Prof. RNDr. Jaroslav Spížek, DrSc. itute of Microbiology, Academy of Sciences of the Czech Repub Vídeňská 1083 142 20 Praha 4 Telephone: +420 2 4106 2212 Fax: +420 2 4106 2201 E-mail: spizek @biomed.cas.c z Recommended literature: František Kaprálek: Základy bakteriologie V. Fraňková, J. Schindler, A. Souček, J. Vávra: Lékařská mik dmila Šilhánková: Mikrobiologie pro potravináře a biotechnolo T. Brock: Biology of Microorganisms 1 Biology of Microorganisms – 1 Biology of Microorganisms – School of Natural Sciences of the School of Natural Sciences of the University of South Bohemia University of South Bohemia
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Prof. RNDr. Jaroslav Spížek, DrSc.Institute of Microbiology, Academy of Sciences of the Czech Republic
František Kaprálek: Základy bakteriologieM. Bednář, V. Fraňková, J. Schindler, A. Souček, J. Vávra: Lékařská mikrobiologie
Ludmila Šilhánková: Mikrobiologie pro potravináře a biotechnologyT. Brock: Biology of Microorganisms
1 Biology of Microorganisms – 1 Biology of Microorganisms – School of Natural Sciences of the School of Natural Sciences of the
University of South BohemiaUniversity of South Bohemia
1a Biology of Microorganisms – 1a Biology of Microorganisms – School of Natural Sciences of the School of Natural Sciences of the
University of South BohemiaUniversity of South Bohemia Recommended literature continued:Recommended literature continued: G.J. Tortora, B.R. Funke, C.E. Case – G.J. Tortora, B.R. Funke, C.E. Case –
Microbiology – An IntroductionMicrobiology – An Introduction A.A. Salyers, D.D. Whitt – Bacterial A.A. Salyers, D.D. Whitt – Bacterial
Pathogenesis – Pathogenesis –
A Molecular ApproachA Molecular Approach
2 Biology of Microorganisms – School of 2 Biology of Microorganisms – School of Natural Sciences, University of South Natural Sciences, University of South
BohemiaBohemia
What are microorganisms?What are microorganisms? Which organisms are classified as Which organisms are classified as
microorganisms?microorganisms? Significance of microorganisms in natureSignificance of microorganisms in nature Basic life features of microorganismsBasic life features of microorganisms Selected metabolic processes of Selected metabolic processes of
microorganismsmicroorganisms Brief review of bacterial geneticsBrief review of bacterial genetics Pathogenicity and infectionPathogenicity and infection Classical and modern microbial Classical and modern microbial
biotechnologies biotechnologies
3 3 Microorganisms grow on us Microorganisms grow on us and inside usand inside us
Most cells in our body are microbialMost cells in our body are microbial They grow on us – we can find them They grow on us – we can find them
everywhere, on our skin, eyes, mouth, everywhere, on our skin, eyes, mouth, nose and on the whole body surfacenose and on the whole body surface
They grow inside us – they are They grow inside us – they are particularly abundant in our particularly abundant in our gastrointestinal tract, there are more gastrointestinal tract, there are more than 10than 101414 microbes in our intestines microbes in our intestines
We are a walking collection of different We are a walking collection of different species, although we have our own cells, species, although we have our own cells, we carry ten times more microbial cells. we carry ten times more microbial cells.
4 Is our DNA „human“?4 Is our DNA „human“?
We carry many genes identical with those We carry many genes identical with those of other animals but also microorganismsof other animals but also microorganisms
Most of the genetic information we carry is Most of the genetic information we carry is microbial microbial
We do not know most microbes colonizing We do not know most microbes colonizing us as only 1 – 2 % of them can be cultivatedus as only 1 – 2 % of them can be cultivated
DNA analysis shows that each of us carries DNA analysis shows that each of us carries 500 – 1 000 microbial species with more 500 – 1 000 microbial species with more
than 8 000 subspecies than 8 000 subspecies This colonization differs in different This colonization differs in different
individuals and, in a certain sense, can individuals and, in a certain sense, can serve as fingerprints.serve as fingerprints.
