UTA-Microbiology Exam 2-Dr.Parks

Prokaryotes Habitats

-found in hot springs, ice caps, deep ocean, skin, and mucosal surfaces

-are ubiquitous

-why: they are very adaptable and resilient and are able to switch metabolic respiration methods

-diversity is important: stability of ecosystems, carbon and nitrogen fixation, environmental cleanup

-human pathogens and climate change

Microbiomes

-The diverse communities of bacteria that live on or within the body and are essential to bodily function.

-prokaryotes + eukaryote microbes = microbiome

-differ btwn different sites and organisms

-resident: natural there

-transient: not there or there for a short while

Mutualism

-both are benefitted

-ex: gut nutrient metabolism

Amensalism

-A is harmed and B is unaffected

-ex: antimicrobial defense on skin

Commensalism

-A is benefitted and B is unaffected

-ex: skin cells as food source

Neutralism

-both are unaffected

-ex:spores in soil

Parasitism

-A is benefitted and B is harmed

-ex: tuberculosis, leprosy, etc.

Taxonomy of Prokaryotes

-do not reproduce sexually

-not many distinctive morphological features

-molecular, biochemical, microscopi, and nucleotide sequences together is best approach

Gram Negative Phyla

-Proteobacteria

-Spirochete

-CFB group

-Planctomycetes

-Phototrophic bacteria

Gram Postitive Phyla

-Actinobacteria

-Firmicutes

Atypical

-neither

-tenericutes

Alphaproteobacteria

-gram (-) proteobacteria

-oligotrophs: lives in low nutrient environments

-obligate intracellular and must have host to be metabolically active

-Rickettsia spp.: causative agent for Rocky Mountain spotted fever and typhus fever, transmitted from tick, others spread through lice

-Chlamydia spp.: causative agents for lymphogranuloma venereum (STD), spreads rapidly, endospore like

Agrobacterium

-gram-negative bacillus

-plant pathogen, one species

-A.tumefaciens causes tumors in plants

Rhizobium

-gram-negative, rectangular bacilli with rounded ends forming clusters

- nitrogen fixing batters that live in soil and form symbiotic relationship with roots of legumes

Betaproteobacteria

-gram (-) proteobacteria

-eutrophs: require many nutrients (copiotrophs)

-Bordetella spp.: causative agents with whooping cough (pertussis) and kneel cough (dogs), produce toxins to paralyze lung cilia

-Neisseria gonorrhea: causative agent for gonorrhea STD, painful peeing

-Neisseria meningitides: causative agent for bacterial meningitis, difficult to culture, typically live off our blood

Gammaproteobacteria

-gram negative

-most diverse

-Pseudomonas aeruginosa - common infection of wounds, urinary tract, & respiratory tract

-Pasteurella haemolytica - causative agent for severe pneumonia in animals

-Haemophilus influenza - causative agent for upper & lower respiratory infections (does not cause influenza)

-Vibrio spp. - commonly found in alkaline environments such as ocean ports & lagoons, gastrointestinal disease, cellulitis, blood-borne infections

-Vibrio cholera - causative agent of cholera and common to water contamination

-Legionella pneumophila- causative agent for Legionnaire's disease and common to water contamination

-Enterobacter family - includes E. coli, & Salmonella spp., Coliforms - "E. coli - like" microbes that ferment lactose completely, Noncoliforms - fermentation of lactose is incomplete or absent

-E. coli - most mutualistic, some produce Shiga toxin

-Salmonella can have multiple serotypes, many that cause salmonellosis

Deltaproteobacteria

-gram (-) proteobacteria

-small class

-sulfate reducing bacteria

-desulfovibro orale- periodontal disease

-parasitic Bdellovibro app.

-soil dwelling Myxobacteria "slime bacteria"

Epsilonproteobacteria

-gram (-) proteobacteria

-smallest class

-microaerophillic: only like a small amount of oxygen

-Campylobacter spp.: common to food poisoning, aerobic

-Helicobacter spp.: commonly beneficial but can cause ulcers and stomach cancer in susceptible people

Spirochetes

-gram (-) nonproteobacteria

-extremely thin and hard to stain and culture

-have axial filament similar to flagella

-Treponoma pallidum: causative agent for syphillis

-Borrelia burgdorferi: Lyme disease

CFB group

-gram (-) nonproteobacteria

-Genus: Cytophaga•Cytophaga spp. - gliding system for motility (mechanisms mostly unknown)

-Genus: Fusobacterium•Fusobacteria spp. - inhabit mouth and can cause various oral diseases

-Genus: Bacteroides•Bacteroides spp. - 30% of gut microbiome; lower levels correlated with obesity

