2.

Learning Outcomes
By end of this course student should be able to:
• Understand the basics of microbial genetics, evolution and nutrition.
• Understand the various microbiological enviroments i;e soil, air, water and marine.
• Understand the role of microbes in industry.
• Differentiate the different classes of microbes responsible for causing different
infections/diseases.
a. Elaborate the genomic (microbial) data for different bioinformatics analysis.
A. General Information
1. Course code: MIC-643 Title: Fundamentals of microbiology-ll Credit hours: 2+1
2. Description of Course
The fundamental microbiology II is a 3 credit hour course with 2+1 hour lectures per week. The
fundamental of microbiology is appropriate for students with background in biology, chemistry
whose career path intersects the study of microbes with particular emphasis on bacteria, fungi,
viruses. The core content up to 16 week course is designed to develop the advance concepts of
undergrad students examining the microbes that inhabit different biotic and abiotic worlds. This will
also include microbial genetics, evolution and nutrition, environmental microbiology, pathogenicity,
diseases associated with microbes, computational study of microbial genome and tools to study
microbes in compulsory laboratory sessions. Students will explore the influence of this emerging
science and the 21st century challenges and opportunities arise in understanding the microbiome or
holobionts.
Program in which the course is offered:
BS Biological Sciences with major in Microbiology
Name of faculty member responsible for the course:
Year/Semester in which this course is offered: Year
2/Semester 4th
Location, if not on main campus:
B Goal
1. Course Objectives
• This course will introduce students to the diversity of microorganisms, including, bacteria,
viruses, and fungi, and the impact of microbes on everyday life.
• To know about the applications of the science of microbiology in the different fields of life.
• To know about the epidemiology and pathogenicity of the pathogens.
• The computational tools and techniques that are used to classify microbes.
• The course may initiate students interest in medical, industrial, environmental microbiology
and Bioinformatics.

b. To develop good leadership, problem solving, research planning and lab management skills.

C. Course Details
1. Course Syllabus

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 Week Contact Distribution
List of Topics (Theory)
No hours
Microbial Genetics 1 2 Dr. Mahpara
Lecture 1:
Microbiology and Secrets of Life
Structure and Function of DNA
Structure and Function of RNA
Structure and Function of Cellular Genomes

Lecture 2:
Functions of Genetic Material
DNA Replication
RNA Transcription
Protein Synthesis (Translation)
Mutations
Gene Regulation: Operon Theory
Microbial Evolution and Nutrition 2 2 Dr. Mahpara
Lecture 1:
Evolution, Microbial Life, and the Biosphere
Historical Overview
Fundamental Chemistry of the Cell
Structure and Function of Bacteria and Archaea

Lecture 2:
Nutrition, Cultivation, and Isolation of Microorganisms
Microbial Growth
Control of Microbial Growth
Microbes in the environment 3 2 Dr. Mahpara
Lecture 1:
Carbon cycling in the ecosystem
Brown rots and white rot Funji
Nitrogen cycling in the ecosystem
Ammonification, nitrification and de-nitrification

Lecture 2:
Microbial parterships
Microbial association with plats roots
Legumes, rhizobia and nitrogen fixation
Microbial association with animals and insects
Ruminants and hind gut fermenters
Termites and Leaf cutter ants

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Air Microbiology 4 2 Dr. Asma
Lecture 1:
The air as an environment of microorganisms
Adaptation of microorganisms to the air
environment
Biological aerosols
Mechanisms protecting lungs against bioaerosol
penetration

Lecture 2:
Survival and spread of bioaerosols
Biological aerosols as a hazardous source for
humans
Basic sources of bioaerosol emission
Investigation of microbiological air pollutions
Soil Microbiology 5 2 Dr. Asma
Lecture 1:
Soil
Edaphon
Edaphic factors

Lecture 2:
Activity of microorganisms
Symbiosis forms
Soil bioremediation
Water Microbiology 6 2 Dr. Asma
Lecture 1:
Water
Water organisms
Factors limiting growth
Microorganisms

Lecture 2:
Polluted water organisms
Water health standards
Wastewater treatment
Marine Microbiology 7 2 Dr. Asma
Lecture 1:
The role of microorganisms in the oceans
Metabolic diversity
Methods in marine microbiology
Interactions of microbes with other microbes, plants
and animals

Lecture 2:
Biochemical cycling, pollution and

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water quality Microbe-mineral
interactions Extremophiles.