5 Mi5 Miccroorganisms are not roorganisms are not only a bunch of aggressorsonly a bunch of aggressors
Friends or enemies?Friends or enemies? We developed togetherWe developed together Human body is a complex ecosystem, similarly to Human body is a complex ecosystem, similarly to
the biospherethe biosphere Individual species follow their own program, but Individual species follow their own program, but
together they constitute a complex with together they constitute a complex with resulting activities resulting activities
Intestinal microorganisms have some essential Intestinal microorganisms have some essential functionsfunctions;; they help us to digest food, synthesize they help us to digest food, synthesize vitamins and prevent us from some diseasesvitamins and prevent us from some diseases
With microorganisms we form a quasi strategic With microorganisms we form a quasi strategic alliance, symbiosis that had developed for alliance, symbiosis that had developed for millions of years millions of years
6 Are we creators of our own 6 Are we creators of our own development?development?
Can we optimize the activity of our Can we optimize the activity of our own microbial community in our favor?own microbial community in our favor?
What if we finally find (a little unlikely What if we finally find (a little unlikely presumption) that our own presumption) that our own development is essentially a side effect development is essentially a side effect of requirements of microorganisms in of requirements of microorganisms in our intestine?our intestine?
What if the microorganisms needed to What if the microorganisms needed to modify their hosts to make them more modify their hosts to make them more efficient sources of their nutrition?efficient sources of their nutrition?
7 Organisms considered 7 Organisms considered microrganismsmicrorganisms
The term microorganisms is The term microorganisms is somewhat old-fashioned at present; somewhat old-fashioned at present; the modern taxonomy recognizes the modern taxonomy recognizes three primary groups of living three primary groups of living organisms, organisms, viz. Archaebacteriaviz. Archaebacteria, , EubacteriaEubacteria and and UrcaryotaeUrcaryotae. For the . For the sake of simplicity, sake of simplicity, in this lecture in this lecture we we will stick with the old definitionwill stick with the old definition according to which microorganisms according to which microorganisms are all organisms with microscopic are all organisms with microscopic size.size.
8 Classification of 8 Classification of organisms according to organisms according to
rRNA sequence (a)rRNA sequence (a) The conception of comparing rRNA The conception of comparing rRNA
sequences was introduced by Carl Woese at sequences was introduced by Carl Woese at the beginning of the seventiesthe beginning of the seventies
He selected sequences of ribosomal RNAs He selected sequences of ribosomal RNAs since they are ubiquitous and highly since they are ubiquitous and highly conservedconserved
On the basis of rRNA sequencing he coined On the basis of rRNA sequencing he coined the term „archaebacteria“ which in 1990 the term „archaebacteria“ which in 1990 were renamed archaea to emphasize that were renamed archaea to emphasize that they are fundamentally different from they are fundamentally different from bacteriabacteria
According to this classification organisms According to this classification organisms can be divided to: can be divided to:
ArchaeaArchaea BacteriaBacteria EucaryaEucarya
9 Classification of 9 Classification of organisms according to organisms according to
rRNA sequence (b)rRNA sequence (b) The developmental tree of life based The developmental tree of life based
on rRNA represents the evolutionary on rRNA represents the evolutionary flow of the genetic system, the flow of the genetic system, the essence of cellsessence of cells
Developmental trees should thus not Developmental trees should thus not be viewed as „organismic trees“ but be viewed as „organismic trees“ but rather as the more abstract „lines of rather as the more abstract „lines of descent“ of the genetic machinerydescent“ of the genetic machinery
Although we may think of dinosaurs Although we may think of dinosaurs as extinct, the line of descent from as extinct, the line of descent from which dinosaurs emerged is alive which dinosaurs emerged is alive today in the form of birdstoday in the form of birds
10 Molecular tree of life10 Molecular tree of life
11 Molecular tree of life 11 Molecular tree of life continues to expand continues to expand
A lesson from molecular phylogenetics is A lesson from molecular phylogenetics is that all known cellular life is related and has that all known cellular life is related and has a common origin a common origin
The last universal common ancestral „root“ The last universal common ancestral „root“ cannot be inferred only from rRNA datacannot be inferred only from rRNA data
However, other phylogenetic results, as well However, other phylogenetic results, as well as biochemical correlates put the root of the as biochemical correlates put the root of the molecular tree on the bacterial linemolecular tree on the bacterial line
This bacterial line means that the eucaryal This bacterial line means that the eucaryal and archaeal lines separated from one and archaeal lines separated from one another after they separated from the another after they separated from the bacterial linebacterial line
12 The molecular tree of 12 The molecular tree of life continues to expand life continues to expand
(continued)(continued) Eucaryotes and archaea are thus more Eucaryotes and archaea are thus more