Planctomycetes

-gram (-) nonproteobacteria

-aquatic environments: fresh, salt, and brackish

-reproduce via budding instead of binary fission (mother pinches off daughter cell)

-Sessile cells: immobile with holdfast appendage

-Swarmer cells: motile, unable to reproduce

Phototrophic Bacteria

-grouped based on function

-sunlight main source of energy via photosynthesis

Cyanobacteria

-phototrophic bacteria

-highly adaptable and diverse

-chlorphyll; uses as biosorbents and human nutrients

-Microsystis spp.: toxic algal bloom, some of the oldest

purple sulfur bacteria

-oxidize hydrogen sulfide to elemental sulfur and sulfuric acid

-phototrophic bacteria

purple nonsulfur bacteria

-phototrophic bacteria

-use only hydrogen

green sulfur bacteria

-phototrophic bacteria

-oxidize sulfide

green nonsulfur bacteria

-phototrophic bacteria

-oxidize non-sulfide substrates

Gram-positive bacteria

-gram stains purple

-grouped by guanine + cytosine content

-Phylum Actinobacteria - high G+C content (>50%)

-Phylum Firmicutes - low G+C content (<50%)

Actinobacteria (phylum)

-very diverse

-thin filamentous to coccobacilli shaped

-Important to soil ecology

-differnet peptidoglycan in cell wall

-myobacterium, corynebacterium, bifidobacterium, and gardnerella

Mycobacterium spp.

-Acid fast (+) due to mycolic acid in cell wall

-causative agent for tuberculosis & leprosy

Corynebacterium spp.

-Diaminopimelic acids in cell wall

-Most are non-pathogenic; C. diphtheria is causative agent for diphtheria

Bifidobacterium spp.

-Filamentous & anaerobic

-used as probiotic

Gardnerella vaginalis

-Only one species

-Gram variable: inconsistent stain results

-Causative agent for bacterial vaginosis

Firmicutes (phylum)

-low G+C content

-no other common genera

-Clostridium, Streptococcus, Lactobacillus, Enterococcus, Bacillus

Clostridium

-mostly obligate anaerobes

-endospore producers

-soil dwelling

-common food contaminant

-C. perfringens - agent for food poisoning and gangrene

-C. tetani - producer of neurotoxin and agent for tetanus

-C. botulinum - producer of botulinum neurotoxin

-C. difficile - hospital infection, causes severe colitis

Lactobacillus

-contains bacilli and cocci

-genera Steptococus

~S. pyogenes - β-hemolytic cocci associated with pus production (pyogenic), strep throat

~S. pneumoniae - causes pneumonia, respiratory infections, and a wide range of other diseases

-prominent genera: Lactobacillus

~Facultative anaerobes, non-spore formers

~significant component of gut microbiome

~starter cultures for yogurt, cheese, sauerkraut, etc.

-Prominent Genera: Enterococcus

~Diplicocci arrangement

~Anaerobic respiration

~Commensal gut microbe

~Common UTI pathogen

~E. faecium

Bacillius

-firmicutes phylum

-bacillus shaped aerobes or facultative anaerobes

-endospore producers

-Important to industrial mircobiology

Prominent species:

•B. anthracis - causative agent for anthrax

•B. cereus - common food poisoning agent

•B. thuringiensis - producer of insecticide compounds

•Genus Staphylococcus - cocci shaped facultative anaerobes

•Halophilic (like salt)

•Nonmotile

•Prominent species

•S. aureus - common agent of skin infections; some can produce enterotoxins for food poisoning Some are very antibiotic resistant (MRSA & VRSA)

•S. epidermidis - common flora on skin; can cause infection to open wounds

Tenericutes Phylum

-Genus Mycoplasma - no cell wall and do not retain crystal violet

pleomorphic

-Extremely small

-Cell wall antibiotics do not work

-Only classified by genome

-Prominent species

•M. pneumoniae - agent for walking pneumonia

Deep Branching Bacteria

-bacteria that appear to have diverged the earliest from ancestral archaea and eukaryotes

-last common universal ancestor (LUCA)

-provide clues to structure and functions of ancient forms of life

-Prominent classes:

~Aquificae - gram (-) hyperthermophiles living in hot springs and oven vents

~Thermotogae - gram (-), hyperthermophilic anaerobes; sheath-like outermembrane

~Deinococci - gram (+) polyextremophile (heat, vacuum, acidity tolerant)

Archaea

-Membranes with branched isoprene chains & ether linkages to phosphate head

-Walls of surface layer proteins(some pseudopeptidoglycan)

