) cell count
- most probable #
- plate count
- pour plate
- spread plate
- membrane filtration
- lag-extensive macromolecule & ATP synthesis
- Exponential or log – cells multiply exponentially
- primary metabolite – used as flavoring agents & food supplements
- secondary metabolites produce antibiotics
- stationary phase-#of viable (living) cells stay constant
- death-#of viable cells decrease exponentially
- phase of prolonged decline-gradual decrease in # of viable cells overtime (days, weeks, years, and decades)
- physical – heat, wash, filter, irradiate
- chemical-antimicrobial chems
sterilization – removing of or destroying all microbes on or in a product. Disinfection-eliminating most or all disease
- daily life
- food & food production
Using heat to destroy
- moist heat
- dry heat
Why is heat so good? It is cheap quick
Potential risk of infection
- critical items – scalpel, gloves, needles
- semi-critical – endoscope, trachea tube
- non -critical – bp cuff
Selecting the appropriate germicide
- activity in the presence of organic matter
- storage & stability
- environment risk
- refrigerate, freeze, lypophilize – freeze dry
Classes of Germicides
- alcohol-antiseptic kill bacteria & fungi
- aldehydes – formaldehyde, inactive proteins & nuclei acids
- br guanides – antiseptic, chlorhexide kills bacteria & fungi
- ethylene oxide – gas, kills microbes & endospores
- halogens, CHI disinfect drinking waste water
- ozone- same as halogens
- metals silver, inhibits protein & enzyme function Copper is the best of these
- peroxygen H2O2 – sterilize juice & milk juice containers
- Pheholic compounds triclosan & hexachlorophene – denatures proteins
- Quats – food prep surfaces
Disinfection in clinical and non-clinical setting ways to disinfect non-porous surface
- liquid disinfectants
- microbiocide surfaces
Most are ineffective and harmful. Why? Very, very long contact time}hospital centered or a hospital setting
Gases, Mists, Foams
sit for 2-24 hours, seal the room and be unoccupied
Disinfect rooms, use it as a gas, Dangerous- lead to free radical formation in cells.
Questions they must ask if a tumor appears cancerous
- Size of primary tumor
- Has it invaded surrounding tissue
- Has it metastasized (spread)
- Has it invaded any regional lymph nodes
TNM System for Identification
T = Tumor
T0 = no tumor;
T1 = very small;
T2 = small;
T3 = medium;
T4 = large
N = Lymph node
N0 = no nodes involved;
N1 = 1 node involved less than 3 cm;
N2 = medium node involved 3-6 cm & multiple small nodes;
N3 = single node larger than 6 cm
M = Metastasized
M0 = no spread;
M1 = spread
Diagnosis = clinical symptoms
Prognosis = probable outcome
Cancer Warning Signs
- lump or thickening in the breast or elsewhere
- nagging cough or hoarseness
- changing appearance of mole or wart
- indigestion or difficulty in swallowing
- change in bladder or bowel
- unusual bleeding or discharge
- sore that doesn’t heal
Staph – becoming XDR
Pyogenic – pus producer
- Gram positive
- Produces no spores
- Colonies are round, raised, golden yellow
Toxin and Enzymes
- Staph produces an enzyme called betalactamase – makes it resistant to penicillins and cephalosporins
- Cell wall structure is unique and resistant to methicillin (MRSA – methicillin resistant Staph aureus)
Side note: CAMRSA – Communicative associative methicillin resistant staph aureus
- Plasmids (round circular piece of DNA) – carry genes resistance tetracyclines, amino glycosides, and erythromycins
- Exhibits “tolerance”. Inhibits but not killed
- Exotoxin – skin necrosis (rotting)
- Exotoxin C – fever producing (106° F)
- Hemolysins – cause red blood cells to burst
- Leukocidins – kills white blood cells
- Enterotoxin – food poisoning
- Coagulase – causes plasma to clot
- Hyaluronidase – spreading factor
- Exfoliative toxin – causes “scalded skin” syndrome
- Postulated toxin – causes TSS – toxic shock syndrome
- Empyema – accumulation of pus in a body cavity
- Severe acne
- Impetigo – small pustules that ooze a yellowish mustard like liquid
- Pneumonia (pus in the lung)
- No vaccines
- Drain lesion
- Best medications – vancomycin, clindamycin, rifampin, mupirocin (cream that can be used in the nasal cavity)
Vaccines – substances that are found in vaccines: (1.2 – 2B people saved from vaccinations)
- Aluminum – act as an adjuvant (enhances) to promote a more potent response and a more persistent response.
- Antibiotics – prevents the growth of germs during production and storage of the vaccine.
- Egg protein – used in production of influenza and yellow fever drugs.
- Formaldehyde – inactivates bacterial products for toxoid vaccines, kills unwanted viruses and bacteria that might contaminate the vaccine during production. It is removed from the vaccine before packaging.