related to one another than either is to related to one another than either is to bacteria bacteria
Bacteria use Bacteria use σσ factors to control factors to control transcription initiation transcription initiation
Both archaea and eucaryotes use a Both archaea and eucaryotes use a different mechanism, TATA-binding different mechanism, TATA-binding proteins proteins
Bacteria wrap their DNA in a variety of Bacteria wrap their DNA in a variety of basic proteins, while eucaryotes and basic proteins, while eucaryotes and archaea use histonesarchaea use histones
13 Microbial kingdom – 13 Microbial kingdom – cultured and non-cultured cultured and non-cultured
microorganismsmicroorganisms Among bacteria only 12 phyla were Among bacteria only 12 phyla were
identified in 1987, and all had identified in 1987, and all had representative cultured organismsrepresentative cultured organisms
Now more than 70 phylum-level Now more than 70 phylum-level bacterial lines are known, but only bacterial lines are known, but only about 20 have representatives that about 20 have representatives that have been culturedhave been cultured
Only seven of the cultured phyla, Only seven of the cultured phyla, those that contain human pathogens, those that contain human pathogens, have significant representation have significant representation through culture studiesthrough culture studies
Archaeal phylogeny also proves much Archaeal phylogeny also proves much more complex than originally thoughtmore complex than originally thought
14 Cultured and non-14 Cultured and non-cultured microorganisms cultured microorganisms
(continued)(continued) Based on limited culture studies Based on limited culture studies
crenoarchaeotes are commonly crenoarchaeotes are commonly described as extreme thermophiles described as extreme thermophiles
In the light of environmental In the light of environmental sequences, the cultured, thermophile sequences, the cultured, thermophile crencrenooarchaeotes are only one line archaeotes are only one line among many other low-temperature among many other low-temperature organisms occurring globally organisms occurring globally
Although these environmental Although these environmental crenoarcheotes are among the most crenoarcheotes are among the most abundant kinds of organisms on abundant kinds of organisms on Earth, their roles in the global Earth, their roles in the global ecosystem remain obscure. ecosystem remain obscure.
The complete genome of the bacterium The complete genome of the bacterium Mycoplasma genitalium Mycoplasma genitalium was prepared was prepared synthetically (synthetically (in vitro)in vitro)
It is the smallest genome of a living organism It is the smallest genome of a living organism containing 485 active genescontaining 485 active genes
M. genitalium M. genitalium containscontains a single chromosomea single chromosome The next step will be to clone this genome in The next step will be to clone this genome in
the cell and investigate, whether it is functional the cell and investigate, whether it is functional This represents one of the next steps aimed at This represents one of the next steps aimed at
the production of synthetic microorganismsthe production of synthetic microorganisms It is estimated that there are about 100 genes It is estimated that there are about 100 genes
that cannot be deleted without endangering the that cannot be deleted without endangering the cell’scell’s viability viability
18 Some definitions18 Some definitions Autotrophic organisms Autotrophic organisms are those that can synthesize all are those that can synthesize all
their cell material from carbon dioxidetheir cell material from carbon dioxide Photosynthetic autotrophs Photosynthetic autotrophs derive their energy for this derive their energy for this
synthesis from sunlightsynthesis from sunlight; ; greeen plants, algae and some greeen plants, algae and some bacteria fall into this categorybacteria fall into this category
Chemosynthetic autotrophs Chemosynthetic autotrophs are represented only by a are represented only by a small number of bacteria. They derive their energy for small number of bacteria. They derive their energy for carbon dioxide fixation from the oxidation of inorganic carbon dioxide fixation from the oxidation of inorganic moleculesmolecules
Heterotrophic organisms Heterotrophic organisms include animals, fungi, include animals, fungi, protozoans and most bacteria. They require an organic protozoans and most bacteria. They require an organic carbon sourcecarbon source
Photosynthetic heterotrophs Photosynthetic heterotrophs derivederive their energytheir energy from from sunlight, require organic compounds as carbon sources and sunlight, require organic compounds as carbon sources and are represented by only a small number of bacteriaare represented by only a small number of bacteria
Chemosynthetic heterotrophs Chemosynthetic heterotrophs – require organic – require organic molecules as both carbon and energy sources. Higher molecules as both carbon and energy sources. Higher animals, including you and me, protozoans, fungi and most animals, including you and me, protozoans, fungi and most bacteria fall into this group bacteria fall into this group
19 Microorganisms – 19 Microorganisms – friends or enemies? (a)friends or enemies? (a)
Microorganisms and diseaseMicroorganisms and disease A major characteristic of some microorganisms A major characteristic of some microorganisms
is that they cause diseases of humans, animals is that they cause diseases of humans, animals and plantsand plants
Why are some microbes disease-causing or Why are some microbes disease-causing or pathogenicpathogenic andand others not? others not?
