Introduction to microbiology. Classification and nomenclature of microorganisms

Course Introduction Instructor: Instructor: Dr Elena Romancenco Department of Microbiology, Virology and Immunology Department of Microbiology, Virology and Immunology WEBSITE:

Course objectives List major groups of microorganisms and their habitats. List major groups of microorganisms and their habitats. Overview and history of Microbiology. Overview and history of Microbiology. Describe the system of scientific nomenclature used to name microorganisms. Describe the system of scientific nomenclature used to name microorganisms.

Definition Microbiology (mikros bios logos – small, live, study) study microorganisms and their activities. Microbiology (mikros bios logos – small, live, study) study microorganisms and their activities. Microbiology is the study of microorganisms usually less than 1mm in diameter which requires some form of magnification to be seen clearly. Microbiology is the study of microorganisms usually less than 1mm in diameter which requires some form of magnification to be seen clearly. Microbiology - study the organisms that can exist as single cells, contain a nucleic acid genome for at least some part of their life cycle, and are capable of replicating that genome themselves or getting replicated with the help of host cells Microbiology - study the organisms that can exist as single cells, contain a nucleic acid genome for at least some part of their life cycle, and are capable of replicating that genome themselves or getting replicated with the help of host cells

Branches of Microbiology Bacteriology: study of bacteria Bacteriology: study of bacteria Mycology: study of fungi Mycology: study of fungi Virology: study of viruses Virology: study of viruses Beijerinck, NE: discovered intracellular reproduction of TMV; coined the term virus (1899) Beijerinck, NE: discovered intracellular reproduction of TMV; coined the term virus (1899) Parasitology: study of protozoa and parasitic worms Parasitology: study of protozoa and parasitic worms

Branches of Microbiology Immunology: study of immunity Immunology: study of immunity Edward Jenner, UK: developed vaccination (1798) Edward Jenner, UK: developed vaccination (1798) Metchnikoff, RU: discovered phagocytes (1884) Metchnikoff, RU: discovered phagocytes (1884) Paul Ehrlich, DE: theory of immunity (1890) Paul Ehrlich, DE: theory of immunity (1890) Chemotherapy Chemotherapy Treatment of disease by using chemical means Treatment of disease by using chemical means Antibiotics produced naturally Antibiotics produced naturally Synthetic drugs Synthetic drugs Paul Ehrlich (1878) – used arsenic compounds to fight disease Paul Ehrlich (1878) – used arsenic compounds to fight disease

Branches of Microbiology Chemotherapy Chemotherapy Alexander Fleming, Scotland (1928) discovered penicillin Alexander Fleming, Scotland (1928) discovered penicillin Selman Waksman, Ukraine (1944) discovered streptomycin Selman Waksman, Ukraine (1944) discovered streptomycin Problems Problems Toxicity of drugs => Selective toxicity Toxicity of drugs => Selective toxicity Resistance of bacteria to drugs Resistance of bacteria to drugs

Microorganisms are everywhere, but why is so important to learn about them? Affect our lives in many different ways.

Microbes are capable of growing in a wide variety of environments. Microbes are capable of growing in a wide variety of environments. Bacteria will grow in frigid glaciers to boiling volcanic springs, dry sands to the open ocean. Bacteria will grow in frigid glaciers to boiling volcanic springs, dry sands to the open ocean.

IMPORTANCE OF MICROORGANISMS Microorganisms are the oldest forms of life. Microorganisms are the oldest forms of life. Nutrient production & energy flow Nutrient production & energy flow Production of foods Production of foods Decomposition (bioremediation) Decomposition (bioremediation) Without certain microorganism life could not exist; produce O 2 and N 2 Without certain microorganism life could not exist; produce O 2 and N 2 Production of drugs & vaccines Production of drugs & vaccines Genetic engineering Genetic engineering Causing disease Causing disease Microorganisms have killed more people than have ever been killed in war.

