Microbio Exam 3

phenotype identification- microscope morphology

important initial step. Quickly determines size shape, staining characteristics. Sometimes enough to diagnose eukaryotic infections Gram stain distinguishes between Gram-positive and Gram-negative bacteria Result may be enough to start appropriate therapy Special stains may help with identification Acid-fast stain may help identify Mycobacterium tuberculosis

Crynebacterium blutamicum

makes large amount of glutamate so used industrically as food supplement

if bacteria have the same 16S ribosome sequence, are they the same?

not always

anaerobic chemotrophs

Atmosphere anoxic for first approximately 1.5 billion years that prokaryotes inhabited Earth Early chemotrophs likely used anaerobic respiration- Terminal electron acceptors likely abundant CO_2 or S. Others may have used fermentatio- Passed electrons to organic molecule like pyruvate

obligate anaerobes that cannot ferment

Micrococcus: Gram-positive cocci Found in soil, dust particles, inanimate objects, skin Pigmented colonies Tolerate dry, salty conditions

Ecophysiology

Study of the adaptations of physiological mechanisms that prokaryotes use to live in terrestrial and aquatic environments As a group, prokaryotes show remarkable diversity in their physiological adaptations to a wide range of habitats, including the bodies of animals.

pulsenet

makes it easier to use RFLP data to track foodborne disease outbreaks Established by CDC Labs can submit RFLP patterns to database and quickly receive information about other isolates

DNA hybridization

relatedness of organisms determined by similarity of nucleotide sequences. Measured by how completely single strands of their DNA hybridize with each other. Extent of hybridization reflects degree of similarity. Bacterial strains with over 70% similarity are considered members of the same species. Shigella and Escherichia would be grouped in same species based only on DNA hybridization

Basic strategy for identification using biochemical tests

relies on dichotomous key- Series of alternative choices. Simultaneous tests speed process and provide more conclusive results Some tests accomplished without culturing (breath test to assay urease and identify Helicobacter pylori)

phage typing

relies on differences in susceptibility to bacteriophages (phages) Susceptibility pattern determined by adding different bacteriophage suspensions to agar plate growing bacteria If phage lyses cells, a clear area forms Largely replaced by molecular methods, but still useful in labs lacking equipment for molecular typing

antibiograms

reveal differences in susceptibility to antimicrobial medications Bacteria grown on agar plate Discs containing different antimicrobials placed on agar If cells are susceptible, a clear area forms Largely replaced by molecular methods

Which bacterial genus is a prolific producer of antibiotics?

streptomyces

taxonomy

the science that characterizes and names organisms to arrange them into hierarchical groups (taxa)

Current classification

three-domain system based on nucleotide sequences in rRNA Replaces Whittaker's five-kingdom system (1969)

Facultative anaerobes

use aerobic respiration, but can ferment if O_2 is not available

genotype identification- Nucleic acid amplification tests (NAATs)

used to increase number of copies of specific DNA sequences. Allows detection of small numbers of organisms. Often from body fluids, soil, food, water. Detection of organisms that cannot be cultured. Polymerase chain reaction (PCR) is common technique

molecular typing

uses differences in DNA sequences to distinguish strains. Cut DNA samples with same restriction enzyme. Separate via gel electrophoresis Patterns called restriction fragment length polymorphisms (RFLPs) Different RFLPs indicate different strains

biochemical typing

Group with characteristic pattern: biovar, or biotype. Can trace Vibrio cholerae El Tor.

bacteriophages (phages)

viruses that infect bacteria. Easy to grow in the lab as a good model for how animal viruses interact with their hosts. Vehicle for horizontal gene transfer. Their ability to kill bacteria is important ecologically and medically

three separate but interrelated areas

Identification- Process of characterizing in order to group Classification- Arranging organisms into similar or related groups Nomenclature- System of assigning names

today anaerobic habits common

Aerobes contribute by depleting O_2 Mud, tightly packed soil limit diffusion of gases Aquatic environments can become limiting Human body (especially intestinal tract) Anaerobic microenvironments in skin, oral cavity

phenotype identification- Metabolic capabilities revealed by biochemical tests

Catalase test: positive if O_2 bubbles are seen after H_2 O_2 is added to colony on microscope slide Many tests rely on pH indicators Sugar fermentation lowers pH and may trap gas in inverted tube Urease raises pH

bacteria in the intestinal tract

Clostridium, Enterobacteriaceae

Comparisons of rRNAs revolutionized classification

Comparisons of rRNAs revolutionized classification Small subunit (SSU) RNAs most useful rDNAs that encode rRNAs used due to ease of DNA sequencing methods Culturing not necessary Environmental samples may be amplified by PCR May not resolve at species level because closely related prokaryotes can have identical SSU rDNA sequences DNA hybridization a better tool in these cases Analysis of ribosomal proteins accounts for novel organisms; more gene products compared