Pathogenic microorganisms are often much Pathogenic microorganisms are often much less robust than their free-living relativesless robust than their free-living relatives
They may require a supply of particular They may require a supply of particular complex organic molecules which can only be complex organic molecules which can only be provided by the host plant or animalprovided by the host plant or animal
The body of a human or other warm-blooded The body of a human or other warm-blooded animal can provide the conditions which a animal can provide the conditions which a pathogen may require to survive and which may pathogen may require to survive and which may not exist in the outside worldnot exist in the outside world
20 Microorganisms 20 Microorganisms causing serious health causing serious health
Etiological agent – protozoans Etiological agent – protozoans Plasmodium falciparumPlasmodium falciparum, , P. vivaxP. vivax, , P. P. ovale ovale and and P. malariaP. malaria
300 – 500 million people get sick every 300 – 500 million people get sick every yearyear
Of them about 3 million die, mostly Of them about 3 million die, mostly children younger than 5 years children younger than 5 years
Three thousand children per dayThree thousand children per day Total number of deaths higher than Total number of deaths higher than
that caused by AIDSthat caused by AIDS
23 Tuberculosis (a)23 Tuberculosis (a) It is caused by It is caused by Mycobacterium tuberculosis Mycobacterium tuberculosis
andand comes back as the „disease of the poor“ comes back as the „disease of the poor“ Most sick live in India, 1 000 people die Most sick live in India, 1 000 people die
every day every day Similarly to leprosy, the sick are often Similarly to leprosy, the sick are often
rejected by the society and even by their rejected by the society and even by their families families
It has exploded into a pandemic – 9 million It has exploded into a pandemic – 9 million people get sick every year and 2 million diepeople get sick every year and 2 million die
Even in this country tuberculosis comes Even in this country tuberculosis comes back due to the antibiotic resistant strains of back due to the antibiotic resistant strains of Mycobacterium tuberculosisMycobacterium tuberculosis
24 Tuberculosis (b)24 Tuberculosis (b) It is said that in this country ouf of tenIt is said that in this country ouf of ten
tuberculosis cases as many as four are tuberculosis cases as many as four are lethal lethal
Mycobacterium tuberculosis Mycobacterium tuberculosis successfully cooperates with the HIV successfully cooperates with the HIV virus impairing the immune system. virus impairing the immune system. Tuberculosis is then the main death Tuberculosis is then the main death cause in AIDS patientscause in AIDS patients
Tuberculosis is highly contagious – it is Tuberculosis is highly contagious – it is air-borne, inhalation of only a very air-borne, inhalation of only a very small amount of bacsmall amount of bacteriateria is infective is infective
Every non-treated person can infect 10-Every non-treated person can infect 10-15 people per year 15 people per year
2004 – 20 million infected2010 - estimated 70 million infected
Worldwide 16 000 people are infected every day95 % new cases in Africa
More than 60 virostatics are usedAbout 200 new drugs are currently clinically tested
Most of them help to decrease the disease progressionIn spite of this the number of new cases increases
geometrically and the therapeutic results are not very satisfactory
25 A I D S (Acquired 25 A I D S (Acquired Immunodeficiency Immunodeficiency
Syndrome)Syndrome)
Massive and often not justified uses of antibiotics support selection of resistant microorganisms
Global warming may increase distribution and survival of natural reservoirs and vectors resulting in the occurrence
and spread of diseases, e.g. malaria, cholera and Hantavirus infections
26 26 Factors contributing to Factors contributing to the spread of infectious the spread of infectious
diseases (a)diseases (a)
Known diseases move to new geographical regions thanks to modern transportation means, which would have been highly
unlikely 100 years ago Originally unknown infections can occur in individuals living or working in areas with subject to
