INTRODUCTION TO MICROBIOLOGY

Dr. Rose Elaine D. Tan

What is Microbiology?
  

Micro - too small to be seen with the naked eye Bio life

ology - study

Definition Microbiology


branch of biology which deals with the study of minute living microorganism not visible to the naked eye and their effects on other living organisms

Microorganisms included :  1. Bacteria - simple, single cell  2. Fungi - single & multi cell forms - yeast, filamentous molds, complex fungi  3. Protists - single cell, some multicellular - algae, protozoans, slime molds  4. Viruses - acellular, intracellular parasites  5. Parasites - multicellular, more complex

Scope of Microbiology


    

Bacteriology - study of Bacteria - Group of microscopic, single-celled organisms that inhabit virtually all environments, including soil, water, organic matter, and the bodies of multicellular animals. Phycology - study of Algae Virology - study of Virus Mycology - study of Fungi Parasitology - study of Parasites Immunology - study of cells, molecules and mechanisms responsible for immunity

Health related:  1. Etiology

  

2. 3. 4. 5.

identification of causative agent of diseases Epidemiology study of spread of disease Immunology study of immune system Chemotherapy treatment of disease with chemical compounds Infection control control of spread of infectious diseases

BENEFICIAL APPLICATIONS (WHY STUDY MICROBIOLOGY ?)



A. Causative agents of infectious diseases and food poisoning (Pathogenic Organisms) B. Normal flora/Microbiota: - microorganisms that are normally found on or in the body and do not cause disease 1. Beneficial metabolic functions 2. Prevents invasion of pathogens and over growth of potential pathogens 3. Normal flora vs. identification pathogen

C. Environmental importance 1. Bacteria act as decomposers and produce oxygen 2. Food chain 3. Sewage treatment D. Industrial Importance 1. Food and Brewing industry - involved in the production of vinegar, cheese, bread, beer, and wine 2. Pharmaceutical industry - Probiotics - are dietary supplements of live beneficial bacteria (Lactobacillus & Bifidobacterium) or yeast which confer a health benefit on the host - Antibiotics - Produce industrial chemicals such as ethanol and acetone

E. Bioremediation clean up technology that uses naturally occurring microorganisms to degrade or neutralize hazardous substances into non/less toxic compounds in polluted soil or water - Exxon Valdez oil spill - 1989 - 2 Genera: Pseudomonas sp. & Bacillus sp F. Biotechnology: Recombinant DNA Technology, Gene Therapy, and Genetic Engineering - bacteria & fungi can be manipulated to produce enzymes and proteins they normally would not produce - Ex. Insulin, Human Growth Hormone, Interferon Vaccines and Antibiotic G. Research

BRIEF HISTORY

before microorganism were discovered, ancient people regarded diseases as a form of punishment sent by GOD for the sins of men Biblical disease - Leprosy - Tuberculosis - Syphilis - Plague

treatment and prevention of these diseases were sought by sacrifices to appease the anger of God

Marcus Terentius Varro  during the 2nd century B.C postulated the concept of contagion q diseases are transmitted by invisible creature


In De re rustica, a book on agriculture, he speculated that contagion from stagnant water might affect a person's health. (This theory of disease was first formulated scientifically in 1546 by Girolamo Fracastoro.)

Girolamo Fracastoro (1546)  Latin Hieronymus Fracastorius

 

He is best known for Syphilis His intense study of epidemic diseases led to his book On Contagion and Contagious Diseases He postulated that each disease is caused by a different type of rapidly multiplying minute body (invisible living things), transmitted by direct contact or by intermediary inanimate fomites or through the air.

Roger Bacon (13th century)  postulated that invisible living creatures called germs produce disease
 

He constructed the first magnifying lenses in 1267 Useful to enlarge detail on small organisms

Anton Van Leeuwenhoek  Father of Bacteriology  1st to describe bacteria in 1677 with the use of a simple microscope utilizing crude lenses


1st person to actually see live microorganisms animalcules that he observed in teeth scrapings, rain water, and peppercorn infusions Submitted detailed descriptions and drawings to the Royal Society of London described the 3 major forms of bacteria (rod, spherical, spiral) and fungi, protozoa, spermatozoa