Why Study Medical Microbiology? The majority of serious diseases in humans (especially those of early childhood) are due to microbial infections. The majority of serious diseases in humans (especially those of early childhood) are due to microbial infections. Prior to the discovery of antibiotics and vaccines, a large proportion of children died before adulthood because of infectious disease. Prior to the discovery of antibiotics and vaccines, a large proportion of children died before adulthood because of infectious disease. Till 1900, the average life expectancy in the United States was 40 years of age. Till 1900, the average life expectancy in the United States was 40 years of age. In years, largely due to the near eradication of most serious early childhood diseases. In years, largely due to the near eradication of most serious early childhood diseases. This trend is seen in the gap between developed and developing countries in terms of causes of death (mortality). This trend is seen in the gap between developed and developing countries in terms of causes of death (mortality).

MICROBES MICROBES includes all those living organisms that can not be viewed (seen) in any detail by the human eye. MICROBES includes all those living organisms that can not be viewed (seen) in any detail by the human eye. Alternatively, a MICROBE is any living creature that must be examined with a magnifying lens in order to see its unique physical characteristics (size, shape, motility, color). Alternatively, a MICROBE is any living creature that must be examined with a magnifying lens in order to see its unique physical characteristics (size, shape, motility, color).

Microbes Pathogen or pathogenic - capable of producing disease. Pathogen or pathogenic - capable of producing disease. Though only a minority of microorganisms are pathogenic, practical knowledge of microbes is necessary for their treatment so is highly relevant to medicine and related health sciences. Though only a minority of microorganisms are pathogenic, practical knowledge of microbes is necessary for their treatment so is highly relevant to medicine and related health sciences.microorganismsmicrobesmicroorganismsmicrobes Normal flora [ normal microbiota ] - n ot typically- disease-causing Normal flora [ normal microbiota ] - n ot typically- disease-causing microorganisms normally found in and on healthy individuals. microorganisms normally found in and on healthy individuals. microorganisms on the skin,on the skin, in the eyes,in the eyes, in the nose,in the nose, in the mouth,in the mouth, in the upper throat,in the upper throat, in the lower urethra,in the lower urethra, in the lower intestine.in the lower intestine.

the Bacterium Escherichia coli; a photosynthetic cyanobacterium a fungus Ebola virus the malaria parasite (a protozoan

A, Influenza virus; A, Influenza virus; B, West Nile Virus; B, West Nile Virus; C, Staphylococcus aureus; C, Staphylococcus aureus; D, Streptococcus pneumoniae.

Microbial morphology Microbial morphology Microbial cytology Microbial cytology Microbial physiology Microbial physiology Microbial ecology Microbial ecology Microbial genetics and molecular biology Microbial genetics and molecular biology Microbial taxonomy Microbial taxonomy Microbiologists may be interested in various characteristics or activities of microbs and may study:

Classification of life

For many years, living organisms were divided into two kingdoms: For many years, living organisms were divided into two kingdoms: Animalia (animal) and Animalia (animal) and Plantae (vegetable). Plantae (vegetable).

Classification Schemes Plantae Animalia Plantae Two kingdoms

But after 1800s, scientists realized that these two kingdoms could not adequately express the diversity of life. But after 1800s, scientists realized that these two kingdoms could not adequately express the diversity of life. Since the 1960s, the most widely used scheme - five kingdoms. Since the 1960s, the most widely used scheme - five kingdoms. five kingdoms five kingdoms Viruses are separate group of biological entities, although not organisms in the same sense as Eukaryotes, Archaea and Bacteria. Viruses are separate group of biological entities, although not organisms in the same sense as Eukaryotes, Archaea and Bacteria.