-Genomes are much large

-Capable of methanogenesis

-usually not in human microbiota

-not directly associated with infectious diseases

Phylum Crenarchaeota

-archaea

-all aquatic microbes, many extremophiles

-Sulfolobus ssp. - thermophiles & acidophiles; facultative anaerobic; used in biotech for production of affitins

-Thermoproteus spp. - strict anaerobic thermophiles; arguably deepest branching Archaea

Phylum Euryarchaeota

-archaea

-mostly methanogens and anaerobes

-methoanobacteria, methanomicrobia, methanococci

-D. radiodurans

Characteristics of Viruses

-infectious, acellular pathogens

-Obligate intracellular parasites with host and cell-type specificity

-DNA or RNA genome (Never Both)

-Genome is surrounded by a protein capsid and, in some cases, a phospholipid membrane studded with viral glycoproteins

-Lack genes for many products needed for successful reproduction, requiring exploitation of host-cell genomes to reproduce

Virions

parasites that invade host cells and hijack cellular machine to produce new virus particles

Transmission of viruses

-host can vary

-can infect eukaryotes or prokaryotes

-can get infected by

1. direct contact with infected individual

2. fomite (eating utensil, doorknobs, bedding)

3. mechanical vector- organisms carries the virus on outside of body (ex. roaches and flies)

4. biological vector- organism carries viruses inside (ex. mosquitoes and biting flies)

Virus Sizes

-virons: viral particles assembled in infected host cell

-range of size: 20 nm - 900 nm

-are also some novel giant virus species that are almost the size of a bacterial cell

components of a virus

1. capsid (capsomere subunit)

2. genomic material (RNA or DNA)

3. envelope (not in all)

4. spikes (not in all)

Bacteriophage

A virus that infects bacteria

Caspid Shape (classification)

-caspid: protein coating surrounding genomic material

- shapes: helical, polyhedral, or complex

Envelope

-enveloped viruses: phospholipid membrane surrounding capsid

-naked viruses: capsid only with no envelpope

Virus structure

-grouped by genomic material

1. single strand DNA

2. double strand DNA

3. single strand RNA

4. double strand RNA

Taxaonomy of Viruses

-not in tree of life

-based on genetics, chemistry, morphology, and mechanism for replication

-use binomial nomenclature: family = viridae genus = virus

-7 orders, 96 families, and 350 genera

ICD codes

-international classification of diseases

-used for clinically prescribed treatments, ordering lab tests, health care management, medical billing and insurance reimbursement, vital records keepers for cause of death, epidemiology studies

-assigns a code to every type of viral infection

Viral Life Cycle

- goal is to invade the host cell, hijack machinery to make proteins and replicate

-varies deepening on host

Phage life cycle

-virulent phages: lead to death of host cell by lysis

-temperate (latent) phages: become part of host genome until induced to start making new viruses

lytic cycle (virulent phage)

The virus uses host DNA to build more virus structures in side the cell. Then the infected cell bursts (lyses) and releases the virus.

lysogenic cycle (temperate phages)

A phage replication cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage and does not kill the host.

generalized transduction

-DNA is random when transferred during lytic cycle

specialized transduction

-occurs at end of lusogenic cycle and can transfer host DNA

Viral Life Cycle of Eukaryotes

-similar to phage life cycle: different mechanism of penetration, nucleic acid biosynthesis, and release of viral particles (lysis or budding)

-after binding to host receptors, animal viruses ender via endocytosis or membrane fusion

-many are host and tissue specific

-ex: poliovirus (bran and spinal cord tissue) and influenza virus (respiratory tract tissue)

-steps: attachment, penetration, uncaring, biosynthesis, assembly, release

Nucleic acid biosynthesis

-dictates how proteins and nucleic acid are replicated

-dsDNA: normal flow of host cell

-ssDNA: complementary strand is synthesized and then normal flow

-+ssRNA: acts like normal mRNA

--ssRNA: converted to +ssRna thru special RNA polymerase

-rdRP = viral RNA dependent RNA polymerase

Retrovirus

-use reverse transcriptase enzyme to synthesize complementary ssDNA (cDNA) from +ssRNA template

-dsDNA integrated into host chromosome

-Intergrated viral genome called provirus

Persistent Viral infections

-not all eukaryotic infections kill the host cell quickly some can last for extended time

-Latent infections: viruses remain hidden in host cell after initial infection (ex. herpes simplex virus)

-chronic infections: occurs when host cannot successfully eradicate virus (ex. HIV becomes chronic after latency period)

Viral Life Cycle of Plants

-most similar two eukaryotic than prokaryotic viruses

-most have +ssRNA fgnomes

-host range can be broad or narrow

-usually transferred via insect of fungal mechanical vectors

Viroids

-small circular RNA molecules that infect plants and disrupt their growth

-self replicate

-virus like but not a virus

-no protein coating (Capsid)

- example: potato tuber spindle disease

virusoids

-Infectious agents composed only of single-stranded RNA. They are unable to replicate without the aid of specific viruses that coinfect the host cell.

