Microbial Taxonomy, Identification, and Classification Methods

What is taxonomy?

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

What are the three interrelated areas of taxonomy?

Identification, classification, and nomenclature.

What is the process of identification in microbiology?

Characterizing microorganisms in order to group them.

What is classification in microbiology?

Arranging organisms into similar or related groups.

What does nomenclature refer to in taxonomy?

The system of assigning names to organisms.

What are some strategies used to identify microorganisms?

Microscopic examination, culture characteristics, biochemical tests, nucleic acid analysis, and patient symptoms.

What is point-of-care testing (POCT)?

Testing done at or near the site of patient care, such as a Rapid Strep Test.

What is phylogeny in the context of classifying microorganisms?

The consideration of evolutionary relatedness among organisms.

What is the basic unit of classification in prokaryotes?

Species, defined as a group of closely related isolates or strains.

How can species be further divided?

Species may be divided into subspecies, such as E. coli K-12 and E. coli O157:H7.

What are some informal groupings used for microorganisms?

Lactic acid producers, anoxygenic phototrophs, endospore-formers, and sulfate reducers.

What is the order of taxonomic hierarchies from most specific to least specific?

Species, genus, family, order, class, phylum, kingdom, domain.

What does the three-domain system of classification reflect?

Cell characteristics based on nucleotide sequences in rRNA.

What does Bergey's Manual of Systematic Bacteriology describe?

All known prokaryotic species and classifies them according to genetic relatedness.

What is the purpose of the International Code of Nomenclature of Prokaryotes?

To provide rules for naming bacteria and archaea, ensuring consistency in bacterial taxonomy.

What is the significance of Gram staining in microbiology?

It distinguishes between Gram-positive and Gram-negative bacteria, aiding in diagnosis and treatment.

What can culture characteristics reveal about microorganisms?

They can provide clues to the identity of the organism, such as color or odor of colonies.

What is a differential media in microbiology?

A culture medium that aids in the identification of microorganisms based on their growth characteristics.

What does a catalase test indicate?

A positive result shows oxygen bubbles after adding hydrogen peroxide to a colony.

How does sugar fermentation affect pH in biochemical tests?

It lowers pH and may trap gas in an inverted tube.

What is the role of urease in biochemical tests?

It raises pH by converting urea into carbon dioxide and ammonia.

What is a dichotomous key in biochemical testing?

A series of alternative choices used to identify organisms based on their biochemical characteristics.

What is the role of urease in detecting Helicobacter pylori?

Urease breaks down urea into CO2, which can be detected in breath tests.

What is the purpose of commercial kits like API in microbial identification?

They allow rapid identification via biochemical tests, requiring an incubation period.

How does serological testing identify specific microorganisms?

It uses antibodies to detect specific proteins or polysaccharides on prokaryotic cells.

What are the key surface structures used in serological testing?

Cell wall, capsule, flagella, and pili.

What is the significance of the 16S rRNA in microbial identification?

It provides a stable sequence for comparison and identification of microbes.

What is the function of MALDI-TOF Mass Spectrometry in microbial identification?

It measures the masses of various components to create protein 'fingerprints' for rapid identification.

What are nucleic acid probes used for in microbial identification?

They locate nucleotide sequences characteristic of specific species or groups.

What is the purpose of nucleic acid amplification tests (NAATs)?

To increase the number of copies of specific DNA sequences for detection.

What is Whole Genome Sequencing (WGS) and its significance?

WGS detects subtle differences among strains and has replaced older methods like RFLP.

What is the role of PulseNet in tracking foodborne outbreaks?

It is a CDC network that collects WGS data from foodborne pathogens.

How does phage typing work in microbial identification?

It relies on differences in susceptibility to bacteriophages, forming clear areas on agar plates.

What is an antibiogram?

A test revealing differences in bacterial susceptibility to antimicrobial medications.

What are the limitations of phenotypic methods in microbial classification?

They may not accurately reflect genetic relatedness among organisms.

How is DNA-DNA hybridization used to determine relatedness of organisms?

By measuring how completely single strands of DNA hybridize, indicating sequence similarity.

What does a G + C content analysis indicate about organisms?