Classification schemes, 5 kingdoms Plantae AnimaliaPlantaeProtistaMoneraFungi Domain Bacteria (Eubacteria) Domain Archaea (Archaeabacteria) Prokaryotes Eukaryotes

Classification of Life 3 major Domains of life 3 major Domains of life Bacteria Bacteria Archaea Archaea Eukaryota (Eukarya) Eukaryota (Eukarya) The first two are Prokaryotes (Bacteria and Archaea)- without true nucleus, while the Eukaryotes all have a true nucleus in each cell. The first two are Prokaryotes (Bacteria and Archaea)- without true nucleus, while the Eukaryotes all have a true nucleus in each cell. The 3 Domains. Source:

Kingdom Monera All organisms in the Kingdom Monera are prokaryotes. All organisms in the Kingdom Monera are prokaryotes.prokaryotes lack nuclei and organelles lack nuclei and organelles most of their cell walls are made of peptidoglycan (the exceptions are the archaebacteria). most of their cell walls are made of peptidoglycan (the exceptions are the archaebacteria). The archaebacteria have cell walls that lack peptidoglycan, cell membranes that utilize different lipids, and ribosomes similar to those found in eukaryotes. The archaebacteria have cell walls that lack peptidoglycan, cell membranes that utilize different lipids, and ribosomes similar to those found in eukaryotes.lipidseukaryoteslipidseukaryotes The bacteria (eubacteria-true bacteria) are characterized by how they metabolize resources, their means of motility, and their shape. The bacteria (eubacteria-true bacteria) are characterized by how they metabolize resources, their means of motility, and their shape. Most organisms in the Kingdom Monera reproduce through binary fission (asexual) or conjugation (sexual). Most organisms in the Kingdom Monera reproduce through binary fission (asexual) or conjugation (sexual).

Bacteria Most utilize flagella for movement. Most utilize flagella for movement. Digestion is extracellular (outside the cell) and nutrients are absorbed into the cell. Digestion is extracellular (outside the cell) and nutrients are absorbed into the cell. Circulation and digestion in Kingdom Monera is accomplished through diffusion. Circulation and digestion in Kingdom Monera is accomplished through diffusion.

Bacterial Classification by Metabolism Metabolism Morphology (shape) Morphology (shape) Staining, etc Staining, etc

According the metabolism Autotrophs manufacture their own organic compounds. Autotrophs manufacture their own organic compounds. Heterotrophs obtain their energy by feeding on other organic substances. Heterotrophs obtain their energy by feeding on other organic substances. Saprophytes, a special kind of heterotroph, obtain energy by feeding on decaying matter. Saprophytes, a special kind of heterotroph, obtain energy by feeding on decaying matter.

According the symbiotic relationships with other organisms: In parasitism, harm is caused to the host. In parasitism, harm is caused to the host. In commensalism, one organism benefits while the other is unaffected. In commensalism, one organism benefits while the other is unaffected. In mutualism, both organisms benefit. In mutualism, both organisms benefit.

According the respiration: In obligate aerobes, the prokaryotes must have oxygen to live. In obligate aerobes, the prokaryotes must have oxygen to live. In obligate anaerobes, the organisms cannot survive in the presence of oxygen. In obligate anaerobes, the organisms cannot survive in the presence of oxygen. And in facultative anaerobes they can survive with or without oxygen. And in facultative anaerobes they can survive with or without oxygen.

According the shapes: cocci (spherical), cocci (spherical), bacillus (rod shaped), and bacillus (rod shaped), and spirillum (spirals). spirillum (spirals).

Classification of bacteria CocciCocci Micrococcus Micrococcus Staphylococci Staphylococci Irregular clusters of cocciIrregular clusters of cocci Diplococci Diplococci Pairs of cocciPairs of cocci Streptococci Streptococci Chains of cocciChains of cocci

Classification of bacteria Bacilli Bacilli Rod like Rod like Diplobacilli Diplobacilli Pairs of bacilliPairs of bacilli Streptobacilli Streptobacilli Chains of bacilliChains of bacilli Spirochetes Spirochetes SpiralSpiral

Size of bacteria Unit of microbial measurement Unit of microbial measurement micrometers (um) micrometers (um) 1 um being 10-6 m or m(1/25,000 inch)1 um being 10-6 m or m(1/25,000 inch) nanometers nanometers 1 nm being 10-9 or m.1 nm being 10-9 or m. Pathogenic bacterial species vary from approximately 0.4 to 2 um in size Pathogenic bacterial species vary from approximately 0.4 to 2 um in size