Serological Typing

E. coli distinguished by antigenic type of flagella, capsules, lipopolysaccharide molecules E. coli O157:H7 (O antigen is lipopolysaccharide; H antigen is flagella) Group with characteristic antigens: serovar, or serotype

bacteria Genitourinary system

Lactobacillus (vagina)

anerobic chemotrophs- Anaerobic Chemoorganotrophs—Fermentation

Numerous anaerobic bacteria ferment- ATP via substrate-level phosphorylation, Many different organic energy sources, end products. Clostridium are Gram-positive, endospore-forming rods- common in soils; vegetative cells live in anaerobic microenvironments created by aerobes consuming O_2. Endospores tolerate O_2, survive long periods of heat, drying, chemicals, irradiation- Germinate when conditions improve. Diverse metabolism; some cause diseases

Which of the following would typically NOT be a common, abundant inhabitant of the human gut

Porphyromonas

new molecular techniques are more accurate

Provide relative measure of time elapsed since divergence from common ancestor Random mutations accumulate over time DNA sequencing allows construction of phylogenetic tree

Phenotypic methods have been largely replaced by methods that rely on DNA sequence data

Some taxonomists believe classification should be based on more than just genotypic traits Phenotypic methods still important since provide foundation for microbial identification

bacteria in Respiratory system

Streptococcus, Corynebacterium

how many base pairs can sanger sequencing reliable sequence?

about 800 base pairs

Myxobacteria

aerobic Gram-negative rods with unique developmental stage and resting form. Favorable conditions: secrete slime layer, form swarm. Nutrients depleted: cells congregate into fruiting body- Cells differentiate, form dormant microcysts (resist heat, drying, radiation). Degraders of complex organic substances. Model for studying developmental biology

whole genome sequencing

can trace outbreaks caused by closely related stains. Genome Trakr established by FDA Network of labs that use WGS data for tracking outbreaks

Obligate Intracellular Parasites

cannot reproduce outside a host cell: host cells supply compounds they would otherwise need to synthesize. Most have lost ability to synthesize needed substances. Multiple bacterial examples; tiny Gram-negative rods or coccobacilli

Three-domain system expanded by

comparing amino acid sequences of ribosomal proteins- Shows many bacteria not grown in culture

phylogeny

considers evolutionary relatedness

Magnetotactic bacteria

contain a string of magnetic crystals that align cells with Earth's magnetism. Allows movement up or down in water or sediments. Likely allows location of their required microaerophilic habitats Magnetospirillum are Gram-negative; spiral-shaped

Bergey's Manual of Systematic Bacteriology

describes all known prokaryotic species, newest edition in five volumes- classifies according to genetic relatedness (phylogeny), provides info on ecology, methods of enrichment, culture and isolation, and methods for maintenance

Enterobacteriaceae

enterics or enterobacteria- Gram-negative rods found in intestinal tract of humans, other animals; some thrive in soil. Normal intestinal microbiota include Enterobacter, Klebsiella, Proteus, most E. coli strains. Diarrheal disease caused by Shigella, Salmonella enterica, and some E. coli strains. Life-threatening: typhoid fever (Salmonella enterica serotype Typhi) and bubonic and pneumonic plague (Yersinia pestis). Facultative anaerobes that ferment glucose. Lactose fermenters termed coliforms- Include E. coli, Indicator of possible fecal pollution. Been research suggesting that when the "normal intestinal microbiota" bloom, it can cause issues such as IBS or Crohns but everyone has low levels of it in their system

Deinococcus

extraordinarily radiation resistant- Dose shatters genome into many fragments, yet enzymes repair damage- Scientists hope to genetically engineer species to help clean up radioactive wastes- Stain Gram-positive

Genus Vibrio

facultative anaerobes- found in marine environments, require some Na^+ for growth Gram-negative straight or slightly curved rods Pathogens include V. cholerae, which causes cholera. Some are bioluminescent. Some vibrio associated with marine organisms ability to light up- how quorum sensing was discovered

corynebacterium

facultative anaerobes. Gram-positive pleomorphic rods- Wide-spread, Often club-shaped and form V shapes or palisades. Referred to as coryneforms or diphtheroids. Generally facultative anaerobes; some strict aerobes. Many harmless in normal microbiota- C. diphtheriae causes diphtheria

why characterizing different strains is important

foodborne illnesses, forensic investigations of bioterrorism or bio-crimes, diagnosis certain diseases