- MSG – stabilizer for the vaccine in the presence of heat, light, acidity or humidity.
- *Thimerosol – mercury containing preservative that prevents growth of harmful bacteria.
Herd immunity – protecting a whole community from disease by immunizing a critical mass of its populace.
Vaccine protects not only the one person, but breaks the chain of an infection’s transmission, it also protects non-immunized individuals. To do this a certain % of the populace must be vaccinated.
Ways to become immune to a disease
- Be exposed to a pathogen
Infectious features of a microbe.
These affect a disease’s threshold (minimum % of an immune individuals and community needs to prevent an outbreak
To set a threshold one uses a value – basic reproductive # or RO
The RO represents how many people in an unprotected population, one infected person can pass the disease along to
RO for measles is 12-18
Higher the %, higher the immunity threshold must be to protect the community
Factors involved in calculating a specific threshold:
- How effective the vaccine for a given disease is?
- How long lasting the immunity is from vaccination and infection?
- Which populations form critical links in transmission of the disease (very young, very old, immune compromised, religion groups)
Koch and germ theory of disease
Robert Koch (1843-1910), physician, studied anthrax early on in his work. It is a disease of cattle, sometimes people. Caused by Bacillus anthracis – endospore former. Koch established that anthrax bacteria were ever present in the blood of an animal with anthrax disease. He demonstrated that one could take a small amount of blood from a diseased mouse and inject it into a 2nd disease-free mouse. This mouse then contracted anthrax and died. He took blood from the dead mouse, injected it into another mouse and it got the disease. Furthermore, he found that one could cultivate the bacteria in nutrient-rich fluid outside of an animal body and that after many transfers in other cultures, the bacteria was still highly pathogenic. From these experiments he formulated his famous Koch’s Postulates.
- The organism should be constantly present in animals suffering from the disease and should not be present in healthy individual.
- The organism must be cultivated in a pure culture away from the animal body.
- Such a culture, when inoculated into susceptible animals, should initiate the characteristic disease symptoms.
- The organism should be reisolated from these experimental animals and cultured again in the lab after which it should be the same as the original organisms.
Summary of the postulates: specific organisms cause specific diseases.
Stenotrophomonas maltiphilia (aerobe)
Multi-drug resistant, Gram (-) bacillus, opportunistic pathogen particularly in hospitalized patients.
It has an inherent ability to adhere to foreign materials and form a biofilm, thus, it is protected from host antimicrobial agents.
It has intrinsic or acquired resistance mechanisms to: betalactamases, penicillinase, cephalo-sporinase, aminoglycoside acetyl transferase to confer resistance.
High morbidity (clinical symptoms – fever, etc)
High mortality (21-69%)
Risk factors for acquiring an S-malt infection: ICU, vented, HIV, cancer, CF, catheters, surgery, broad-spectrum antibiotic treatment.
Need strict hand hygiene and contact isolation.
Clinical manifestations – pneumonia, bacteremia, endocarditis, mastoiditis, peritonitis, UTIs, soft wound infection, ocular infection, meningitis.
Treatment – hard to discern from other infections. Need much clinical data. Only somewhat effective treatment is:
TCA +/or ciproflaxin
14 day treatment span
About 41% effective
Diversity of Prokaryotes
Organohalide respiring bacteria – use chlorinated molecules
Methanogens – oxidize hydrogen gas, make methane
Purple sulfur and green sulfur bacteria – use sulfur compounds, grow in large masses in sulfur springs.
Lactic acid bacteria – make lactic acid. Can cause disease and make dairy products (yogurt) – Lacto bacillus
Streptococcus pyogenes – cause disease – wound infections, strep throat, rheumatic fever, glomerular nephritis, flesh-eating, TSS
Nitrifers – oxidize NH3 and nitrate, breakdown N
Bioluminescent bacteria – utilize luminol, glow in the dark, symbiosis with deep sea fish (angler fish, shrimp) to help attract a mate and score off predators, attract prey.
Prochlorococcus – smallest known microscopic phytoplankton, marine, numbers are trillion-trillion, responsible for ½ of all global photosynthesis (CO2)
Ice nucleators (IN) – microbes such as Pseudomonas syringae that are found in the upper atmosphere. They influence weather. Dust and soot particles act as seed nuclei for the bacteria to attach to them. Once this happens, the bacteria catalyze ice formation which can then fall to Earth’s surface as rain, sleet or snow.
Snottites – biofilm of chemotrophic bacteria that oxidize hydrogen sulfide. They are found in caves and produce stalagmite and stalgtite-like columns. Also etch vertical and horizontal lines in cave walls.