Taxonomy Taxonomy is the classification of organisms. The most common system in use today is the Five Kingdoms: Taxonomy is the classification of organisms. The most common system in use today is the Five Kingdoms: Monera (Prokaryota), Monera (Prokaryota), Monera (Prokaryota) Monera (Prokaryota) Protista, Protista, Protista Fungi, Fungi, Fungi Plantae, and Plantae, and Plantae Animalia. Animalia. Animalia Organisms in each kingdom are divided into phyla. Organisms in each kingdom are divided into phyla. In each phylum, organisms are separated into classes. In each phylum, organisms are separated into classes. In each class, organisms are segregated into orders. In each class, organisms are segregated into orders. In each order, organisms are divided into families. In each order, organisms are divided into families. In each family, organisms are separated by genus. In each family, organisms are separated by genus. And finally, in each genus organisms are divided into species. And finally, in each genus organisms are divided into species. Just remember that King Philip Can Order For Genial Students. Just remember that King Philip Can Order For Genial Students.

Naming micoorganisms Binomial (scientific) nomenclature Binomial (scientific) nomenclature Gives each microbe 2 names Gives each microbe 2 names Genus - noun, always capitalized and may be abbreviated Genus - noun, always capitalized and may be abbreviated species - adjective, lowercase, never abbreviated species - adjective, lowercase, never abbreviated A genus name may be used alone to indicate a genus group; a species name is never used alone A genus name may be used alone to indicate a genus group; a species name is never used alone eg: Bacillus subtilis B. subtiliseg: Bacillus subtilis B. subtilis Both italicized or underlined Both italicized or underlined Staphylococcus aureus (S. aureus) Staphylococcus aureus (S. aureus) Bacillus subtilis(B. subtilis) Bacillus subtilis(B. subtilis) Escherichia coli(E. coli) Escherichia coli(E. coli)

Nomenclature Common or descriptive names (trivial names) Common or descriptive names (trivial names) Names for organisms that may be in common usage, but are not taxonomic names Names for organisms that may be in common usage, but are not taxonomic names eg: tubercle bacillus (Mycobacterium tuberculosis)eg: tubercle bacillus (Mycobacterium tuberculosis) meningococcus (Neiserria meningitidis)meningococcus (Neiserria meningitidis) Group A streptococcus (Streptococcus pyogenes )Group A streptococcus (Streptococcus pyogenes )

Eukaryotes

Prokaryotes Kingdom - Monera Kingdom - Monera Domain - Bacteria Domain - Bacteria Phylum – Proteobacteria Phylum – Proteobacteria Class – Gammaproteoba Class – Gammaproteoba Order – Enterobacteriale Order – Enterobacteriale Family – Enterobacteriace Family – Enterobacteriace Genus – Escherichia Genus – Escherichia Species – Escherichia coli Species – Escherichia coli

Louis Pasteur "The role of the infinitely small in nature is infinitely large"

Historical Perspectives

HistoricalYEARNAMEACHIEVEMENT 1 st century BC Varo Concept of Animalia minuta 1546Fracostorius Contagion- Cause of syphilis 1590Jensen Hand lens 1683 Antony van Leeuwenhoek First Microscope Animalcules 1678 Robert Hook Compound microscope 1745 Needham (Priest) Abiogenesis 1836 Schulze & Schwan Air contains microbes 1840 Oliver Homes, Poet physician Contageousness & Puerperal fever 1846 Ignaz Semmelweis Cause, concept & prophylaxis of child-bed fever 1853 Augustino Bassi Silk worm disease due to a fungus

Pioneers of Microbiology Robert Hooke, UK (1665) Robert Hooke, UK (1665) Proposed the Cell Theory Proposed the Cell Theory Observed cork with crude microscope Observed cork with crude microscope All living things are composed of cells All living things are composed of cells Spontaneous generation Spontaneous generation Some forms of life could arise spontaneously from non-living matter Some forms of life could arise spontaneously from non-living matter Francesco Redi, IT (1668) Francesco Redi, IT (1668) Redis experiments first to dispprove S.G. Redis experiments first to dispprove S.G.