Sequencing a short part of the 16S rRNA gene (35 bp) is enough information to identify at what level?

genus?

spirochetes

group of Gram-negatives with spiral shape and flexible cell wall. or axial filament contained within periplasm at each end of the cell allow corkscrew-like motion. Can move through viscous environments like mud. Spirochaeta live in muds, anaerobic waters. Leptospira are aerobes; some free-living, others inhabit animals- L. interrogans causes leptospirosis

Bacteroides are most commonly found in which human microbiome?

gut

Which of the following human microbiome has the greatest diversity?

gut by far then mouth then vagina and skin tied for third/last

Bdellovibrio

highly motile Gram-negative curved rods Prey on E. coli and other Gram-negatives Strikes forcefully; prey propelled short distance Parasite attaches, rotates, secretes digestive enzymes; forms hole in cell wall of prey Parasite divides while attached; daughter cells released when host cell lyses

Thermus and Deinococcus

obligate anerobes. related genera with unusual cell walls

streptomyces

over 500 species of aerobic Gram- positive bacteria. Growth resembles fungi: form mass of branching hyphae called mycelium. Chains of spores (conidia) develop at tips. Conidia resistant to drying; easily spread by air currents. Produce extracellular enzymes, geosmins, and medically useful antibiotics including streptomycin, tetracycline, erythromycin

Aerobic chemoorganotrophs

oxidize organic compounds for energy Use O_2 as terminal electron acceptor Some inhabit specific environments, others ubiquitous

G+C Content

percentage of G-C base pairs in DNA. If G+C content differs by more than a few percent, organisms are not related. similarity of G+C does not guarantee relatedness. DNA with higher G+C content melts at a higher temperature due to 3 hydrogen bonds between the bases

Classification historically based on

phenotypic traits- Size, shape, staining, metabolic capabilities. But phenotypically similar organisms may be only distantly related; conversely, closely related organisms may appear dissimilar

Anaerobic Chemoorganotrophs—Fermentation Lactic Acid Bacteria

produce lactic acid. Most can grow in aerobic environments; lack catalase so they only ferment Streptococcus inhabit oral cavity; normal microbiota. Some pathogenic (for example, β-hemolytic S. pyogenes). S. thermophilus used to make yogurt. Lactococcus species used to make cheese. Enterococcus inhabit human, animal intestinal tract. Lactobacillus rod-shaped, common in mouth, vagina- Break down glycogen deposited in vaginal lining so resulting low pH helps prevent infection, also present in decomposing materials and important in production of fermented foods.

international code of nomenclature of bacteria

provides rules for naming bacteria and archea- less than 97% identical considered new species

Which of the following would NOT be a common inhabitant of the human oral microbiome?

Akkermansia (muncin in intesitines) not found in mouth but streptococcus, treponema (unique spiricite found in mouth not thought to be pathogenic like syphilis and lymes disease species), aggregatibacter and tannarella found in mouth

What species is most abundant in human microbiome?

Bactaroidies and clostrialies species- high diversity is good

bacteria found in gut

Bacteroides, Clostrididales, Lachnospiracea, Rumminococcus, Blautia, Holdemania, Roseburia, Blautia, Akkeramensia, Faecalibacterium, Enterobacteriaceae

Coxiella

C. burnetii is only characterized species Obligate intracellular bacterium; can survive outside host cell as spore-like structures called small-cell variants (SCVs) formed during intracellular growth Not as resistant as endospores to heat, disinfectants C. burnetii causes Q fever; most often acquired by inhaling bacteria shed from infected animals

Legionella

Gram-negative obligate aerobe. Use amino acids, but not carbohydrates, as source of carbon and energy. Common in aquatic environments; also found in water from air conditioners, and in produce misters. Often reside in protozoa L. pneumophila can cause respiratory disease when inhaled in aerosolized droplets

Rhizobia

Gram-negative rods that often fix nitrogen and form relationships with legumes. Includes Rhizobium, Sinorhizobium, Bradyrhizobium, Mesorhizobium, Azorhizobium. Live as endosymbionts in nodules on roots of legumes Plants synthesize leghemoglobin, which binds and controls O_2 levels to yield microaerobic conditions. Allows bacteria to fix nitrogen

agrobacterium

Gram-negative rods. Can genetically alter plants for their own benefit. Ti plasmid of A. tumefaciens is transferred through wounded plant tissue Transferred DNA encodes ability to synthesize plant growth hormone; results in plant tumor. Also encodes synthesis of unusual amino acid derivative, an opine. Agrobacterium use opine as nutrient

obligate aerobes- Pseudomonas

Gram-negative rods; polar flagella; often produce pigments. Most are strict aerobes; no fermentation; oxidase positive. Extreme metabolic diversity important in degradation- ability sometimes from plasmids. Widespread: soil, water Most harmless but some pathogens: P. aeruginosa common opportunistic pathogen

