MODULE 1 Microbiology Lecture

Microbiology

Microbiology

study of living organisms that are too small to be visible with the naked eye

Virus

Bacteria n Archaea

Protozoa (Protist)

Microalga (Protist)

Yeast

Microorganism

• Microscopic ( < 1mm)

• Unicellular or colonial

• Multicellular without highly differentiated tissues

Microbes description

Atom size

0.1 nm

C60, Lipids, Protein size

1nm - 10nm

Virus size

100 nm

Size of mitochondria and Bacteria

1 um

Red Blood Cell size

Between 1um and 10 um

Animal Cell and Plant Cell

Between 10 um and 100 um

Protein and human egg size

Between 100 um and 1 mm

Frog Egg size

1mm

Smallest of all microbes, requires host cell to replicate cause range of disease, some cancers

Virus

Cellular and Acellular

organisms can be:

1. Fungi

2. Protist

3. Bacteria

4. Archaea

Cellular Bacteria

Fungi

What kind of cellular microbes is yeast and molds

Protists

What kind of cellular Microorganism is Algae, Protozoa, Sime Molds

Bacteria

What kind of cellular Microorganism is Escherichia coli

Archaea

What kind of cellular Microorganism is Methanogens

• viruses

• Viroids

• Satellites

• Prions

Acellular microorganism

Viruses

Composed of protein and nucelic acid

Viroids

Composed of RNA

Satellites

Composed of Nuceleic acid enclosed in a protein shell

Prions

Composed of protein

1 Trillion

Earth is a home to ——- microbial species

Fermentation

Microbial processes to produce Alcoholic Beverages

Fermentation

Microbial processes to produce soy sauce

Microbial Growth

Microbial processes to produce cheeses

Fermentation, Leavening

Microbial processes to produce Bread

Ferementation, breakdown of pulp

Microbial processes to produce Coffee

Fermentation, breakdown of pulp

Microbial processes to produce Chocolate

Botulinum toxin - highly diluted

Microbial processes to produce botox

Biodegradation

Microbial processes for composting

Biodegradation

Microbial processes for sewage treatment

Fermentation, growth

Microbial processes for antibiotic production

Molecular biology

Microbial processes to produce Vaccine

Source of genes or as vectors for genetic engineering

Microbial importance to generate GMO’s

Basic

Microbiology as a field of study

• concerned with achieveing a deeper understanding of the workings of the microbial cell and its interaction

Basic

Microbial Physiology ( microbiology as a field of study)

Basic

Microbial ecology ( microbiology as a field of study)

Basic

Genetic and molecular biology ( microbiology as a field of study)

Basic

Taxonomy and systematics ( microbio as a field of study)

Applied

Disease and its control ( microbio as a field of study)

Applied

Water and Food production ( microbiology as a field of study)

Applied

Industrial Microbiology ( microbiology as a field of study)

Applied

Micrbiology as a field of study that is concerned with practical problems

Agricultural microbiology

Plant pathogens, food safety, plant-beneficial microbes

Immunology

How the body protects a host from pathogens

Industrial microbiology

Production of antibiotics, biofuel, fermentation

Medical microbiology

Diseases of humans and animals

Microbial ecology

Microbial interactions

Microbial genetics

Control of gene expression, genomics

Microbial physiology

Metabolic pathways

Public health microbiology

Control of communicable diseases

Controverset over spontaneous generation > germ theory of disease > industrial application [ fermentation, Pasteurization] > Microbial ecology [ enrichment, physiology]

Development of ideas about microbes

Development of the microscope > culture techniques [petri dish] > control of microbes [ vaccines and antibiotics] > molecular genetics and genomics

Development of tools and methods

General Antonio Luna

• scientist, soldier and revolutionary

• Got his doctorate degree in phramacy from university of madrid where he studied malaria

• Post doctoral at Pasteur Institute in Paris

Etiology

Study of the cause of disease

Germ Theory

Infections by pathogenic microorganism cause disease

Robert Koch

Developed postulates to prove particular pathogen causes a disease

1.5 bya

Multicellular eukaryotic organism first appear

2.5-2.0 bya

eukaryotic cells with mitochondria or chloroplasts first appear

3.5 bya

fossilsof primitive microbes

3.8 - 3.5 bya

first cell appear

RNA world hypothesis

what hypothesis states that RNA may have been an importat molecule in the pre-cellular stage of cellular evolution