Antonie van Leeuwenhoek First to observe living microbes First to observe living microbes his single-lens magnified up to 300X his single-lens magnified up to 300X ( )

Louis Pasteur French chemist French chemist Father/Founder of Modern Microbiology Father/Founder of Modern Microbiology Fermentation – a microbiological process Fermentation – a microbiological process Beer/Wine not produced without microbes Beer/Wine not produced without microbes Showed microbes caused fermentation & spoilage Showed microbes caused fermentation & spoilage Disproved spontaneous generation of m.o. Disproved spontaneous generation of m.o. Developed aseptic techniques. Developed aseptic techniques. Developed a rabies vaccine. Developed a rabies vaccine. ( )

Louis Pasteur Methods & Techniques of cultivation Methods & Techniques of cultivation Introduced sterilization Introduced sterilization Tyndalization (Tyndal-1877) Tyndalization (Tyndal-1877) Studied Silkworm disease, anthrax, chicken cholera, hydrophobia. Studied Silkworm disease, anthrax, chicken cholera, hydrophobia. Introduced live vaccines – Jenner (Cow- pox vaccine) Introduced live vaccines – Jenner (Cow- pox vaccine) Antirabic vaccine Antirabic vaccine Pasteur Institutes Pasteur Institutes

Joseph Lister 1867 Prof of Surgery, Glasgow Royal Infirmatory Prof of Surgery, Glasgow Royal Infirmatory Introduced Antiseptic Surgery Introduced Antiseptic Surgery Called Father of Antiseptic Surgery Called Father of Antiseptic Surgery

Robert Koch German general practitioner German general practitioner Perfected bacteriological techniques Perfected bacteriological techniques Isolated pure cultures of bacteria for the first time Isolated pure cultures of bacteria for the first time Discovered Anthrax bacilli, Cholera vibrio, M. tuberculosis Discovered Anthrax bacilli, Cholera vibrio, M. tuberculosis Father of Medical Microbiology Father of Medical Microbiology Hypersensitivity Hypersensitivity Established a sequence of experimental steps to show that a specific m.o. causes a particular disease. Established a sequence of experimental steps to show that a specific m.o. causes a particular disease. ( )

Highlights in the History of Microbiology 1887 Invented Petri Dish Invented Petri Dish (R.J. Petri) (R.J. Petri)1892 Discovered viruses (Dmitri Iosifovich Ivanovski) Discovered viruses (Dmitri Iosifovich Ivanovski)(Dmitri Iosifovich Ivanovski)(Dmitri Iosifovich Ivanovski)1899 Recognized viral dependence on cells for reproduction (Martinus Beijerinck) Recognized viral dependence on cells for reproduction (Martinus Beijerinck)(Martinus Beijerinck)(Martinus Beijerinck)1900 Proved mosquitoes carried the yellow fever agent (Walter Reed) Proved mosquitoes carried the yellow fever agent (Walter Reed) (Walter Reed) (Walter Reed)1910 Discovered cure for syphilis (Paul Ehrlich) Discovered cure for syphilis (Paul Ehrlich) (Paul Ehrlich) (Paul Ehrlich)1928 Discovered Penicillin (Alexander Fleming) Discovered Penicillin (Alexander Fleming) (Alexander Fleming) (Alexander Fleming)

Highlights in the History of Microbiology Developed a method to sequence DNA (W. Gilbert & F. Sanger) (W. Gilbert & F. Sanger)(W. Gilbert & F. Sanger) Polymerase Chain Reaction invented (Kary Mullis) (Kary Mullis)(Kary Mullis) First microbial genomic sequence published (H. influenzae) (TIGR) (H. influenzae)(TIGR)(H. influenzae)(TIGR)