ecological changes
27 Factors contributing to 27 Factors contributing to the spread of infectious the spread of infectious
diseases (b)diseases (b)
Infections caused by bacteria and fungi affect hundreds of millions people all over
the worldFinancial burden amounts to about $ 30
billion in USA aloneSome programs aimed at the development of new antibiotics and other antimicrobial
drugs (not too many) are in general motivated by the occurrence of
microorganisms resistant against currently used drugs
28 Research and 28 Research and development of new drugs development of new drugs against infectious diseasesagainst infectious diseases
Selected projects:
Liposomal nystatin against fungal infectionsGlyminox against mouth candidosesGatifloxacin against most varied bacterial infectionsAmikacin against bacterial infectionsAntibiotics against vancomycin and teicoplanin resistant enterococciAzithromycin against bacterial infectionsStreptogramin against vancomycin resistant enterococciNew virostatics (some of them developed at the Institute of Organic Chemistry and Biochemistry) are currently clinically tested
29 Search for new antiviral, 29 Search for new antiviral, antibacterial and antifungal antibacterial and antifungal
Intestinal tract of animals including man Intestinal tract of animals including man depends on the presence of microorganisms – depends on the presence of microorganisms – e.ge.g. degradation of cellulose. degradation of cellulose
Synthesis of vitamins in intestinal tract – Synthesis of vitamins in intestinal tract – vitamins B and Kvitamins B and K
Nitrogen fixation from the air – production of Nitrogen fixation from the air – production of organic compoundsorganic compounds
Photosynthesis – production of saccharides Photosynthesis – production of saccharides from carbon dioxidefrom carbon dioxide
Industrial applications of microorganisms – Industrial applications of microorganisms – synthesis of acetone, organic acids, alcohols, synthesis of acetone, organic acids, alcohols, enzymes, antibiotics and many other drugsenzymes, antibiotics and many other drugs
Degradation of waste materialsDegradation of waste materials
31 Microorganisms in the 31 Microorganisms in the environment (a)environment (a)
Nitrogen fixation – some free living bacteria Nitrogen fixation – some free living bacteria (number of blue-green bacteria) and symbiotic (number of blue-green bacteria) and symbiotic bacteria (bacteria (Rhizobium – Rhizobium – root nodules of leguminous root nodules of leguminous plants). Nitrogen from the atmosphere is plants). Nitrogen from the atmosphere is incorporated into the proteins and nucleic acids of incorporated into the proteins and nucleic acids of nitrogen fixing bacterianitrogen fixing bacteria
Ammonification – to be made available to plants Ammonification – to be made available to plants and animals, these microbes must die. Protein and animals, these microbes must die. Protein amino acids are enzymatically deaminated to amino acids are enzymatically deaminated to release fixed nitrogen as the ammonium ions release fixed nitrogen as the ammonium ions (NH(NH44
++)) Nitrification – Nitrification – although although some plants can also use some plants can also use
other inorganic compounds as their nitrogen other inorganic compounds as their nitrogen source, it is the nitrate ion (NOsource, it is the nitrate ion (NO33
--) which is the ) which is the major source of nitrogen used by plants. To major source of nitrogen used by plants. To produce nitrate produce nitrate from from ammonium, two oxidation ammonium, two oxidation steps are carried out by steps are carried out by nitrifying bacterianitrifying bacteria. .
32 Microorganisms in the 32 Microorganisms in the environment (b)environment (b)
The ammonium ion is initially oxidized to The ammonium ion is initially oxidized to the nitrite ion (NO the nitrite ion (NO 2 2
--) by bacteria ) by bacteria NitrosomonasNitrosomonas, , Nitrosococcus Nitrosococcus and and NitrosobolusNitrosobolus. Nitrite is then oxidized to . Nitrite is then oxidized to nitrate by nitrate by NitrobacterNitrobacter. In this way the . In this way the nitrate required as the major source of nitrate required as the major source of nitrogen for plants is produced.nitrogen for plants is produced.