Applied Microbiology and Biotechnology 8 2 Dr. Asma

Lecture 1:
Microbes Involved in Industrial Processes
Major Industrial Products
Foods, Flavoring Agents and Food
Supplements, and Vitamins
Beverages Containing Alcohol
Ethanol as Fuel
Organic Acids

Lecture 2:
Enzymes
Inhibitors
Genetically Engineered Microorganisms

Mid-Term Examination 9 --
Microbial Pan-genome 10 2 Dr. Mahpara
Lecture 1:
Pan-genomics of Animal pathogens
Pangenomics of animal pathogenic Bacteria
Pangenomics of animal pathogenic Fungi
Pangenomics of Sexually transmitted pathogens

Lecture 2:
Application of Pan-genomics
Genome Plasticity
Pathogenic Islands

Microbial Pan-modelome 11 2 Dr. Mahpara

Lecture 1:
Bacterial Genome
Fungal Genome
Viral Genome
Application of Pan-modelome

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Microbes as Pathogens 12, 13, 6 Dr. Saima
Pathogens of Skin and Eyes 14
Pathogens of Urogenital Tract Infections & STD’s
Pathogens of the Nervous System
Pathogens of the Cardiovascular System
Pathogens of the Respiratory System
Pathogens of the Digestive Tract
Pathogens of the Urinary and Reproductive Tract
(Bacterial, Viral and Fungal)
Principles of Disease and Epidemiology 15 2 Dr. Saima
Lecture 1:
Epidemiology
Carriers and Reservoirs
Modes of Transmission of Infectious Diseases
Nosocomial (Hospital-Acquired) Infections
Public Health Measures

Lecture 2:
Control Measures for Communicable Diseases
World Health
Clinical and Diagnostic Methods
Identifying Pathogens
Antibiotic Sensitivity

Pathogenicity and Resistance 16 2 Dr. Saima

Lecture 1:
Characteristics of Infectious Disease
How Pathogens Cause Disease
Virulence Factors of Bacterial and Viral Pathogens
Virulence Factors of Eukaryotic Pathogens

Lecture 2:
Concept of Drug Resistance
How microorganisms develop or acquire drug
resistance Different Mechanisms of antimicrobial drug
resistance
MDRs
XDRs
Revision and Preparation 17 --

Final Examination 18 --

List of Topics (Practicals) Week Contact

No hours

86
Sampling Methods in Microbiology 3 2 Dr. Asma
 Sampling from various environments

Microbiology of surface waters and wastewaters, hygienic control 5,7 4 Dr. Asma
(membrane filter technique)
• Filter 100mL of water sample through a 150µm thick and
0.45µm pore size sterile membrane filter.
• Remove the membrane filter and place it facing up onto the
surface of adequate differential medium (Endo-or
EosinMethylene Blue agar plates) using sterile forceps.
• Incubate the plates at 37°C for 24 hours and count the number
of colonies formed. If the filtered water sample was not
diluted prior to filtration, the Coli-count of 100 mL water
sample is equal to the number of coliform colonies counted on
the agar surface.

Pan-genomics of Bacterial Genome 10,11 4 Dr.

• Introduction to the available tools Mahpara
• Statistical analysis
• Pathogenic Island identifications

Pan-modelomics of Bacterial Genome 12 4 Dr.

• Introduction to the available tools Mahpara
• Statistical analysis
• Drug target identification

Sampling Methods in Microbiology 13,14 2 Dr. Saima

• Sampling for diagnostic purposes

Identification and Isolation of pathogen from given sample. 15 4 Dr. Saima

2. Learning Resources
List of Textbooks, Journals, Electronic Materials:
1. Prescott Microbiology 10th edition
2. Microbiology by Nina Parker, Mark Schneegurt, Anh-hue Thi Tu, Brian m.
Forster, Philip Lister, 2016.

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3. Brock Biology of Microorganisms, 14th Edition By Michael T. Madigan,
John M. Martinko,
Kelly S. Bender, Daniel H. Buckley, David A. Stahl, Thomas Brock
Published by Pearson Copyright © 2015 Published Date: Jan 2, 2014
4. Foundations in Microbiology 10th Edition By Kathleen Park Talaro and Barry
Chess 5. Baker , S., Khan , N., Nicklin, J. and Killington, R., 2011. Instant
Notes in Microbiology, 4TH Ed edition, Taylor and Francis.
6. Foundations in Microbiology: Basic Principles, McGraw-Hill Companies,
N.Y. 4. Tortora, G. J., Funke, B. R. and Case, C. L. 2012.
7. Microbiology: An Introduction, Benjamin-Cummings Publishing Company,
U.S.A.
8. Tortora, G. J., Funke, B. R. and Case, C. L. Study Guide for Microbiology:
An Introduction.
13th edition. Benjamin-Cummings Publishing Company, U.S.A.

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