If G + C content differs significantly, the organisms are not related.

What is the average nucleotide identity (ANI) and its use?

A measure calculated by comparing shared genes of genome sequences to assess relatedness.

Why are ribosomal RNA comparisons important in microbial classification?

They provide reliable indicators due to the crucial and constant functions of ribosomes.

What is the significance of using environmental samples in microbial identification?

They can be amplified by PCR without the need for culturing the organisms.

What does the term 'biovar' or 'biotype' refer to in microbial classification?

Groups of organisms with characteristic biochemical patterns.

What distinguishes E. coli O157:H7 from other E. coli strains?

It is distinguished by its specific antigenic types of flagella and lipopolysaccharides.

What is the role of fluorescence in situ hybridization (FISH) in microbial identification?

It uses probes for 16S rRNA to identify specific microorganisms without amplification.

What is the importance of characterizing strain differences in microbiology?

It is crucial for foodborne illness investigations, forensic studies, and disease diagnosis.

How do random mutations contribute to microbial classification?

They accumulate over time and can be used to construct phylogenetic trees.

What is the significance of ribosomal genes in microbial classification?

They are stable and not commonly transferred, making them reliable for classification.

What is the limitation of using SSU rRNA for species-level identification?

Closely related prokaryotes can have identical SSU rDNA sequences, making differentiation difficult.

What is the estimated number of bacterial species described by scientists?

Approximately 6,000 out of an estimated 1 million species.

What role do final electron acceptors play in prokaryotic metabolism?

They are necessary for the oxidation of NADH back to NAD+, allowing glycolysis to continue and ATP to be produced.

How do methanogens influence the carbon cycle?

They produce methane as a byproduct of using hydrogen for energy and carbon dioxide as an electron acceptor.

What is the primary energy source for anaerobic chemoorganotrophs?

They oxidize organic compounds, such as glucose, to obtain energy.

What are the byproducts of anaerobic fermentation?

Various organic compounds, with low ATP yield produced only by substrate-level phosphorylation.

What type of environments do anaerobes dominate?

Oxygen-free habitats such as sediments, the gut, and deep subsurface areas.

What distinguishes lactic acid bacteria from other bacteria?

They are Gram-positive and produce lactic acid as a product of fermentation.

What is the role of Clostridium species in food safety?

They are common fermenters linked to food spoilage and safety issues, causing conditions like tetanus and botulism.

What is the significance of sulfate-reducing bacteria in anaerobic environments?

They use sulfate as an electron acceptor and produce hydrogen sulfide, contributing to sulfur cycling.

What are the characteristics of cyanobacteria?

They are photosynthetic bacteria that can fix nitrogen and are important in aquatic environments.

What are the ecological roles of nitrifiers?

They play a key role in the nitrogen cycle by oxidizing ammonia to nitrite and then to nitrate.

How do extreme halophiles adapt to their environment?

They thrive in high-salinity environments and have specialized mechanisms to maintain osmotic balance.

What are the habitats of extreme thermophiles?

They inhabit extremely hot environments, such as hot springs and hydrothermal vents.

What is the significance of facultative anaerobes?

They can switch between aerobic and anaerobic metabolism, allowing them to thrive in varying oxygen conditions.

What distinguishes coliforms from other members of the Enterobacteriaceae family?

Coliforms are a subgroup of Enterobacteriaceae that can ferment lactose and are commonly found in the intestines of warm-blooded animals.

What is the role of Agrobacterium species?

They are known for their ability to transfer DNA to plants, causing tumor formation.

How do bacteria in aquatic environments obtain and store nutrients?

They utilize various mechanisms such as nutrient uptake from the surrounding water and storage in intracellular granules.

What are the implications of hydrogen sulfide (H2S) production by sulfate-reducing bacteria?

H2S is corrosive to metals and is associated with health issues such as IBS and colorectal cancer.

What is the importance of anaerobic chemolithotrophs in the carbon cycle?

They oxidize inorganic molecules for energy and play a major role in greenhouse gas emissions.

What are the common genera of lactic acid bacteria used in food production?

Streptococcus, Lactococcus, Enterococcus, and Lactobacillus.