• came with the discovery of catalytic RNA

Ribozymes

discovery of catalytic RNA

RNA

have the ability to store and copy geneti information

lipid membrane

encloses the RNA genetic information

symbiogenesis

endosymbiotic theory on the origin of the eukaryotic cells

Systematics

scientific study of organisms with the ultimate objective of arranging them in an orderly manner

natural classification

arranges organism into groups whose members shares many characteristic

Carl von Linne’ or Carolus Linnaeus

developed the frist natural classification

Polyphasic taxonomy

determining the genus and sepcies of a newly isolated microbe

• phenotypic

• phylogenetic

• genotypic features

phenetic system

• Succeededin bringing order to biological diversity and clarified the function of morphological structures.

• classifies organisms according to their phenotypic siimilarity

Genotypic classification

• seeks to compare the genetic similarity between organisms

  • Individual genes or whole genomes can be compared

Phylogenetic or phyletic classification systems

• sought to compare organisms on the basis of evolutionary relationships

• developed due to the publication of Charles Darwin’s On the Origin of Species in 1859

phylogeny

term referring to evolutionary development of a species

Carl Woese

George Fox

• proposed small subunit (SSU) rNA nucleotide sequences to assess evolutionary relationships among microorganisms

• this opened the door to the resolution of long-standing inquiries regarding the origin and evolution of themajority of life forms on earth-- Microbes

superphylum

• recent development of the taxonomic classification

• below domain and above phylum

• includes organisms of several phyla that share a number of distinctive characteristics such as unusual morphological or metaboloc features

Species

collection of strains that share stable properties and differ significantly from other groups of strains

Strain

consists of descendant of as single, pure, microbial culture

Biovars

variant strains characterized by biochemical or physiological differences

Morphovars

differ morphologically

serovars

have distinctive antigenic (immunologically reactive) properties

type strain

• holder of the species name

• Ensures permanence of names when nomenclature revisions occur because the type species must remain within the original species

genus

well-defined group of one or more species that is clearly separate from other genera

binomial system

latinized, italicized consists of two names

International Journal of Sytematic and Evolutionary Microbiology

to be recognized as an new species, genomic, metabolic, morphological, reproductive, and ecological data must be accepted and pubish in the _____

bergey’s manual of systematic bacteriology

contains only recognized baterial and archaeal species

clinical microbiology and immunology

methods employed in routine laboratory identification of pathogenic bacteria

classical approaches

makes use of morphological, physiological, biochemical, and ecological characteristics.

fatty acid methyl ester (FAME) analysis

reveal specific differences in chain length, degree of saturation, branched chains, and hydroxyl groups

APPLICATION

public health, food and water microbiology

where microbiologists seek to identify specific micorbial pathogens

matrix-assisted laser desorption/ionization-time of flight (MALDI-ToF)

enables the analysis of complex biomolecules that could not previously be studies by MS

DNA-DNA hybridization

similarity between gennomes can be compared more directly by the use of nucleic acid hybridization studies, called ________

Average nucleotide identity (ANI)

• uses pairwise alignment between sequenced DNA from two organisms, is a promising replacement for DDH

• used to compare complete genome sequences

• used to compare short stretches of nucleotides

16S ; Bacteria

18S ; Eukaryotes

rRNA’s from small ribosomal subunits that have become the molecules of choice for inferring microbial phylogenies and making taxonomic assignments at the genus level

oligonucleotide signiture sequences

short, conserved, nucleotide sequences that are specific for phylogenetically defined groups of organisms

The Ribosomal Database Project website

a repository of hundred of thousands of rRNA sequences and facilitates accurate comparative analysis

Indels

• taxon specific insertion and deletions

• useful when flanked by conserved regions

Restriction fragment length polymorphism

requires PCR amplification of the gene encoding the rRNA to provide enought DNA fro analysis

ribotyping

omits the need for PCR because the rRNA genes are detected by a labeled nucleotide probe.