Denitrification – nitrate (NODenitrification – nitrate (NO33--) is reduced ) is reduced
all the way to gaseous nitrogen in the all the way to gaseous nitrogen in the process carried out by process carried out by denitrifying bacteriadenitrifying bacteria – – PseudomonasPseudomonas, , BacillusBacillus, , ThiobacillusThiobacillus,, chemolitotrophic bacteria chemolitotrophic bacteria Paracoccus Paracoccus denitrificansdenitrificans
33 Nitrogen cycle33 Nitrogen cycle
34 34 Advantages of Advantages of microorganisms as microorganisms as
experimental subjectsexperimental subjects Many are relatively simple and inexpensive to grow and Many are relatively simple and inexpensive to grow and
maintain in laboratory culturesmaintain in laboratory cultures So far, no one has protested against the use of So far, no one has protested against the use of
microorganisms as experimental organisms and there are microorganisms as experimental organisms and there are no ethical objections to experimenting with such organismsno ethical objections to experimenting with such organisms
Microorganisms exist as essentially homogenous Microorganisms exist as essentially homogenous populations of cells. That is, we do not encounter the populations of cells. That is, we do not encounter the situation we find with multicellular organisms which situation we find with multicellular organisms which consist of a large variety of different cell types. In addition, consist of a large variety of different cell types. In addition, biochemical investigations of plant And animal cells biochemical investigations of plant And animal cells require preliminary dissection and separation of different require preliminary dissection and separation of different cell types. This is usually not the case with unicellular cell types. This is usually not the case with unicellular microbes because all the cells are the same microbes because all the cells are the same
Microbial populations rapidly increase in size because of Microbial populations rapidly increase in size because of the very short times between successive generations. Some the very short times between successive generations. Some bacteria can reproduce as often as every 20 minutes bacteria can reproduce as often as every 20 minutes meaning that genetics experiments can be set up on a meaning that genetics experiments can be set up on a particular day and the offspring will be produced either the particular day and the offspring will be produced either the next day or within a few daysnext day or within a few days
35 Relationships among 35 Relationships among radius, surface and volumeradius, surface and volume
36 Microorganisms in 36 Microorganisms in industryindustry
Microorganisms have been essential for production Microorganisms have been essential for production of dairy products and alcoholic drinks for thousands of dairy products and alcoholic drinks for thousands of yearsof years
Initially people apparently did not know of their Initially people apparently did not know of their involvement in such processes involvement in such processes
Modern era of industrial microbiology is said to have Modern era of industrial microbiology is said to have begun with the production of a number of organic begun with the production of a number of organic solvents – acetone, isopropanol and butanol by solvents – acetone, isopropanol and butanol by Clostridium acetobutylicumClostridium acetobutylicum
Acetone provided the raw material for the production Acetone provided the raw material for the production of the high explosive trinitrotoluene (TNT)of the high explosive trinitrotoluene (TNT)
((The use of Clostridium acetobutylicum for acetone The use of Clostridium acetobutylicum for acetone production was developed by Chaim Weizmann in production was developed by Chaim Weizmann in Manchester during World War I. It is said that the grateful Manchester during World War I. It is said that the grateful British government agreed to support the establishment of British government agreed to support the establishment of the State of Israel after World War II as an expression of the State of Israel after World War II as an expression of gratitude to Weizmann, who became Israel‘ s first gratitude to Weizmann, who became Israel‘ s first President)President)
37 Microorganisms in 37 Microorganisms in industry (continued)industry (continued)
Major progress of the uses of Major progress of the uses of microorganisms in industry came with the microorganisms in industry came with the development of the techniques of genetic development of the techniques of genetic engineeringengineering
By means of these techniques, genes from By means of these techniques, genes from any organism, including humans, can be any organism, including humans, can be incorporated into bacteria or other microbesincorporated into bacteria or other microbes
Once the genes are incorporated, Once the genes are incorporated, engineered bacteria can then be used to engineered bacteria can then be used to synthesize a variety of therapeutic synthesize a variety of therapeutic compounds such as hormones and other compounds such as hormones and other compounds, e.g. industrial enzymes etc. compounds, e.g. industrial enzymes etc.
