Microbiology: The Human Experience PowerPoint Lecture ch 1

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JOHN W. FOSTER ZARRINTAJ ALIABADI JOAN L. SLONCZEWSKI

MICROBIOLOGYTHE HUMAN EXPERIENCE

Microbes Shape Our History1

© 2016 W. W. Norton Co., Inc. 2

Chapter Objectives• Describe the discovery of microbes

related to human health, including the tools of microscopy and medical statistics.

• Explain Koch’s postulates for showing that a microbe causes disease.

• Describe how environmental microbes are essential for human life.

Microbes Shape Our History


Half a Lung Is Better than None – 1ScenarioDebi was an ordinary teenager attending an affluent American public high school when she contracted tuberculosis (TB). She did not know the person who infected her. Infection requires inhalation of the causative bacteria.


Half a Lung Is Better than None – 2Signs and SymptomsDebi coughed all the time,felt tired, and was losingweight.

Her coughing brought upblood.

An X-ray revealed the signs of infection in her lung, including a large hole eaten away by the bacteria.


Half a Lung Is Better than None – 3DiagnosisFrom Debi’s sputum sample,a DNA sequence was amplified by PCR (polymerase chain reaction).

The DNA sequence revealedMycobacterium tuberculosis, the cause of TB.


Half a Lung Is Better than None – 4TreatmentDoctors prescribed isoniazid and rifampin, antibiotics that kill moststrains of M. tuberculosis.But Debi’s TB strain provedresistant to nearly all known drugs (MDR-TB).Because drugs failed to eliminate the MDR strain, surgeons removed nearly half of her right lung to help the antibiotics overcome the infection.


Half a Lung Is Better than None – 5TreatmentDebi recovered andreturned to high school. She would have to continuetaking antibiotics for yearsafterward. All the teachers and students in Debi’s school were screened, and over 200 were found to have been infected by a student with tuberculosis misdiagnosed for two years. All required treatment to prevent disease.


Section Objectives• Describe how we define a microbe, and

explain why the definition is a challenge.• Describe the three major domains of life:

Archaea, Bacteria, and Eukarya. Explain what the three domains have in common and how they differ.

• Define viruses, and explain how they relate to living cells.

1.1 From Germ to Genome: What is a Microbe? – 1


Where did life come from?• Life on Earth began early in our planet’s

history with microscopic organisms.• Microbial life has shaped our atmosphere,

our geology, and the energy cycles of all ecosystems.

• Early microbes eventually evolved into multicellular plants and animals, including humans.



Microbes• generate the air we breathe

oxygencarbon dioxidenitrogen gas

• fix nitrogen into forms used by plants• make essential vitamins

vitamin B12

vitamin K• produce food webs



Microbes• Human body contains 10x as many

microbes as human cells.• Human relationship with microbes

• food production• food preservation• mining for precious minerals• biotechnology tools

• Small, but critical proportion are pathogens.• disease causing• remain the principal cause of human mortality



1.1 From Germ to Genome: What is a Microbe? – 5A Microbe Is a Microscopic OrganismSimple definition of a microbe leaves us with contradictions:• Some protists and algae can be seen with

the naked eye.• amebas

• Pelomyxa


Simple definition of a microbe leaves us with contradictions:• Some form complex multicellular

assemblages.• mycelia (multicellular filaments)• biofilms

• Some complex multicellular organisms require a microscope for us to see but are not considered microbes.• mites• roundworms



Classified as members of a species, according to a shared set of genes and traits

Scientific name of the species consists of a capitalized genus name and a lowercase

species name, which are both italicized.• Staphylococcus epidermidis• Escherichia coli



• The more closely related organisms are, the more recently they diverged from a common ancestor.

• Degree of relatedness is determined by comparing the DNA sequences of their genomes, the total DNA sequence content of an organism.



Major trait that distinguishes different types of microbes is the possession or absence of a membrane-enclosed nucleus.• Prokaryotes

• lack a nuclear membrane• include bacteria and archaea

• Eukaryotes• possess a nuclear membrane (nucleus)• include fungi, protozoa, and algae



Bacteria• prokaryotic• 0.2–20 µm• may grow as single cells, filaments,

communitiesArchaea

• prokaryotic• genetically distinct from bacteria• “extremophiles”• nonpathenogenic



Protozoa• eukaryotic• motile, single-celled organisms• may be free-living or parasitic

Algae• eukaryotic• contain chloroplasts and conduct

photosynthesis• base of the food web



Fungi• eukaryotic• nonmotile• grow by absorbing nutrients from

surroundings• grow as single cells or as filaments• can cause disease

Viruses• noncellular• genetic material (DNA or RNA) that can take

over the metabolism of a cell to generate more viruses

• can cause disease• also used as biotechnology tools



Section Objectives• Explain how microbial diseases have

changed human history.• Describe how microbes participate in human

cultural practices such as production of food and drink.