Neisseria species

Gram-negative, typically kidney bean-shaped cocci found in pairs. Common microbiota of animals, humans; grow on mucous membranes Typically strict aerobes; some grow anaerobically N. gonorrhoeae (gonorrhea), N. meningitidis (meningitis) medically important. Nutritionally fastidious

Epulopiscium

Gram-positive cigar-shaped bacteria Live in intestinal tract of surgeonfish Much larger than most prokaryotes (600×80 micrometer) Thousands of copies of the chromosome are scattered within the cell and allow protein synthesis throughout Instead of binary fission, they enlarge considerably and then lyse to release up to seven daughter cells

Anaerobic Chemoorganotrophs—Fermentation Propionibacterium

Gram-positive pleomorphic rods- produce propionic acid via fermentation, Can also ferment lactic acid, Important in dairy industry: Swiss cheese for Typical nutty flavor and CO_2 creates signature holes

Informal groupings also used for microorganisms

May share phenotype and physiology, but are not genetically unrelated Lactic acid bacteria Anoxygenic phototrophs Endospore-formers Sulfate reducers

strategies used to identify bacteria

Microscopic examination Culture characteristics Biochemical tests Nucleic acid analysis Patient symptoms (for pathogens)- Identification may be more important than determining evolutionary relationshipso

obligate anaerobes

Mycobacterium are acid-fast bacteria Mycolic acid in cell wall prevents Gram-staining; acid-fast staining used Related Nocardia species also acid-fast Generally pleomorphic rods Many saprophytes, living on dead and decaying matter Notable pathogens: M. tuberculosis, M. leprae More resistant to disinfectants, often resistant to antimicrobial drugs

Chlamydia, Chlamydophila

Obligate Intracellular Parasite. transmitted person to person; unique growth cycle. Inside host initially as non-infectious reticulate bodies. Reproduce by binary fission. Later, differentiate into dense-appearing infectious elementary bodies. Released when cell ruptures. Chlamydia trachomatis causes eye infections and STI similar to gonorrhea. Chlamydophila species cause types of pneumoniaf

Rickettsia, Orientia, Ehrlichia

Obligate Intracellular Parasites. include species responsible for several serious arthropod-transmitted human diseases R. rickettsii (Rocky Mountain spotted fever) R. prowazekii (epidemic typhus) O. tsutsugamushi (scrub typhus) E. chaffeensis (human ehrlichiosis)

sequence analysis of ribosomal components

Reliable indicators because ribosomes perform crucial and functionally constant tasks in all organisms Only a limited number of mutations can be tolerated Some sequences will be similar even if organisms diverged long ago Ribosomal genes are not commonly horizontally transferred

diversity of prokaryotes

Scientists just beginning to understand vast diversity of microbial life Only a fraction of over a million species of prokaryotes described Vast majority have not been isolated New molecular techniques aiding in discovery, characterization

genotype identification- Sequencing Ribosomal RNAs (rRNAs) or the DNA that encodes them (rDNA)

Sequences relatively stable. 16S rRNA most useful because of moderate size. Approximately 1,500 nucleotides. Sequence compared with extensive databases. Can identify organisms thatcannot be grown in culture

phenotype identification- culture characteristics can give clues

Serratia marcescens colonies often red at 22 degrees Celsius. Pseudomonas aeruginosa often produces green pigment- cultures also have distinct fruity odor. Differential media aids in identification- Streptococcus pyogenes (strep throat) yields β-hemolytic colonies on blood agar E. coli (urinary tract infection) ferments lactose, forms pink colonies on MacConkey agar

phenotype identification- commercial kits

allow rapid identification via biochemical tests Require incubation period Pattern of results is scored and a computer identifies the organism

viruses

are genetic information — DNA or RNA — contained within protective protein coat. Inert particles: no metabolism, replication, motility. Genome hijacks host cell's replication machinery Inert outside cells; inside, direct activities of cell. Infectious agents, not organisms. Viruses require live organisms as hosts; cannot be grown in pure culture. Cannot be seen with light microscopy. Classified generally based on type of cell they infect: eukaryotic or prokaryotic

Endospore-formers

are most resistant to environmental extremes. Bacillus, Clostridium are most common. Gram-positive rods. Clostridium species are obligate anaerobes. Bacillus include obligate and facultative anaerobes. Both can cause disease: C. tetani causes tetanus; B. anthracis causes anthrax

thermus

are thermophilic, valuable for their heat-stable enzymes. Stain Gram-negative. Particularly stable in environmental conditions. Thermus aquaticaus- taq enzyme derived from

Bioluminescent bacteria

emit light. Symbiotic relationships with certain fish, squid. Help with camouflage, confuse predators and prey. Luminescence catalyzed by enzyme luciferase. Luciferase controlled by quorum sensing (used in 454 sequencing). Gram-negative straight or curved rods, facultative anaerobes, marine environments.