Robert Hooke (1665)



developed the compound microscope that used reflected light and was able to confirm Leeuwenhoek s discoveries Founded the field of Microscopic Biology through his published work "Micrographia first person to coin the word cell to describe the tiniest components of the living system

ABIOGENESIS THEORY VS BIOGENESIS THEORY

The discovery of microbes both generated and spurred enough interest not only in the fundamental origin of living things but also augmented argument and speculations alike

Spontaneous Generation Theory (Abiogenesis)

This theory existed to explain the origin of some forms of life Living organisms arose spontaneously from nonliving, decaying organic matter. Believed to explain the origin of animalcules Spontaneous generation theory took another 200 years to disprove

 

Aristotle  proposed the Spontaneous Generation Theory  living things could develop spontaneously from non-living materials  Supported by appearance of living creatures in decaying meat, stagnating ponds, fermenting grain, and infected wounds

Experiments to disprove Spontaneous Generation Theory

1. Francesco Redi (1626-1697)  Introduced experimental procedure for disproof S.G  Utilized jars containing meat. Some were covered, some were not.  he challenged the idea that maggots arose spontaneously from rotting meat  Results not accepted for microscopic organisms.

Unsealed demonstrated the appearance of maggots in decomposing meat as a result on the deposition of eggs by flies 2. Sealed no maggots on meat 3. Partially covered -- realizing that the sealed containers were deprived of air, he used "fine Naples veil", and observed no worm on the meat, but they appeared on the cloth
1.

2. John Needham (1713-1781)



claimed that vital life is needed for the spontaneous generation of microbes Introduced the first culture medium for microbial growth utilizing infusion broth prepared by boiling meat & grain, to extract nutrients. Broth put in flasks, some were sealed with corks, some were not. Believing that boiling would kill all living things, he showed that when sealed right after boiling, the broths would cloud, allowing the belief in spontaneous generation to persist He added that the reason why no living organisms emerged from heated and sealed solutions in containers is that the vital life was destroyed by the heat and new vital life was not supplied to the solutions because they cannot enter the sealed containers

3. Lazzaro Spallanzani (1729-1799)



Repeated Needham s experiments but attempting to exclude the possibility of introducing a contaminating factor between boiling and sealing


Broth is boiled after placing in sealed flasks. (done by melting neck of the flask)

Although he did not see growth, the exclusion of air left the question of whether air was an essential factor in spontaneous generation Results more consistent with Redi s Occasionally sealed flask p cloudy

 

4 . Rudolph Virchow  in 1858, he challenged the spontaneous generation with his concept/theory of biogenesis.  He claimed that living cells can arise only from preexisting living cells  This concept would somehow explain the origin of animalcules seen under a microscope.  Although Virchow was correct with this concept, he lacked the needed experimental evidences demonstrating his concept of biogenesis.

5. John Tyndall
 

proved that dust carried germs also found out that bacterial spores could be killed by successive heating tyndallization (Fractional sterilization) - heating with free -flowing steam for 30-60min for 3 consecutive days at 100rC

6. Louis Pasteur

  

Placed boiled infusion broths in swan-necked flasks Flasks remained sterile unless tilted or neck broken The idea being that the bend in the neck prevented any particles from reaching the broth, while still allowing the free flow of air. The flask remained free of growth for an extended period. When the flask was tilted so that particles could fall down the bends, the broth became quickly clouded suggesting bacterial contamination

His experiment was accepted as disproof of theory of SG. Thus he claimed the prize for the contest conducted to disprove the spontaneous generation theory in 1864 Additional work:  Pasteurization - to prevent spoilage of wine.  Introduced Germ Theory of Disease after discovering silk worm disease caused by protozoan.