38 Taxonomic criteria and 38 Taxonomic criteria and methods for classification and methods for classification and identification of bacteria (a)identification of bacteria (a)
MethodMethod ClassificatioClassificationn
IdentificatioIdentificationn
MorphologyMorphology yesyes yesyes
StainingStaining yesyes yesyes
Biochemistry Biochemistry nono yesyes
SerologySerology nono yesyes
PhagotypizatPhagotypizationion
nono yesyes
A.a. A.a. sequencesequence
yes yes no no
F.a. profileF.a. profile nono yesyes
39 Taxonomic criteria and 39 Taxonomic criteria and methods for classifiction and methods for classifiction and identification of bacteria (b)identification of bacteria (b)
MethodMethod ClassificatiClassificationon
IdentificatioIdentificationn
Flow Flow cytometry cytometry
nono yesyes
DNA DNA composition composition
yesyes yesyes
DNA DNA fingerprint fingerprint
nono yesyes
rRNA rRNA sequencesequence
yesyes nono
PCRPCR yesyes yesyes
DNA DNA hybridizationhybridization
yes yes yes (DNA yes (DNA probes) probes)
40 History of 40 History of microbiology (a)microbiology (a)
Robert Hook (1665) – microscope Robert Hook (1665) – microscope with two sets of lenses – could see with two sets of lenses – could see „little boxes“, „cells“ – gave basis to „little boxes“, „cells“ – gave basis to cell theory – all living things consist cell theory – all living things consist of cells of cells
Antoni van Leeuwenhoek (1674) – Antoni van Leeuwenhoek (1674) – microsmicrosccope in which he could see ope in which he could see microbesmicrobes,, „animalcules“ „animalcules“,, in rain in rain water, in preparations from tooth water, in preparations from tooth surface, actually protozoa and surface, actually protozoa and bacteriabacteria
41 History of microbiology - 41 History of microbiology - biogenesis (b)biogenesis (b)
Spontaneous origin of life – toads, snakes and Spontaneous origin of life – toads, snakes and mice from wet soil, flies from manure, larvae mice from wet soil, flies from manure, larvae from decomposing dead bodiesfrom decomposing dead bodies
Redi (1668) – demonstrated that fly larvae do Redi (1668) – demonstrated that fly larvae do not originate spontaneously from not originate spontaneously from decomposing meatdecomposing meat
Needham (1745) – demonstrated spontaneous Needham (1745) – demonstrated spontaneous origin of microorganisms even origin of microorganisms even in in boiled mediaboiled media
Spallanzani (1765) – miSpallanzani (1765) – miccroorganisms do not roorganisms do not grow in a boiled medium closed in a cultivation grow in a boiled medium closed in a cultivation flaskflask
Edward Jenner (1798) – first vaccinationEdward Jenner (1798) – first vaccination
42 History of 42 History of microbiology (c)microbiology (c)
Rudolf Virchow (1858) – live cells can only Rudolf Virchow (1858) – live cells can only originate from live cellsoriginate from live cells
Louis Pasteur (1861) – microorganisms are Louis Pasteur (1861) – microorganisms are present in the air, can contaminate present in the air, can contaminate seemingly sterile solutions, experiment in seemingly sterile solutions, experiment in „swan-neck“ flasks, can be found on „swan-neck“ flasks, can be found on inorganic matter, on solid materials, in inorganic matter, on solid materials, in liquids and in the air. They can be killed by liquids and in the air. They can be killed by boiling, methods can be developed to boiling, methods can be developed to prevent air-borne microorganisms from prevent air-borne microorganisms from contaminating nutrient media – aseptic contaminating nutrient media – aseptic techniquestechniques
43 History of microbiology – 43 History of microbiology – golden age – (a) golden age – (a)
Pasteur begins the golden age of microbiology Pasteur begins the golden age of microbiology (1857 – 1914)(1857 – 1914)
1857 – Pasteur – fermentation1857 – Pasteur – fermentation 1861 – Pasteur – spontaneous origin of life 1861 – Pasteur – spontaneous origin of life
impossibleimpossible 1864 – Pasteur – pasteurization1864 – Pasteur – pasteurization 1867 – Lister – aseptic surgery1867 – Lister – aseptic surgery 1870 – Semmelweis – post partum fever 1870 – Semmelweis – post partum fever 1876 – Koch – germ theory of infectious diseases, 1876 – Koch – germ theory of infectious diseases,