Bifidobacterium

inhabit mucous membrane. Gram-positive irregular rods. Anaerobes; reside primarily in intestinal tract of humans and other animals. Most common members of intestinal microbiota of breast-fed infants; thought to exclude pathogens

Bordetella

inhabit mucous membrane. small, Gram-negative coccobacilli. Aerobic. Nutritionally fastidious. B. pertussis causes whooping cough in humans B. bronchiseptica causes "kennel cough" in dogs

Bacteroides

inhabit mucous membranes. Gram-negative rods and coccobacilli. Small; strict anaerobes that inhabit mouth, intestinal tract, genital tract of humans and other animals. Important in digestion. Make up approximately one third of bacteria in human feces. May be responsible for abscesses and bloodstream infections following abdominal surgery

Treponema

inhabit mucous membranes. Gram-negative spirochetes. are obligate anaerobes or microaerophiles; often inhabit mouth, genital tract. T. pallidum causes syphilis, has never been cultured

Borrelia

inhabit mucous membranes. Gram-negative spirochetes. includes three pathogens, transmitted by arthropods such as ticks and lice B. recurrentis and B. hermsii cause relapsing fever B. burgdorferi causes Lyme disease Borrelia genome is linear chromosome and many linear and circular plasmids

mycoplasma

inhabit mucous membranes. lack cell wall Most have sterols for added strength and rigidity Among smallest forms of life; genomes thought to be minimum size encoding essential functions Colony growth produces characteristic "fried egg" appearance. M. pneumoniae causes walking pneumonia;" antibiotics that target peptidoglycan synthesis not effective

Campylobacter and Helicobacter

inhabit mucous membranes. microaerophilic Gram-negative curved rods C. jejuni typically lives in intestinal tract of poultry- Causes diarrhea in humans H. pylori causes ulcers- Produces urease, which breaks down urea to ammonia to neutralize local pH

Haemophilus

inhabits mucous membranes. Gram-negative coccobacilli. "Blood-loving": require hematin and/or NAD, both of which are found in blood Many are common microbiota of respiratory tract H. influenzae causes ear infections, respiratory infections, meningitis. H. ducreyi causes the STI chancroid

species

is basic unit: in prokaryotes, a group of closely related isolates or strains. Difficulty is determining separate species or separate strains within a species. Species may be divided into subspecies

microorganisms that live in soil

must tolerate a variety of conditions. Wet and dry, warm and cold, abundant to sparse nutrients. Several genera form structures that help them to survive dry periods. Clostridium, Bacillus, Azotobacter, Myxobacteria, Streptomyces. Two genera have unique means to obtain nutrients from plants- Agrobacterium, Rhizobium

Azotobacter

species are Gram-negative pleomorphic rods. Form resting cell called a cyst. Withstand drying and UV radiation, but not high heat. Fix nitrogen in aerobic conditions. High respiratory rate maintains low O_2 in cell. Protein binds nitrogenase, protects from O_2 damage

Staphylococcus

species inhabit the skin. Skin typically dry, salty; inhospitable to many microbes. Staphylococcus are Gram-positive cocci. Facultative anaerobes; catalase-positive. Most are harmless normal microbiota- S. epidermidis. Some are medically important- S. aureus (skin and wound infections; food poisoning), S. saprophyticus (urinary tract infections)

genotype identification- detecting specific nucleotide sequences

tests can identify sequences unique to species or group- nucleic acid probes, nucleic acid amplification tests (NAATs), limitation is each only detects single possibility, need to run multiple probes if organism being tested could be one of multiple different species or related groups- most often 16S used.Nucleic acid probes locate nucleotide sequence characteristic of species or group. Most methods first increase DNA in sample Inoculation on agar or in vitro DNA amplification Fluorescence in situ hybridization (FISH) probes for 16S rRNA. Amplification step not needed Signature sequence characterizes certain group

One way of defining whether two bacteria belong to the same species is if...

they have a 16S rRNA sequence greater than 97% identical