The Theory of Biogenesis

 

states that living things can only arise from living things and cannot be spontaneously generated Virchow introduced the Theory of Biogenesis attributed to Louis Pasteur - He provided the evidence that any appearance of spontaneous life in nonliving solutions can be attributed to microbes that already exist in the air or in the fluids themselves. Pasteur's (and others) empirical results were summarized in the phrase, Omne vivum ex vivo, Latin for all life [is] from life

Germ Theory of Disease

 

developed by Louis Pasteur it states that each specific infectious disease is caused by a specific microorganism Scientists hypothesized that since microorganisms have the ability to modify non-living organic matter, they may also have the ability to do the same in living plants and animals that the modifications (whether physical or chemical) they made to these organisms are the causes of disease. They later called this hypothesis as the germ theory of disease

Important Events That Strengthened the Germ Theory 1. Louis Pasteur (1865)  was able to prove that the new silk worm disease affecting the silk industry was caused by a protozoan.  He formulated a way to identify afflicted silkworm moths so that they would be destroyed and would not infect others.  He proved that the invisible protozoans cause disease to the silk worms.  Note that the invisibility of the protozoans is due to their very tiny sizes (a few micrometers) which can only be seen under a microscope

2. Joseph Lister (1878)  used the germ theory of disease to promote his idea that disinfection is necessary to prevent the spread of diseases caused by microorganisms  He promoted carbolic acid (phenol solution) as the disinfectant, knowing that it effectively kills bacteria.  When surgeons found out that the phenol solution has dramatically reduced the incidence of infections and deaths to patients, more doctors began using it until it became a standard operating procedure.  also developed the first pure culture technique using liquid medium which was the key to identification of bacteria

3. Robert Koch  first scientist to devise a series of proofs used to verify the germ theory of disease  used the germ theory of disease to prove that the disease anthrax, which kills cattle and sheep, is caused by a bacterium  Koch s Postulates - sequence of experimental procedures for directly associating a specific microorganism to a specific disease  Established proof of the microbial etiology of 3 important diseases of this day:  Cholera (V. cholerae)  Tuberculosis (M. tuberculosis)  Anthrax (Bacillus anthracis)

KOCK S POSTULATE
(Postulate 1) The organism must always be found in diseased animals and not in healthy one

(Postulate 2) Organisms isolated from the diseased animals must be grown in pure culture away from the diseased animals

(Postulate 4) Organisms must be re-isolated from experimentally infected animals

(Postulate 3) Organisms grown in pure culture must initiate and reproduce the disease when re-inoculated into susceptible animal

Exceptions to the Kock s Postulate : # 1) Carrier - some individual harbors the organism but do not manifest the disease and can transmit the disease to others # 2) Some or certain organisms/bacteria cannot be cultured in vitro (cannot grow in artificial culture media) Ex. Mycobacterium leprae / Treponema pallidum # 3) Certain animals not susceptible to certain microorganism - some animals are by nature immune cannot replicate even with the same specie - some bacterial specie are host specific Ex. Vibrio cholerae cannot cause chicken cholera or vice versa

The Golden Age of Microbiology 18571857-1914

 

Period (about 50 years) of rapid development. Causes of diseases identified, control methods developed, work began on viruses Beginning with Pasteur s work, discoveries included the relationship between microbes and disease, immunity, and antimicrobial drugs Edward Jenner  Developed small pox vaccination utilizing vaccinia virus.

Robert Koch  While studying anthrax ( a disease of cattle)  Identified a bacterium as cause of anthrax (first bacterium that caused a disease).  Introduced solid medium using agar.  Observed differences in colony morphology.  Introduced the inoculating loop to transfer bacteria and prepare pure cultures.  Introduced Koch s Postulates and the concept that a disease is caused by a single organism. Joseph Lister (1865)  Introduced the antiseptic technique .  Use of phenol (carbolic acid) as disinfectant.

Martinus Beijerink (1884-1885)  Discovered filterable agents called viruses (latin for toxins, poisons).  Infectious agents in tobacco plant fluid  Assumed soluble toxin in filtrate caused disease Paul Ehrlich (1912)  Introduced concept of chemotherapy.  Use of salvarsan for the treatment of syphilis. Alexander Fleming (1928)  Discovered the first antibiotic penicillin.  Produced by mold that contaminated bacterial culture plate.  Led to discovery of other fungi that secreted antibacterial substances (antibiotics)

Carl Linnaeus - the Father of Taxonomy - His system for naming, ranking, & classifying organisms is still in wide use - He established the system of scientific nomenclature: Genus & specie

MICROBIAL TAXONOMY


area of biologic science comprising of 3 distinct but highly interrelated disciplines that include: - Classification - Nomenclature - Identification

1. Establish phylogenic relationships between groups of organisms 2. Provides reference for identification by describing physical, chemical characteristics of previously identified and classified organisms 3. Provides universal language of communication