1.2 Microbes Shape Human History – 1


Have microbes changed the course of human history?devastation of human populations by microbial diseases

• tuberculosis• leprosy• smallpox• bubonic plague




Microscopes Reveal the Microbial WorldRobert Hooke built the first compound microscope.



Microscopes Reveal the Microbial WorldAnton van Leeuwenhoek observed bacteria with a single lens.



Spontaneous generationthe theory that living microbescan arise spontaneously withoutparental organisms.

• Spallanzani’s sealed flask experiment • opponents argued that since the flask was sealed,

oxygen was not present and microbes could not grow.

• Pasteur’s “swan neck” flask allowed oxygen to enter, but kept the boiled contents free of microbes.


Have microbes changed the course of human history?The Origin of Life• If all life on Earth shares descent from a

microbial ancestor, how did the first microbes arise?

• Earliest fossil evidence of cells appears in sedimentary rock that formed over 2 billion years ago.

• Living cell components may have formed from spontaneous reactions sparked by UV absorption or electrical discharge.

• Stanley Miller’s experiment• origins of life remain a mystery



Section Objectives• Define the germ theory of disease.• Explain how Florence Nightingale first drew

a statistical correlation between infectious diseases and human mortality.

• Explain how Koch’s postulates can show that a specific kind of microbe causes a disease. Explain the problems in interpreting Koch’s postulates in practice.

1.3 Medical Microbiology and Immunology – 1


1.3 Medical Microbiology and Immunology – 2Linking Infectious Disease with Mortality• Germ Theory of Disease

• Specific diseases are caused by specific kinds of microbes.

• Disease is common in overcrowded areas like cities and during warfare.• Florence Nightingale demonstrated the significance of mortality due to disease.


Epidemiology• Statistical analysis continues to serve as a

crucial tool for determining causes of disease.

• Public Health is now a major field of service.• Centers for Disease Control and

Prevention(CDC)• World Health Organization (WHO)



1.3 Medical Microbiology and Immunology – 5The CDC tracks epidemics of seasonal influenza and tries to predict which strains will require vaccination in a given year.


1.3 Medical Microbiology and Immunology – 6Case History 1.1 Sickened by Dead Cattle

In 2000, on a farm in North Dakota, 67-year-old Caleb helped bury 5 cowsthat had died of anthrax.

Wearing heavy leather gloves, Caleb placed chains around the heads and hooves of the carcasses and moved them to the burial site. Four days later, he noticed a small lump on his left cheek. Over two days, the lump enlarged and a lesion opened.



Caleb sought medical attention. The physician reported a firm, superficial nodule surrounded by a purple ring, with an overlying black eschar (piece of dead tissue sloughed from the skin).

The physician prescribedciprofloxacin, the standard antibiotic for cutaneous anthrax.



Testing the patient’s serum with a bacterial antigen revealed the presence of antibodies, confirming the diagnosis of anthrax.

The ciprofloxacin wascontinued and the patient slowly improvedover several weeks.


Growth of Microbes in Pure Culture

Diagnosis for a patient requires more direct evidence that a given microbe causes a given disease.

Robert Koch developed the first scientific method for establishing the microbial cause of a disease.



Koch’s postulates link a pathogen with a disease.1. The microbe is found in all cases of the disease, but

absent from healthy individuals.2. The microbe is isolated from the diseased host and

grown in pure culture.3. When the microbe is introduced into a healthy,

susceptible host (or animal model), the same disease occurs.

4. The same strain of microbe is obtained from the newly diseased host. When cultured, the strain shows the same characteristics as before.



Individual diseases and pathogens may confound one or more of the criteria:

• M. tuberculosis is now known to cause symptoms in only 10% of people infected.

• HIV is difficult to detect in early stages and is an exclusively human pathogen. Experimenting with humans would be unethical.



Immunization Prevents DiseaseBy 1000 BCE in India and China, it was known that individuals could be made immune to smallpox by transferring secretions from a diseased individual to healthy ones.

In the 18th century, the incidence of smallpox was decreased by deliberately inoculating children with material from smallpox pustules.



1.3 Medical Microbiology and Immunology – 15The practice of smallpox inoculation was introduced from Turkey to other parts of Europe by Lady Mary Wortley Montagu, a smallpox survivor and the wife of the British Ambassador.She brought the practice back to England, where itbecame widespread.



Preventative inoculation with smallpox was dangerous, as some infected individuals still contracted serious disease and were contagious.

Dr. Edward Jenner deliberately infected patients with matter drawn from cowpox lesions. The processof cowpox inoculation was called vaccination.


Louis Pasteur was the first to show that infecting with attenuated (weakened) strains of bacteria was able to confer immunity and he applied this principle to other organisms.

We now know that the molecular components of pathogens generate immunity to a specific disease by stimulating the immune system.