-ex: subterranean clover mottle virus ( virus contains virusoid in capsid)

Prions

-not all infectious agents have genomic material

-misfolded rogue proteins that can cause others to become misfolded

-causative agents of transmissible spongiform encephalopathy (mad cow disease)

-transmitted btwn animals and then to humans by eating contaminated meet/feed

-transmitted human to human thought heredity

-difficult to destroy; no treatment

isolation of viruses

-Study of tobacco mosaic virus dates back to 1890s

-Dmitri Ivanovski used porcelain to filter out virus (Chamberland porcelain filters)

-Filters with 0.1 μm pores

-Filters are now used to remove all material except viruses from cell cultures

cultivating viruses

-Recall: viruses are intracellular pathogens

-Grown in vivo (in organism) orin vitro(outside organism)

-Can be bacterial or animal cell cultures

Viral Growth Curve (bacteriophage)

-Bacteriophages can be grown in dense layer of bacteria (bacterial lawn)

-four phases

1.Inoculation - virus causes infection

2.Eclipse - virus binds and penetrates (no virions detected)

3.Burst - virions released from lysed host cell

4.Burst size - number of virions released per bacterium

Importance of Animal Virus Cultures

-identification of viruses

-production of vaccines

-other virology research studies

Production of influenza vaccine

-Predictive analysis of next influenza strain is determined w/ bioinformatics

-Virus is genetically modified to become attenuated

-Grown in vivo from chicken/turkey embryo

In Vitro Growth

-primary cell line is obtained from desired tissue

-cells are grown in Petri dish to allow attachment

-mitosis is allowed to continue but limited

HeLA cell lines

-immortal cell line

-obtained from cervical cancer patient Henrietta Lacks in 1951

-cells still alive today

Viral Detection

1. effects on cells

2. hemagglutination assay

3. nucleic acid test

4. enzyme immunoassay

cytopathic effect (CPE)

- cell abnormalities due to viral infection•Loss of adherence

•Change of cell shape

•Shrinkage of nucleus

•Vacuoles formed

•Fusion of cytoplasmic membranes to form multiple nuclei

•Inclusion bodies

•Cell lysis (death)

•Other pathological changes include disruption of host genome and alteration of cells (carcinomas, sarcomas)

Hemagglutinin Assay (HA)

-detection of virus from patient serum

-observes clumping of red blood cells

-can be done without a microscope

-viruses attach to RBCs via spikes

Nucleic Acid Amplification Test

-detection of unique viral sequences

-polymearse chain reaction (PCR) for DNA

-reverse transcriptase PCR (RT-PCR) for RNA

Enzyme immunosorbent assay (EIA)

rapid enzyme immunochemical method for identifying the presence of antigens, antibodies, or other substances in the blood, used as a primary diagnostic test for many infectious diseases including syphilis and HIV; formerly called enzyme-linked immunosorbent assay (ELISA)

Eukaryotic microbes

-Fungi, Algae, Protozoa, Parasitic worms (helminths), lichens

-extremely diverse

-different life cycles and reproduction modes, many morphologically specialized structures, and specialized nutritional needs

Protozoa

-huge variety of unicellular, non-photosynthetic, motile eukaryotic microbes

-Life stages: 1.trophozoites (feeding and growing stages) 2.cysts (encapsulated stage to protect against harsh environments)

-reproduce asexually and sexually

-prominent groups: amoebozoa, excavata, and chromalveolata

Asexual

-binary fission, budding, or schizogeny

sexual

fusing of haploid gametes (syngamy) or conjugation (but different from bacteria)

Protozoa cell structures

-Plasmalemma - protozoan membrane

-Pellicle - membranes with bands of protein to provide rigidness

-Shape can also be created by outer gel-like layer (ectoplasm) and inside fluid in cytoplasm (endoplasm)

Protozoa feeding structures

-Cytostome - taking up food/nutrients;Cilia sweep food towards openings

-Holozoic protists - take in whole particles

-Saprozoic protists - take in smaller molecules

-Cytoproct - structure for exocytosis of waste

protozoa locomotive structures

-flagella and cilia (both made of microtubules)

-Pseudopodia - cytoplasmic extensions to attach cell to surface

protozoa unique organelles

-Contractile vacuoles - help regulate osmotic pressure

-mitochondria may be absent or modified: 1.kinetoplast: DNA bundles located by basal body of flagella 2.hydrogenosomes: to produce ATO without O2

