Microbial Classification and Identification Methods

Three Domains

Classification system by Woese based on rRNA sequences. (eukarya, bacteria, archaea)

what is common to all life

ribosomes

Eukarya

Domain including animals, plants, and fungi.

Bacteria

Domain consisting of prokaryotic microorganisms.

Archaea

Domain of prokaryotes with extreme environments.

Methanogens

Archaea producing methane in anaerobic conditions.

Extreme Halophiles

Archaea thriving in high-salt environments.

Hyperthermophiles

Archaea that live in extremely hot environments.

Prokaryotic Cells

Cells without a defined nucleus or organelles.

Eukaryotic Organelles

Membrane-bound structures within eukaryotic cells.

Endosymbiotic Theory

Eukaryotes originated from symbiotic prokaryotes.

Prokaryotic cell wall

contains peptidoglycan

eukaryotic cell wall

contains carbohydrates

Phylogenetic Tree

Diagram showing evolutionary relationships among organisms. (common ancestor)

endosymbiotic theory

a theory that states that certain kinds of prokaryotes began living inside of larger cells and evolved into the organelles of modern-day eukaryotes

Molecular Clock

Method using mutation rates to estimate evolutionary time.

stromatolites

Oldest known fossils formed from many layers of bacteria and sediment. (>2billion years)

Binomial Nomenclature

Two-part naming system for organisms, genus and species.

Taxonomic Hierarchy

System of classification from domain to species.

Prokaryotic Species

Population of cells with similar characteristics

eukaryotic species

a group of closely related organisms that breed among themselves

Culture

Bacteria grown in laboratory media for study.

Clone

Population derived from a single parent cell.

Strain

Genetically distinct cells within a clone.

Protista

Diverse kingdom of autotrophic and heterotrophic organisms.

clades

a group of organisms believed to have evolved from a common ancestor, according to the principles of cladistics.

Fungi

Chemoheterotrophic organisms with chitin cell walls. (uni/multicellular) develop from spores or hyphen fragments

Plantae

Multicellular organisms with cellulose walls, photosynthetic.

Animalia

Multicellular organisms lacking cell walls, chemoheterotrophic.

chemoheterotrophic

an organism that uses organic molecules as a source of carbon and energy

Viral Species

Population of viruses with similar characteristics that share ecological niches.

Bergey's Manual of Determinative Bacteriology

Reference for identifying bacteria and archaea.

transport media

used to maintain and preserve specimens that have to be held for a period of time before clinical analysis

morphological characteristics

useful for identifying eukaryotes; tells little about phylogenetic relationships

phylogenetic relationships

Connections between species based on evolutionary history.

Differential Staining

Techniques like Gram staining to identify bacteria with cell walls

Biochemical Tests

Tests determining presence of specific bacterial enzymes without cell walls

rapid identification methods

perform several biochemical tests simultaneously

automated rapid identification system

available for medically important bacteria and yeast

EnteroPluri Test

Rapid identification method for enteric bacteria.

Code Number

Unique identifier derived from test results.

Mass Spectrophotometry

Technique comparing cellular proteins to databases.

Serology

Study of serum and immune responses.

Antiserum

Solution of antibodies tested against unknown bacteria.

Slide Agglutination Test

bacteria agglutinate (clumping) when mixed with antibodies produced in response to the bacteria

serological testing

can differentiate between species and strains within species

Enzyme linked immunosorbent assay (ELISA)

Test using known antibodies to identify unknown bacteria.

Western Blotting

Technique to identify antibodies in patient serum. (ex. HIV, Lyme disease)

Electrophoresis

Separates proteins based on charge and size.

Phage

a type of virus that infects and kills bacteria. (to eat)

phage typing

test for identifying which phages a bacterium is susceptible to

Nitrocellulose Filter

Medium for transferring proteins from gel.

Antigen

Substance that induces immune response.

Fatty acid methyl esters (FAMEs)

provide profiles that are constant for a particular species

Flow Cytometry

Technique using electrical conductivity and fluorescence.

Fluorescence activated cell sorter (FACS)

A device that can count cells and sort them according to differences in fluorescence.

Plaques

Clearings on plates where phages lyse bacteria.

Antibody Reaction

Visible indication of antigen presence in tests.

Lysed Bacteria

Bacteria broken down for antigen detection.

Antihuman Antibodies

Antibodies tagged for detection in serological tests.

Gel Electrophoresis

Technique to separate proteins by size.

Patient Serum

Blood component used in serological testing.

Fluorescent-Antibody Markers

Labels specific antigens for detection in flow cytometry.

Laser Beam

Strikes droplets for cell identification in FACS.

Fluorescence Detector

Identifies cells based on emitted fluorescent light.

Electrically Charged Plates

Directs positively charged cells towards negative plate.

Collection Tubes

Holds separated cells post-sorting in FACS.

DNA Sequencing

Determines base composition of DNA samples.

Online Databases

Resources like NCBI for genomic information.

DNA Fingerprinting

Analyzes DNA fragments for genetic comparison.

Nucleic Acid Hybridization

Measures DNA strand hybridization between organisms.

Hybridization Degree

Indicates relatedness based on DNA strand pairing. (greater degree of hybrid =greater degree of relatedness)

Nucleic acid amplification tests (NAATs)

a lab test that looks for DNA or RNA from a virus or bacteria by making lots of copies of it so it can be easily detected

Southern Blotting

Identifies microorganisms using DNA probes.

DNA Probe

Labeled DNA fragment used for hybridization detection.

DNA Chip (Microarray)

a small, flat surface with thousands of DNA probes attached that can be used to detect specific DNA or RNA sequencesin a sample all at once.

Ribotyping

Uses rRNA sequencing for microbial identification.

Fluorescent in situ hybridization (FISH)

uses fluorescently labeled DNA probes to find and visualize specific DNA or RNA sequences directly inside cells or tissues under a microscope.

Dichotomous Keys

Identification keys based on successive questions.

Cladograms

Maps showing evolutionary relationships among organisms.