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3 distinct but highly interrelated disciplines of Taxonomy

- Classification


- Nomenclature (naming)


- Identification of organisms

Provides a consistent means to classify, name and identify organisms

Taxonomy

- Consistency allows biologists to use common label for every organism studied


- Common language that taxonomy provides minimizes confusion about names

Evolutionary history of organisms

Phylogeny

Taxonomy is important not only in phylogeny but also in virtually every other biologic discipline, including microbiology


This method of classification combines the traditional


- genotypic


- phenotypic, and


- phylogenetic or evolutionary relationships


into a general purpose classification system


Classic/Polyphasic Taxonomy

At the molecular level this process is multifaceted, using


- ribosomal ribonucleic acid (rRNA) sequences


- whole genome sequences


- epigenetic (variations not caused by nucleic acid sequence similarities or difFerences) factors


Provides a more detailed but very complex analysis of the current classification system

Polyphasic Taxonomic Approach

- Not all parameters clearly delineate each organism to the species level



(some characteristics may strengthen the organization of the genus, and some may be useful at the species level)


Have provided means for identifying the historical core genomes used in classification and species identification

Molecular Methods

Happens among organisms, particularly bacteria which creates difficulty in the classification of organisms according to phenotypic traits or biochemical traits and genotypic criteria

Lateral Gene Transfer

- The movement of DNA between diverse organisms


- Genotypic criteria such as DNA G + C content, which is the hallmark of diagnostic microbiology

Expression and classification of organisms will continue to be compounded by the

Variation in genomes

Result of lateral gene transfer among organisms

Examples of Chemotaxonomic methods

- Protein studies


- Fatty acid analysis


- Cell wall composition

More frequently being applied to the identification and classification of microorganisms

Use the separation and analysis of high abundance peptides for the classification and identification of bacterial isolates

Mass spectrometry and


Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)

Uses a protein array chip that captures proteins directly without the loss of sample and decreased sensitivity (evident in MALDI-TOF MS)


Surface-enhanced laser desorption ionization time-of-flight mass spectrometry

Method for organizing microorganisms into groups or taxa based on similar morphologic, physiologic, and genetic traits

Classification

Hierarchical Classification

Domains


Kingdom


Phylum


Class


Order


Family


Genus


Species

The 3 Domains

Bacteria


Archaea


Eukarya

Bacteria


- Contain the environmental prokaryotes (blue green or cyanobacteria) and the heterotrophic medically relevant bacteria


Archaea


- Environmental isolates that live in extreme environments such as high salt concentrations, jet fuel, or extreme temperatures


Eukarya


- Eukaryotes (true nucleus), also contains medically relevant organisms, including fungi and parasites


Encompasses a group of organisms that may contain multiple genera and consists of organisms with a common attribute

Family

The name of a family is formed by adding the suffix

-aceae

Added to the root name of one of the group’s genera, called the TYPE GENUS


Except:


Enterobacteriaceae


- Named after enteric group of bacteria rather than the type species E. coli

Contains different species that have several important features in common

Genus

- Each species within a genus differs sufficiently to maintain its status as an individual species



- Placement of a species within a particular genus is based on various genetic and phenotypic characteristics shared among the species

- A collection of bacterial strains that share common physiologic and genetic features


- Most basic of the taxonomic groups

Species

Differ notably from other microbial species

Taxonomic subgroups within a species

Subspecies

- Do not display significant enough divergence to be classified as a biotype or a new species


Designations given to groups below the subspecies level that share specific but relatively minor characteristics

- Biotype


- Serotype


- Genotype

Is considered the same species with the same genetic makeup but displays differential physiologic characteristics


Biotype

- Naming of microorganisms according to established rules and guidelines



- Provides the accepted labels by which organisms are universally recognized

Nomenclature

- Set forth in the International Code of Nomenclature of Bacteria (ICNB) or the Bacteriological Code (BC)

Each organism has a scientific “label” consisting of two parts:


1. Genus Designation


2. Species Designation

Genus = Always capitalized


Species = Always lowercase



- Printed in italics


- Underlined in script

Process by which a microorganism’s key features are delineated

Identification

- Once those features have been established, the profile is compared with those of other previously characterized microorganisms



- The organism can then be assigned to the most appropriate taxa (classification) and can be given appropriate genus and species names (nomenclature)


Role of Taxonomy in Diagnostic Microbiology:

- Establishes and maintains records of key characteristics of clinically relevant microorganisms



- Facilitates communication among technologists, microbiologists, physicians, and scientists by assigning universal names to clinically relevant microorganisms