discovery of discovery of Bacillus anthracisBacillus anthracis 1879 – Neisser – 1879 – Neisser – Neisseria gonorrhoeaeNeisseria gonorrhoeae 1881 - Koch – pure cultures of microorganisms1881 - Koch – pure cultures of microorganisms 1882 – Koch - 1882 – Koch - Mycobacterium tuberculosisMycobacterium tuberculosis
44 History of microbiology – 44 History of microbiology – golden age (b)golden age (b)
clinical practice as late as in 1944clinical practice as late as in 1944 Howard Florey, Ernst Chain, 1940 – Howard Florey, Ernst Chain, 1940 –
increased production and isolation increased production and isolation of pure penicillin of pure penicillin
46 History of microbiology – 46 History of microbiology – Nobel prizes for microbiologyNobel prizes for microbiology
(a)(a) Robert Koch, 1901, Robert Koch, 1901, Mycobacterium Mycobacterium
tuberculosistuberculosis; ; Hans Krebs,Hans Krebs, 1935, Krebs 1935, Krebs cyclecycle;; Beadle and Tatum, 1941, Beadle and Tatum, 1941, relationship between genes and enzymesrelationship between genes and enzymes; ; AverAveryy, MacLeod, McCart, MacLeod, McCarty, 1944, DNA is y, 1944, DNA is genetic materialgenetic material;; Alexander Fleming, Ernst Alexander Fleming, Ernst Chain, Howard FloreChain, Howard Florey, y, 1945,1945, discovery of discovery of penicilpenicilllinin;; Selmon Waksman, 1952, Selmon Waksman, 1952, discovery of streptomycindiscovery of streptomycin; ; Francois Jacob Francois Jacob and Jacque Monod 1957and Jacque Monod 1957;; regulation of regulation of protein synthesisprotein synthesis;; Joshu Joshua Lederberg, a Lederberg, 19581958;; conjugation in bacteriaconjugation in bacteria;; James Watson, James Watson, Francis Crick, Francis Crick, 19621962;; DNA structure; DNA structure;
47 History of microbiology 47 History of microbiology -Nobel prizes for -Nobel prizes for microbiology (b)microbiology (b)
Robert HoleRobert Holey, y, Gobind Khorana, Marshall Gobind Khorana, Marshall Nirenberg, Nirenberg, 1968,1968, genetic genetic code code; Barbora ; Barbora McClintockMcClintock, , 1983, transposones1983, transposones;; Sidney Sidney Altman and Thomas R. Cech, 1986, RNA Altman and Thomas R. Cech, 1986, RNA exhibits enzyme activityexhibits enzyme activity;; Kary B. Mullis Kary B. Mullis 1993, polymerase chain reaction1993, polymerase chain reaction;; Leland Leland H. Hartwell, R. Timothy Hunt and Paul M. H. Hartwell, R. Timothy Hunt and Paul M. Nurse, 2001Nurse, 2001;; discovery of key regulators of discovery of key regulators of cell cyclecell cycle; ; Barry J. Marshall, J. Robin Barry J. Marshall, J. Robin WarrenWarren,, 2005, 2005, Helicobacter pylori Helicobacter pylori – – bacterium causing stomach ulcersbacterium causing stomach ulcers;; Andrew Andrew Z. Fire, Craig C. MelloZ. Fire, Craig C. Mello,, 2006 2006;; discovery of discovery of RNA interference – gene silencing by RNA interference – gene silencing by double-stranded RNA double-stranded RNA
Attractivity for terroristsAttractivity for terrorists Relatively simple productionRelatively simple production Examples: anthrax, Examples: anthrax, Salmonella typhiSalmonella typhi, ,
Salmonella typhimuriumSalmonella typhimurium, , Vibrio choleraeVibrio cholerae Only simple laboratory devices are Only simple laboratory devices are
required (laboratory shaker, aerated or required (laboratory shaker, aerated or non-aerated flask, sometimes even simple non-aerated flask, sometimes even simple kitchen dishes are sufficient)kitchen dishes are sufficient)
Basic knowledge of cultivation of Basic knowledge of cultivation of microorganisms also requiredmicroorganisms also required
Attractivity for terroristsAttractivity for terrorists Effects are delayed:Effects are delayed: Anthrax 4 – 8 daysAnthrax 4 – 8 days Small pox 10 daysSmall pox 10 days Suitable for subversive Suitable for subversive
operationsoperations Terrorists can easily disappear.Terrorists can easily disappear.
Attractivity for terroristsAttractivity for terrorists Biological weapons induce Biological weapons induce
panicpanic S. typhimurium S. typhimurium in delicatessen in delicatessen
shopshop in Oregon, no deaths in Oregon, no deaths reported reported
„„Anthrax letters“:Anthrax letters“: 22 cases, of 22 cases, of them 11 respiratory, only 5 them 11 respiratory, only 5 deathsdeaths
Sarin in Tokyo underground Sarin in Tokyo underground (toxins can be used in a similar (toxins can be used in a similar way), only 12 deadly casesway), only 12 deadly cases