Classification


organization or level of classification of microorganisms that share similar morphologic, physiologic and genetic traits into specific groups or Taxa / Taxon Genus: comprised of different species that have several important features in common but differ sufficiently to still maintain their status as individual specie Species: most basic taxonomic group and may be defined as a collection of bacterial strains that share many common physiologic and genetic features and as a group differ notably from other bacterial specie

Hierarchical: broad divisions are divided up into smaller divisions: Kingdom Phylum Class Order Family Genus Species

Modern Taxonomy

Identification
 process by which a microorganism s key features are delineated  the profile is compared with those of other previously characterized microorganisms so that the organism in question can be classified within the most appropriate taxa and can be assigned an appropriate Genus and Species name

 General categories of identification method:  Genotypic characteristics  Relate to an organism s genetic make-up including the

nature of the organism s genes and constituent nucleic acid

 Phenotypic characteristics  includes readily observable characteristics  Morphology, staining reaction, antigenic properties,

environmental & nutritional requirements, resistance profiles

Nomenclature
 Scientific name (Systematic Name)  Binomial System of Nomenclature
       

first letter of the genus name - always capitalized first letter of the species name - small letter genus name may be used alone to indicate a genus group a species name is never used alone Genus and species are either:

underlined: Escherichia coli italicized: Eschericia col Abbreviated: E. coli

before microorganisms were discovered all living things were believed to be either plants and animals
-

no transition type were thought to exist after discovery of microorganism it was clear that microorganism combines both plant and animal properties
-

Evolution of Taxonomy Linnaeus 1735 2 kingdoms Haeckel 1866 3 kingdoms Protista Chatton 1937 2 empires Prokaryota Copeland 1956 4 kingdoms Monera

Vegetabilia Animalia

Plantae Animalia * Proposed the Kingdom

Eukaryota

Protista Plantae Animalia

Whittaker 1969 5 kingdoms Monera

Woese et al. 1977 6 kingdoms Eubacteria

Carl Woese et al. 1990 3 domains Bacteria

Protista Fungi Plantae Animalia

Archaebacteria Protista Fungi Plantae Animalia

Archaea Eukaryota

is a branching diagram showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics.  The taxa joined together in the tree are implied to have descended from a common ancestor.

EUCARYOTES higher protists

ex: algae red algae, brown algae green algae fungi Protozoan slime molds

EUKARYOTES


Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota

Possess a true nucleus .  a. Nuclear material surrounded by a nuclear membrane. b. contain the genetic information of the cell in multiple strands of DNA and proteins (chromosomes) c. Nucleus contains nucleolus - sites of ribosome synthesis Cell wall - Occur only on plant cells, fungi ; Composed of cellulose, chitin. cell membrane regulates flow of material in and out of the cytoplasm

cytoskeleton which provides support for the different organelles - contain complex phospholipids, sphingolipids, histones, sterols mitochondria are sites of energy production for cellular work ribosomes (80s) - masses of RNA and proteins that function as the site for protein synthesis golgi apparatus is where protein is packed for export endoplasmic reticulum is involved in the transport of newly synthesized proteins lysosomes are vesicles that contain enzymes for cellular digestive process

 

method of cell division: mitosis  mitosis - one cell divides to produce two genetically identical cells  meiosis - which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes)

PROKARYOTES
 

lower protists Are organisms that lack a cell-nucleus, or any other membrane-bound organelles Most are unicellular Prokaryotes belong to two taxonomic domains:  Bacteria  Archae (Archaebacteria)  Methanogen  extreme halophiles  thermoacidophiles

 

Characteristics:
    

lack a nucleus or nuclear membrane ribosome (70s) absent mitochondria have no organelles, histones and only in rare cases complex phospholipids, sphingolipids and sterols chemical activities takes place in the cytoplasm have a cell wall composed of peptidoglycan with muramic acid

 

are haploid with a single chromosome composed solely of DNA method of cell division: binary fission - is a form of asexual reproduction and cell division used by all prokaryotes, some protozoa, and some organelles within eukaryotic organisms. - This process results in the reproduction of a living prokaryotic cell by division into two parts that each have the potential to grow to the size of the original cell.