1. Introductory Microbiology Dr. Hala Al Daghistani

2. 1. Microbes and Man in Sickness and Health
Why Study Microbes?
1. Microbes and Man in Sickness and Health
Parasitism; Pathogens (disease causing)
Infectious disease is leading cause of death in developing countries (45%).
Commensalisms; Natural Microbiota (do no harm)
Mutualisms; Natural Microbiota (do us good)
2. Major Modern Applications (Biotechnology):
Recombinant DNA technology; cloning
Industrial Applications (antibiotics; chemical production via fermentation)
Sewage treatment to decompose organic matter
Bioremediation of toxic waste
3. The Role of Microbes in Ecosystems
Sources for drug discovery (antibiotics & antiviral drugs)
Cycling of Elements (ecosystem management; global climate change)
Agriculture (crop diseases; nutrient enhancement)

3. Biotechnology & Bioremediation
• Biotechnology- when humans manipulate (micro)organisms to make products in an industrial setting
– Genetic engineering- create new products and “genetically modified organisms” (GMOs)
– Recombinant DNA technology- technology used to engineer GMOs capable of synthesizing desirable proteins (i.e. medicines, hormones, and enzymes)
• Bioremediation - activity of microbes in the environment
helping to restore stability or clean up toxic pollutants
– Oil spills
– Chemical spills
– Water and sewage treatment

4. The microbial world is made up of microorganisms and viruses
The microbial world is made up of microorganisms and viruses.  Microbiology is the branch of biological sciences concerned with the study of these microbes. Microorganisms are unicellular organisms (capable of existence as single cells), too small to be seen with the naked eye. Among all forms of life on the earth, microorganisms predominate in numbers of species and in biomass, but their occurrence is generally under appreciated because of their small size and the need for a microscope to see individual cells. Although a light microscope is generally required to visualize a single microbial cell, microbial colonies and communities can readily be observed in nature. Viruses are noncellular entities and cannot be considered microorganisms. Viruses and cellular microorganisms are considered microbes. The term organism is a descriptive term that implies cellular life.  Hence, micro-organisms are a type of cellular life that is microscopic in size.  Viruses are not considered microorganisms because they are not cells. Viruses consist of nucleic acid (DNA or RNA) enclosed in a protein coat. They lack many essential properties of cells, including membranes, ribosomes and metabolic enzymes. Viruses are considered microbes, but not microorganisms, and hence are not "alive".

5. Which are the microorganisms?
Life forms, or other self replicating entity, that requires microscopy technology to be clearly visualized.
All prokaryotic and many eukaryotic life forms.
Many are unicellular, sometimes cells are organized in filaments or clumps, and others are complex with only a portion of their life cycle being microscopic.
Most can carry out life processes independently from other cells, others are highly parasitic.
They often require specialized techniques for their study: microscopy, culturing, biochemical and molecular.

6. Note the difference in scale
Note the difference in scale. The Eukaryotic cell would be about 50x bigger than the bacterium

9. Biologists recognize the existence of two fundamentally different types of cells in the microbial world, called procaryotic and eucaryotic cells. 1.  Eucaryotic cells have a "true" nucleus (the region of the cell that contains genetic information or DNA) that enclosed in a nuclear membrane 2. Procaryotic cells are said to have a "primitive" nucleus because their DNA is not enclosed within a nuclear membrane. The nuclear region of a procaryotic cell is sometimes referred to as a nucleoid, but never as a nucleus.

10. Procaryotic and Eucaryotic cells Eucaryotic cells are always bounded by a membrane, just as prokaryotic cells are. Some eucaryotic cells are also surrounded by a cell wall, but eucaryotic cells do not have capsules Mitochondria are present in nearly all eucaryotic cells and produce the cell's energy by breaking down food.    Chloroplasts, in contrast, are present only in plants and algae and are used in photosynthesis, the process through which the organism uses energy from the sun to build sugars.  

11. Taxonomy of Life:
The classification, or grouping, of organisms based on common characters used to reflect their evolutionary relatedness. Types of groups, taxa, are arranged in a hierarchy from the most general (Domain) to most specific.
3 Domains based on molecular analysis of ribosomal RNA (Carl Woese 1980s)
Two prokaryote domains: Bacteria and Archaea
A single Eukaryote domain.
Many Phyla within each domain.

12. Difference in taxonomy between us and them.
Humans
Domain: Eukarya
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primata
Family: Hominidae
Group: Homo
Species: sapiens
Intestinal Bacterium
Domain: Bacteria
(no kingdom)
Phylum: Proteobacteria
Class: γ-proteobacteria
Order: Enterobacteriales
Family: Enterobacteriaceae
Genus: Escherichia
Species: coli
Binomial nomenclature: Genus species (italic or underlined)
Just like varieties, or races, there are strains of microbial species (e.g. Escherichia coli K12 versus the pathogenic E. coli O157:H7)

15. Viruses: An infectious particle with an acellular organization of protein and nucleic acids (RNA or DNA), and lacking independent metabolism.
It requires the metabolism of a host cell in order to replicate. Viruses are about 50 to 200 nm in size.
Prion: An infectious aberrant brain protein that causes abnormal aggregation of similar normal brain proteins; no nucleic acids. Causes dementia and madness.