What process converts lactic acid into propionic acid?

Lactic acid is converted into propionic acid, CO2, and H2O.

What gives Swiss cheese its nutty flavor?

Propionic acid.

What gas forms bubbles in Swiss cheese, creating holes?

CO2.

What are anoxygenic phototrophs?

Photosynthetic organisms that do not produce O2 as a waste product, using H2S or organic compounds for electrons.

Where do modern anoxygenic phototrophs typically live?

In low O2 environments where light can penetrate, such as bogs and lakes.

What are the two main groups of purple bacteria?

Purple sulfur bacteria and purple non-sulfur bacteria.

What is a key characteristic of purple sulfur bacteria?

They prefer H2S as an electron donor and play a major role in the sulfur cycle.

What distinguishes purple non-sulfur bacteria from purple sulfur bacteria?

They prefer organic compounds as electron donors and lack gas vesicles.

What is a unique feature of green bacteria?

They contain chlorosomes, specialized light-harvesting structures adapted for low-light environments.

What are cyanobacteria known for?

They are the earliest oxygenic phototrophs and introduced O2 into the atmosphere around 3 billion years ago.

What role do nitrogen-fixing cyanobacteria play in the ecosystem?

They convert N2 and CO2 into organic material, which is critical for other organisms.

What are nitrifiers and what do they oxidize?

Nitrifiers oxidize inorganic N2 compounds, such as ammonium or nitrite, for energy.

What are the two groups of nitrifiers?

Ammonium oxidizers (e.g., Nitrosomonas) and nitrate oxidizers (e.g., Nitrobacter).

What defines obligate aerobes?

They cannot ferment and must use O2 as a terminal electron acceptor.

What are some characteristics of Micrococcus?

They are found in soil and dust, have pigmented colonies, and tolerate dry conditions.

What is a notable pathogen from the Mycobacterium genus?

M. tuberculosis, which causes tuberculosis.

What is the significance of Pseudomonas in the environment?

Most are harmless, but some, like P. aeruginosa, are opportunistic pathogens.

What defines facultative anaerobes?

They prefer to use O2 but can also ferment when O2 is not available.

What is the role of Corynebacterium in human health?

Many are harmless, but C. diphtheriae causes diphtheria.

What are enterics and where are they found?

Gram-negative rods found in the intestinal tract, including normal microbiota and pathogens.

What is the significance of Vibrio species?

They are found in marine water and include pathogens like V. cholerae, which causes cholera.

What challenges do bacteria face in terrestrial environments?

They must adapt to varying conditions such as wet and dry, warm and cold, and nutrient availability.

What are myxobacteria known for?

They can form a resting stage (endospores) to survive unfavorable conditions.

How do sheathed bacteria obtain nutrients?

They have evolved mechanisms to obtain and store sparse nutrients in aquatic environments.

What is Legionella and its significance?

Legionella is a Gram-negative obligate aerobe that can cause respiratory disease and often resides in water systems.

What are obligate intracellular parasites?

Bacteria that cannot reproduce outside a host cell and rely on the host for essential compounds.

What is a notable example of an obligate intracellular parasite?

Rickettsia rickettsii, which causes Rocky Mountain Spotted Fever.

What are the general features of viral structure?

Viruses consist of genetic information (DNA or RNA) within a protective protein coat called a capsid, which is composed of identical subunits known as capsomeres.

How are viruses classified and named?

Viruses are classified based on the type of cell they infect: eukaryotic viruses infect eukaryotic cells, while bacteriophages (or phages) infect prokaryotic cells.

What is a virion?

A virion is any viral particle outside the cell, consisting of nucleic acid surrounded by a capsid.

What is the difference between enveloped and non-enveloped viruses?

Enveloped viruses have a lipid bilayer obtained from the host cell, while non-enveloped (naked) viruses lack this lipid layer and are more resistant to disinfectants.

What are the steps of a generalized infection cycle of animal viruses?

The steps include attachment, penetration, uncoating, replication, assembly, and release.

What are the two types of persistent infections caused by animal viruses?

The two types are chronic infections, where the virus is continuously present, and latent infections, where the virus remains dormant and can reactivate.