1. Microbial genomics

2. Genomics: a field of science that analyzes and compares the complete genome (genetic material of an organism) of organisms or a large number of genes in a simultaneous fashion.
microbial
(Science: biology, microbiology) Pertaining to microorganisms too small to be seen with the naked eye.
Microbial genomic :
the contact of genomics on our understanding of the microbes life
1) Methods for Studying Microbial Genomes
2) Analysis and Interpretation of Whole Genome Sequences

3. Why study microbial genomes?
analysis of whole microbial genomes also provides insight into microbial evolution and diversity beyond single protein or gene phylogenies
in practical terms analysis of whole microbial genomes is also a powerful tool in identifying new applications in for biotechnology and new approaches to the treatment and control of pathogenic organisms
Central role in ecological balance
Commercial opportunities
Pathogens kill millions every year

4. History of microbial genome sequencing
first complete genome to be sequenced was bacteriophage X bp
late 1990’s - many additional microbial genomes sequenced including Archaea (Methanococcus jannaschii ) and Eukaryotes (Saccharomyces cerevisiae )

5. Laboratory tools for studying whole genomes
conventional techniques for analysing DNA are designed for the analysis of small regions of whole genomes such as individual genes or operons
many of the techniques used to study whole genomes are conventional molecular biology techniques adapted to operate effectively with DNA in a much larger size range

6. Some tests :
Pulsed Field Gel Electrophoresis
Large insert cloning vectors – BAC’s and PAC’s
Approaches to whole microbial genome sequencing
Structural genomics
Microarray hybridisation
Random sequencing (shotgun) approach
Genome Annotation

7. A typical Microbial project

8. Genome Annotation The process after sequencing has been completed.
Use of many different tools required:
Bioinformatics
Databases
Literature
Sequence
Experimental

9. Pipelines for the Annotation of Genomes – Web based

10. GLIMMER is a software for gene prediction and used by:
BASYS-
JCVI (formerly TIGR)-
SABIA-

11. Example - Haemophilus influenzae
first complete genome sequence of a free living organism (1995)
important pathogen
genome is around 1.83 megabases in size
random sequencing was done for both small insert and large insert (lambda) libraries
sequencing reactions performed by eight individuals using fourteen ABI 377 DNA sequencers per day over a three month period
in total around sequencing reactions were performed on templates
plasmid extraction performed in a 96 well format
11 mb of sequence was intially used to generate 140 contigs
gaps were closed by lambda linking clones (23), peptide links (2), Southern analysis (37) and PCR (42)