Phenotypic Criteria for Microbial Identification

- Macroscopic Morphology


- Microscopic Morphology


- Staining Characteristics


- Environmental Requirements


- Nutritional Requirements


- Resistance Profiles


- Antigenic Properties


- Subcellular Properties


- Chemotaxonomic Properties

Genotypic Criteria for Microbial Identidication

- Deoxyribonucleic acid (DNA) base composition ratio



- Nucleic acid (DNA and ribonucleic acid [RNA]) base sequence characteristics, including those determined by hybridization assays

- The microbial growth patterns on artificial media as observed when inspected with the unaided eye



- Examples include the size, texture, and pigmentation of bacterial colonies

Macroscopic Morphology

- The size, shape, intracellular inclusions, cellular appendages, and arrangement of cells

Microscopic Morphology

Observed with the aid of microscopic magnification

The ability of an organism to reproducibly stain a particular color with the application of specific dyes and reagents

Staining Characteristics

The ability of an organism to grow at various temperatures, in the presence of oxygen and other gases, at various pH levels, or in the presence of other ions and salts, such as NaC

Environmental Requirements


The ability of an organism to utilize various carbon and nitrogen sources as nutritional substrates when grown under specific environmental conditions

Nutritional Requirements


The exhibition of a characteristic inherent resistance to specific antibiotics, heavy metals, or toxins


Resistance Profiles

The profiles of microorganisms established by various serologic and immunologic methods to determine relatedness among various microbial groups

Antigenic Properties

- Molecular constituents of the cell that are typical of a particular taxon, or organism group, as established by various analytic methods



- Some examples include cell wall components, components of the cell membrane, and enzymatic content of the microbial cell

Subcellular Properties

The chemical constituents of the cell, such as the structure of teichoic acids, fatty acid analysis, and protein profiles, as determined by analytical methods

Chemotaxonomic Properties

Four bases of the DNA

- Guanine


- Cytosine


- Adenine


- Thymine

Order of bases along a strand of DNA or RNA

Base sequence

Relate to an organism’s genetic makeup, including the nature of the organism’s genes and constituent nucleic acids

Genotypic Characteristics

Are based on features beyond the genetic level, including both readily observable characteristics and features that may require extensive analytic procedures to be detected

Phenotypic Characteristics

Are the keys to microbial viability and survival

Microbial


- Genetics


- Metabolism


- Structure

- These processes involve numerous pathways that are widely varied, often complicated, and frequently interactive

Bacterial cellular processes that require energy and nutrients

- Genetic processes


- Biosynthesis


- Assembly of cell structure


- Waste removal


- Motion and other responses to the environment


Where hereditary information resides or is encoded for all living things

Nucleic Acids

The two major classes of nucleic acid

- Deoxyribonucleic Acid (DNA)


- Ribonucleic Acid (RNA)

Most common macromolecule that encodes genetic information

DNA

- In some forms, it encodes genetic information for various viruses



- In other forms, it plays an essential role in several of the genetic processes in prokaryotic and eukaryotic cells, including the regulation and transfer of information



RNA

Do not have membrane-bound organelles, and the cells’ genetic material is therefore not enclosed in a nucleus


Prokaryotic/Pre-nuclear organisms

Organisms have the genetic material enclosed in a nuclear envelope


Eukaryotic (True nucleus)

DNA consists of _________ and connected by _________

Deoxyribose sugars


Phosphodiester bonds

Are the key to genetic code within the DNA molecule

The bases that are covalently linked to each deoxyribose sugar

The four nitrogenous bases include

Two Purines:


- Adenine


- Guanine



Two Pyrimidins:


- Cytosine


- Thymine

These bases are covalently linked to each of the deoxyribose sugar

In RNA the nitrogenous base thymine is replaced by

Uracil

The combined sugar, phosphate, and a base form a single unit referred to as a

Nucleotide

- Adenosine Triphosphate [ATP] - Guanine Triphosphate [GTP] - Cytosine Triphosphate [CTP] - Thymine Triphosphate [TTP] - Uridine Triphosphate [UTP]


- The order of bases along a DNA or RNA strand



- Provides the information that codes for the proteins that will be synthesized by microbial cells

Base Sequence

SEQUENCE = GENETIC CODE

The intact DNA molecule is composed of

2 Nucleotide Polymers

Each DNA strand has a

- 5’ (prime) phosphate


- 3’ (prime) hydroxyl terminus

- The two strands run ANTIPARALLEL, with the 5’ of one strand opposed to the 3’ terminal of the other

Base pairing which results in a double-stranded DNA (dsDNA) molecule (double helix)