Amoebozoa

-group of protists that have amoeba like movement thru pseudopodia

-Entamoeba histolytica - agent for amoebic dysentery

-Naegleria fowleri - causative agent for amoebic meningoencephalitis

-Acanthameoba spp. - causative agent for keratitis associated with contact lenses

Amoebozoa: Slime Molds

-Cellular slime molds - individuals can aggregate into a mobile "slug" and creates a fruiting body to produce haploid spores

-Plasmodial slime molds - large amoeboid cells with multiple nuclei; form reproductive stalks to produce spores

-Life cycle(cellular): 1.mature fruiting body generates spores 2. mature fruiting body releases spores 3. spore germinates 4.germination gives rise to amoeba that divide to form more individual cells 5.two amoebas fuse to form a zygote 6.zygote grows, undergoes meiosis, and several rounds of mitosis 7. new haploid amoebas are releases 8. amoebas aggregate into a structure called a slug 9. slug migrates at 2 mm per hour 10. migration stops, fruiting body forms at end of a stalk

-plasmodial life cycle: 1.sporangia formation begins 2. meiosis restores haploid condition 3.mature sporangium releases spores 4. spore germinates, this gives rise to cells that can convert btwn amoeboid and flagellated forms 5. plasmogamy: fusion of cytoplasm 6. karyogamy: fusion of nuclei

Chromalveolata

-the eukaryotic supergroup that contains the dinoflagellates, ciliates, the brown algae, diatoms, and water molds

-common characteristic is plastids (membrane bound organelle that often contain photosynthetic pigments)

-able to reproduce via conjugation

Ciliates

-use cilia to move and feed

-Balantidium coli: only pathogenic ciliate

-Paramecium: studied in bio labs

-Micro- & Macronucleus

-chromalveolata

Oomycetes (water molds)

-similar to fungi but have cell walls composed of cellulose and are generally diploid

-chromalveolata

-Phytophthorainfestans - potato blight

Apicomplexans

-chromalveolata

-Intra or extracellular parasites

-Apical complex - concentration of organelles, vacuoles, & microtubules that able them to establish infection

-life cycle - infective sporozoites undergo schizogeny

-Prominent Genera:

•Plasmodium spp. - infect a variety of animal cells; life-cycle between multiple hosts; e.g. malaria

•Cryptosporidium parvum - cysts contaminate drinking water and caused intestinal symptoms

Excavata

-most have depression on cell surface

-fornicata, parabasalia, and euglenozoa

Fornicata

-no mitochondria

-have flagella

-Giardia lamblia -agent for giardia disease obtained from contaminated waters; cysts are spread via feces

Parabasalia

-common endosymbionts to termites and cockroaches

-modified mitochondria (kinetoplast)

-Trichomonas vaginalis - agent for STD trichomoniasis

Euglenozoa

-photo & non-photosynthetic;

-Cells have two flagella, a stigma (eyespot), & chloroplast (if applicable)

-Generally non-pathogenic with exception: Genus Trypanosoma - agent for African sleeping sickness and Chagas disease.

Algae

-autothrophic protists

-multi or unicellular

-ecologically and economically important

-Chromalveolata: mostly marine, can be phototrophic, heterotrophic, or mixotrophic

~dinoflagellates: 2 flagella, theca: cellulose armor, some produce neurotoxins (red tide), paralytic shellfish poisonings

~stramenopiles: golden algae (chrysophytes), brown algae (phaeophytes), diatoms (ochraphytes): major produces of oxygen and silicon, frustules, diatomaceous earth

-archaeplastida:

~red algae: cell walls contain agar or carrageenan

~green algae: generally non-path, important in molecular bio research

-Exception: Prototheca spp. - causative agent of protothecosis, found in sewage and soil, infection is rare but possible, localized skin infections

Helminths

-multicellular parasitic organisms commonly called worms or flukes, posses organ systems

-have limited digestive tracts, nervous systems, and locomotion

-complex reproductive cycles and multiple life stages: monoecious; only one sex (both male and female organs), dioecious; either male or female

-groups: roundworms (phylum Nematoda) and flat worms (phylum Platyhelminthes)

Fungi

-many sizes, shapes, and forms

-heterothrophic and mostly saprophytic

-mycoses = illness caused by fungi

-chitin cell walls: ergosterol in membrane

-complex life cycles: seczual (cross or self fertilization) asexual (mitosis, budding, fragmentation of hyphae)

-dimorphic fungi: can appear as either yeast of mold

-ascomycota, basidiomycota, microsporidia, zygomycota