1. Introduction to Microbiology
Anas Abu-Humaidan M.D. Ph.D.
Lecture 9

2. Taxonomy Ordering bacteria in related groups.
Classification uses specific characteristics to group bacteria together.
Identification is the practical use of classification.
Nomenclature is naming according to rules so that it means the same to all microbiologist.
No definitive “species” taxon in bacteria, due to non-sexual reproduction and horizontal gene transfer.
the concept of a species—the fundamental unit of eukaryotic phylogeny—has an entirely different meaning when applied to bacteria.
Linnaean taxonomy is the system most familiar to biologists, The lower ranks are approved by a consensus of experts in the scientific community
different groups of scientists may classify the same organisms differently

3. Classification Bacteria can be classified by their:
Macroscopic and microscopic appearance (Morphology)
Growth conditions
Biochemical characteristics
their antigenicity, and finally
by their genotype.
Classification and identification is important For a medical practitioner since you need to isolate, identify and find antibiotic susceptibility of a certain pathogen.

4. Classification/ Morphologic Characteristics
Gram reactivity/acid-fast
Shape
Flagella organization
Motility
Presence of Spores/capsule/ inclusion bodies.
Colony shape on agar plates.
Such characteristics can be investigated mostly with staining under the microscope.

6. Classification/ Growth conditions
Oxygenation (aerobic, non-aerobic, facultative) .
Type of media used.
Temperature.
pH.
Antibiotic sensitivity.

7. Classification/ Biochemical Characteristics
Classify bacteria based on a series of biochemical reactions, employing differences in metabolism and enzymatic activities among others.
Amount of tests actually used and tests needed to verify the organism usually vary for practical reasons.

9. reducing sulfur, producing indole and walking through gelatin
reducing sulfur, producing indole and walking through gelatin. SIM is generally used to differentiate Enterobacteriaceae members

10. Classification system/ Keys and algorithms
Blood agar used to distinguish between the b-hemolytic streptococci: Streptococcus agalactiae (bacitracin resistant) and Streptococcus pyogenes (bacitracin sensitive).

11. Classification system/ Numerical Taxonomy
The Analytical Profile Index (API) is a method commonly used to identify a wide range of microorganisms. APIs consist of a number of plastic strips, each of which has about 20 miniature compartments containing biochemical reagents static system
When this approach is the only basis for defining a species, it is difficult to know how many and which tests should be chosen; whether and how the tests should be weighted; and what level of similarity should be chosen to reflect relatedness at the genus and species levels.

13. Major Categories and Groups of Bacteria That Cause Disease in Humans as Part of an Identification Scheme Described in Bergey’s Manual of Determinative Bacteriology, 9th Ed, a work in progress.

14. Classification at the species level / Subtyping
Can Use antibodies that react to specific bacterial structures. Like Cell wall (O), flagellar (H), and capsular (K) antigens.
Example: E. coli O157:H7 causes severe, acute hemorrhagic diarrhea
Important in epidemiological studies.
Example: V. cholerae O1 and O139 serogroups are associated with epidemic and pandemic cholera.
We can also use the chemical fingerprint of a bacteria using Mass spectrometry. Or genetic makeup using DNA sequencing.
E. coli O157:H7
Strains of E. coli that express Shiga and Shiga-like toxins gained this ability due to infection with a prophage containing the structural coding for the toxin

15. Classification at the species level / Emerging tools
matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF)
Used for microbial identification and strain typing.

16. Classification above the species level / phylogenetic studies
Genetic relatedness between different bacteria can be done using several methods that investigate homology in nucleic acids.
DNA hybridization, polymerase chain reaction (PCR) amplification, DNA sequencing.
Ribosomal RNA (16s rRNA) is a good candidate for phylogenetic studies.
rRNA, its presence in almost all bacteria, often existing as a multigene family, or operons; (ii) the function of the 16S rRNA gene over time has not changed, suggesting that random sequence changes are a more accurate measure of time (evolution); and (iii) the 16S rRNA gene (1,500 bp) is large enough for informatics purposes

17. The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%

18. Further reading and material:
Murray - Medical Microbiology 8th Edition
Section 4: Bacteriology
Chapter 12: BACTERIAL CLASSIFICATION, STRUCTURE, AND REPLICATION
Jawetz, Melnick & Adelberg's Medical Microbiology, 26th edition- Section 1: Fundamentals of Microbiology-
Chapter 3: Classification of bacteria