Parasite – one that lives at expense of host
- Ectoparasite – lives on surface of host
- Endoparasite – lives within host
Pathogen – any parasitic organism that produces an infectious disease (ex – cold virus, hook worm)
Pathogenicity – ability of a parasitic organism to cause disease
Final outcome of a host/parasite relationship depends upon:
- Virulence of pathogen present – degree or intensity of pathogenicity.
- Number of pathogens present
- Host degree of resistance
Virulence depends on:
- Infectivity ability to establish a focal point of infection
- Pathogenic potential – degree to which the pathogen can cause morbid symptoms
Transport of bacterial pathogen:
- Direct contact – cough, sneeze, body contact
- Indirect contact – soil, H20, food, vectors – insects, fomites – inanimate objects
Studies of the Human Microbiome (full set of microbial genomes that exist in an organism)
Different body habitats are very different from each other in their microbial communities (mouth, earwax, hair, underarm, toe)
Most diverse – mouth, nose, 231 phyla
Least diverse – stomach, toes, 65 phyla
Large differences in stool and intestinal mucosa – 343 genera with the largest genus being Bacteroides.
Fecal bacterium – anti-inflammatory correlated with pulse and bp
4 largest genera of human microbiomes: Bacteroides, Firmicutes, Actinobacteria, Fecal bacterium
Newborns acquire mother’s vaginal microbiome in natural childbirth, but very little if C-section. Breast fed have a far more diverse microbiota than formula fed (virtually none).
Identical twins have quite dissimilar microbial communities.
Gut Ecology and c. diff
AAD – antibiotic associated diarrhea – 1st thought to be associated with Staph, but it is due to killing off healthy gut microbes and leaving a very nasty pathogen present – clostridium difficile (bloating, gas, diarrhea, pain lasting for months).
Hard to get good microbes in high numbers to defeat c. diff. Best way – fecal bacteriotherapy – use host feces (relative), screen it for disease and liquefy, use a feeding tube to ingest. 2-3 days back to normal.
How does our microbiota defend against c. diff?
- Impair it directly (attack)
- Shape the host immune response
- Antimicrobial peptide – Reg III gamma
- IgA antibody
- Short-chain fatty acids
- Occupy space in gut
- Colonization defense
- Filamentous bacteria stimulate lymphocytes
- Use as a possible treatment in prostrate cancer. 1.1 million cases worldwide, mostly in developing countries. It is the 4th most common in both sexes, 2nd in men, 5th leading cause of cancer death.
- Researchers at Swansea University in Wales
- They modified the salmonella to render it harmless and engineered cells to use them as a therapeutic molecule to target cancer cells. Coupled with Salmonella the molecule delivers the “switching off” gene mechanism to genes in the cancer cells, thus, tumor growth is disrupted. Also attached to the gene mechanism is an anti-cancer drug which is non-toxic to normal body cells & only a single dose is needed to achieve positive results.
Prostrate cancer cells have shrunk in the lab when exposed to the modified bacterium
Will be used in clinical application trials.
Helminthes (parasitic worms)
- Nematodes – roundworm, pinworm, hookworm
- Cestodes – tapeworms
- Trematodes – flukes
- Filavial worms
Nematodes-In Phylum Aschelminthes, most common intestinal helminth in man. Diagnose by detection of eggs or larvae in feces, transmission is fecal – oral route (food, water) or skin penetration by larvae (hookworm). Cylindviral body
Cestodes-Flat, ribbon-shaped body, segmented. Head or scolex has suckers and hooks for attachment. No GI tract instead absorb nutrients. Get from undercooked or raw beef, lamb, pork, or fish. Dipylidium caninum (dog tapeworm)-get from playing with a dog. It is the most common.
Trematodes-Phylum Platyhelminthes, bilaterally symmetrical, flat, leaf-shaped, suckers for attachment and sucking. Most are hermaphrodites (box sex organs in same worm). Larval stage within the egg, larvae can escape into environment when they can find an intermediate host, then get released as a tail-bearing larvae-cercaria. Cercaria can penetrate skin, go to the liver and intestines, mature and lay eggs.
Filaviae (dog & cat heart worm)-slender, thread-like nematodes. Transmitted by bite an arthropod vector (fly, mosquito). Live in lymphatic system or deep connective tissue of host. Produce larvae known as microfilaviae.
Wucheria bancrofti & Brugia Malayi – cause lymphatic filiariasis-lymphatic channels become blocked & lymphedema results.
Loa loa – eye worm disease (loiasis)-inhabits deep tissues and can be seen crossing conjunctiva of eye, intense itching, “creeping feeling”.
Onchocerca volvulus-river blindness, major public health problem, worms become encapsulated in fibrous nodules & ocular lesions cause blindness.
Drancunculus medinensis (Guinea worm)-long, slender, soft-bodied worms acquired by drinking contaminated water, exude from any body part with an intense burning.