1. CC1: Introduction to microbiology and microbial diversity
Sem-1
Core Courses (CC) CC1 & 2
2Th + 2P
(2X4+2X2=12 Credits)
CC1: Introduction to microbiology and microbial diversity
CC2: Bacteriology

2. B.Sc (HONOURS) MICROBIOLOGY (CBCS STRUCTURE)
CC-2: BACTERIOLOGY (THEORY)
SEMESTER –1
MCB-A-CC-1-2-TH
TOTAL HOURS: 50 CREDITS: 4
Unit 6 : Bacterial Systematics No. of Hours: 8
Aim and principles of classification, systematics and taxonomy, concept of species, taxa, strain; conventional, molecular and recent approaches to polyphasic bacterial taxonomy, evolutionary chronometers, rRNA oligonucleotide sequencing, signature sequences, and protein sequences. Differences between eubacteria and archaebacteria

3. Five Kingdom Classification Whittaker (1969)
This Scheme Was Based On - 
Structure of Cells - {prokaryotic or eukaryotic }
Structure of Organism - {unicellular or Multicellular}
Mode of nutrition - Photosynthesis in green plants, absorption in fungi and ingestion in animals.

4. The Three Domains Of Life
Genetic Similarity was stressed over outward appearances and behavior. 
Based on the sequence of ribosomal RNA, Carl Woese divided life into three large divisions and referred to them as the "three primary kingdom" 
 In 1990, the name "domain" was proposed for the highest rank.

5. Woese in 2004
Born
Carl Richard Woese July 15, 1928 Syracuse, New York, U.S.
Died
December 30, 2012 (aged 84) Urbana, Illinois, U.S.
Residence
Urbana, Illinois, U.S.
Nationality
United States
Citizenship
American

6. Taxonomy of Bacteria and Archaea
Modern taxonomy comprises the following features:
Nomenclature: giving names of appropriate taxonomic rank to the classified organisms.
Classification: the theory and process of ordering the organisms, on the basis of shared properties, into groups.
Identification: obtaining data on the properties of the organism (characterization) and determination which species it belongs to. This is based on direct comparison to known taxonomic groups.

7. Nomenclature of Bacteria and Archaea
There are a, quite complicated, set of rules for the naming Bacteria and Archaea. They must have two names: the first refers to the genus and the second refers to the species.
The names can be derived from any language but they must be Latinized. Take for example Staphylococcus aureus. The genus name is capitalized and the species name is lower case. The name is italized to indicate that is Latinized. Staphyl is derived from the Greek staphyle meaning ”a bunch of grapes” and coccus from the Greek meaning ”a berry”. Aurous is from Latin and means ”gold”. A golden (yellow) bunch of berries.
The higher taxonomic orders are family, order, class, phylum and domain but except for domain these are rarely used.

9. Bacterial Ribosome

10. Classification of Bacteria and Archaea
Historically, prokaryotes were classified on the basis of their phenotype (morphology, staining reactions, biochemistry, substrates/products, antigens etc). In other words a phenotypic characterization is based on the information carried in the products of the genes. These classification systems were artificial.
Modern characterization is based on the information carried in the genes and the genome. This is genetic information and can also tell us something about the evolution of the organism. In other words phylogenetics.

11. Numerical Taxonomy
Numerical taxonomy is a methods which is used to differentiate a large number of similar bacteria, i.e. species.
A large number of tests (~100) are carried out and the results are scored as positive or negative. Several control species are included in the analysis.
All characteristics are given equal weight and a computer based analysis is carried out to group the bacteria according to shared properties.

12. Homologous genes are used in the construction of phylogenetic trees
Homologous means that genes have a common anscestor
Orthologs are homologous genes that belong to different species but still retain their original function
Paralogs are homologous genes that have arrisen by gene duplication and are found in the same organism
Only orthologes can be used in the construction of phylogenetic trees. The classical example is the 16S ribosomal RNA gene.

13. Secondary structure of the 16S rRNA molecule of Escherichia coli.
The bases are numbered from 1 at the 5' end to 1,542 at the 3' end
Tertiary interactions with strong comparative data are connected by solid lines.

14. Conservation and variation in small subunit rRNA
This diagram shows conserved and variable regions of the small subunit rRNA (16S in prokaryotes or 18S in eukaryotes). Each dot and triangle represents a position that holds a nucleotide in 95% of all organisms sequenced, though the actual nucleotide present (A, U, C, or G) varies among species. Figure by Jamie Cannone, courtesy of Robin Gutell; data from the Comparative RNA Web Site:

15. Conservation and variation in small subunit rRNA
The starred region from part A as it appears in a bacterium (Escherichia coli), an archaean (Methanococcus vannielii), and a eukaryote (Saccharomyces cerevisiae). This region includes important signature sequences for the Bacteria and Archaea. Figure by Jamie Cannone, courtesy of Robin Gutell; data from the Comparative RNA Web Site:

16. Phylogenetic trees Two different formats of phylogenetic trees used to show relatedness among species.

17. Universal phylogenetic tree as determined from comparative ribosomal RNA sequencing.

21. Thank You