A-T and G-C

Complementary Strands

The two single strands of DNA are oriented in an

Antiparallel Configuration/ Twisted Ladder Structure

Provide the essential format for consistent replication and expression of the genetic code

Base Pairs

Dedicated base pairs

Rarely exists as double-stranded molecule

RNA

Four major types of RNA

- Messenger RNA [mRNA]


- Transfer RNA [tRNA]


- Ribosomal RNA [rRNA]


- Noncoding RNA [ncRNA]

ncRNA - Molecules that play key roles in gene expression

- DNA sequence that encodes for a specific product (RNA or protein)



- Encode messages or blueprints for the production of one or more proteins and RNA products that play essential metabolic roles in the cell

Gene

All the genes in an organism comprise the organism’s

Genome

The size of a gene and an entire genome is usually expressed in the

Number of base pairs present

- kilobases [10^3 bases]


- megabases [10^6 bases]

Basis for the development of molecular methods used to detect, identify, and characterize clinically relevant microorganisms

Similarities and differences in gene content and sequences

Base pair sequence for individual genes may be highly conserved (show limited sequence differences among different organisms) or be widely variable

The genome is organized into discrete elements known as

Chromosome

The set of genes within a given chromosome are arranged in a

Linear Fashion

Contains the genes essential for viability and exists as a double-stranded, closed, circular macromolecule

Bacterial Chromosome

- The molecule is extensively folded and twisted (supercoiled) to fit within the confined space of the bacterial cell


The chromosomes of ___________ number more than one per cell, are linear, and are housed within a membrane-bound organelle (the nucleus) of the cell

Parasites and Fungi

This difference is a major criterion for classifying


- Bacteria as Prokaryotes


- Fungi and Parasites as Eukaryotes

The genetic makeup of a virus may consist of DNA or RNA contained within a ________ rather than a cell


Protein Coat

Human cells contain ______ pairs of chromosome

23

DIPLOID

Bacteria contain a ________ chromose

Single

UNPAIRED/HAPLOID

Bacterial elements capable of replication independently of the host chromosome

Episomes

- Not as stable as the chromosome and may be lost during cellular replication, often without any detrimental effects on the viability of the cell

Not all genes are confined to the chromosome, many genes may also be located on the

- Plasmids


- Transposable elements

- Both of these extrachromosomal elements are able to replicate and encode information for the production of various cellular products


- Exist as double-stranded, closed, circular, autonomously replicating extrachromosomal genetic elements



- Do not usually encode for products essential for viability

Plasmids

Ranging in size from 1 to 2 kilobases up to 1 megabase or more

- Pieces of DNA that move from one genetic element to another, from plasmid to chromosome or vice versa



- Many are unable to replicate independently and do not exist as separate entities in the bacterial cell

Transposable elements

2 types of transposable elements

- Simple Transposon/Insertion Sequence (IS)



- Composite Transposon

Transposable elements that are limited to containing the genes that encode information required for movement from one site in the genome to another

Simple Transposon/Insertion Sequence (IS)

- Internal gene embedded in the insertion sequence encodes for an accessory function, such as antimicrobial resistance

Transposable elements that are cassettes (grouping of genes) flanked by insertion sequences

Composite Transposon

Bacteria multiple by

Binary Fission

Four stages of Replication

1. Unwinding or relaxation of the chromosome’s super-coiled DNA


2. Separation of the complementary strands of the parental DNA


3. Synthesis of the new (daughter) DNA strands


4. Termination of replication

Required so that enzymes and cofactors involved in replication can access the DNA molecule at the site where the replication process will originate

Relaxation of supercoiled chromosomal DNA

A specific sequence of approximately 300 base pairs recognized by several initiation proteins

Origin of Replication

- Followed by the separation of the complementary strands of parental DNA



- Where the replication process will originate

Site of active replication

Replication Fork

Each replication fork moves through the parent DNA molecule in opposite directions as a

Bidirectional process

- Two bidirectional forks are involved in the replication process

- Must occur so that there will be a template (pattern) for synthesis of new DNA strands



- Referred to as Semi-conservative Replication

Separation of the complementary strands of the parental DNA

- Each parental strand serves as a template for the synthesis of a new complementary daughter strand

Adds nucleotide bases to each growing daughter strand in a sequence that is complementary to the base sequence of the template (parent) strand

DNA Polymerase

- Plays a central role in the activity at each replication fork together with different cofactors and enzymes

The complementary bases of each strand are then held together by

- Hydrogen bonding between nucleotides



- Hydrophobic nature of the nitrogenous bases