Antiseptics and Antibiotics Control PathogensBefore the work of Koch and Pasteur, many people died of infections transmitted by their own doctors.• Ignaz Semmelweis ordered doctors to

wash their hands in chlorine, an antiseptic (a chemical that kills microbes).

• The mortality rate fell, but other doctors refused to accept Semmelweis’s findings.



Joseph Lister noted that half of his amputee patients died of sepsis. He began to use antiseptic agents (carbolic acid) to treat wounds and surgical instruments.By the 20th century, fully aseptic environments (completely free of microbes) for surgery were in use.



Although the use of antiseptics was a major advance, they could not be taken internally, as they would kill the patient.

Researchers sought a “magic bullet” or antibiotic that would kill only the microbes, leaving the host unharmed.



Alexander Fleming noted that a culture of Staphylococcus contaminated with mold caused a clearing of the bacteria nearby.Fleming showed that the mold secreted a substance that killed only the bacteria. We now know this substance as penicillin.



The second half of the 20th century saw the discovery of many powerful antibiotics.

• H. Florey & E. Chain purified penicillin and it successfully saved the lives of many Allied troops during WWII.

Today, widespread and indiscriminate use of antibiotics has selected for pathogens that are antibiotic resistant (lost effectiveness against certain strains of major pathogens).

• Multi-drug resistant strains of M. tuberculosis are now a serious threat to human health.



The Discovery of VirusesResearchers were puzzled to find contagious diseases whose agents of transmission could pass through a filter with tiny pores that blocked known bacterial cells.• Martinus Beijerinck concluded that the cause of

tobacco mosaic disease could not be bacterial because it passed through a filter that trapped bacteria.

• Wendell Stanley crystallized the infective particle and called it tobacco mosaic virus (TMV).



1.4 Microbes in Our Environment – 1Section Objectives• Describe examples of how microbes

contribute to natural ecosystems.• Explain how mitochondria and chloroplasts

evolved by endosymbiosis.


1.4 Microbes in Our Environment – 2How do microbes shape the Earth’s environment?Microbes are responsible for cycling the many minerals essential for all life.Microbes make up most of the Earth’s biosphere.Earth’s ecology IS microbial ecology.


1.4 Microbes in Our Environment – 3

Microbes Support Natural EcosystemsSergei Winogradsky (1856–1953) was one of the first to study microbes in their natural habitats.• Marshes/wetlands support microbes known as lithotrophs, organisms that feed solely on inorganic molecules.• Winogradsky developed enrichment culture, the use of selective growth media that support certain classes of microbes while excluding others.


1.4 Microbes in Our Environment – 5Microbes Support Natural Ecosystemsgeochemical cycling: the global interconversion of inorganic and organic forms of nitrogen, sulfur, phosphorus, and other minerals

Without essential conversions, such as nitrogen fixation, no plants or animals could live.


1.4 Microbes in Our Environment – 6Animals and Plants Evolved through EndosymbiosisEndosymbiosis (organisms living symbiotically inside a larger organism) is widespread in all ecosystems.

Lynn Margulis (1938–2011) proposed that eukaryotic cells were able to develop complex compartments such as mitochondria and chloroplasts by engulfing and merging with bacterial cells.


1.4 Microbes in Our Environment – 7Endosymbiotic theory:Respiring bacteria similar to E. coli were engulfed by pre-eukaryotic cells, where theyevolved into mitochondria.

Similarly, a phototroph related to cyanobacteria was taken up by a eukaryote, giving rise to the chloroplasts of phototrophic algae and plants.


1.4 Microbes in Our Environment – 9Both mitochondria and chloroplasts contain their own DNA sequences.• Analysis of DNA provides compelling

evidence of the bacterial origin ofmitochondria and chloroplasts.

• Sequences show unmistakable homology

(similarity) to those of modern bacteria, thus supporting their common ancestry.


1.4 Microbes in Our Environment – 10New Microbes Continue to EmergeWe continue to discover surprising new microbes in places previously thought uninhabitable, such as the hot springs of Yellowstone National Park.

Bacterial DNA polymerase

from a hot spring is used

for PCR technology thatidentifies pathogens in

ill patients.


1.4 Microbes in Our Environment – 11In 1977, Carl Woese (1928–2012) discovered that some of the microbes from Yellowstone hot springs have DNA genomes very different from all other known life forms.

The newly discoveredprokaryotes were seen as a new form of life, called archaea.


1.5 The DNA Revolution – 1

Section Objectives• Describe how the structure of DNA was

discovered, and explain the significance of DNA for determining the traits of life.

• Describe how the manipulation of DNA information has transformed the practice of medicine.


1.5 The DNA Revolution – 2How did science change medicine during the 20th century?DNA structure discovered by X-ray crystallography, a method developed in the UK in the early 1900s.Dorothy Hodgkin (1910–1994) and Rosalind Franklin (1920–1958) were pioneers in the X-ray analysis field.



James Watson (b. 1928) and Francis Crick (1916–2004) were the first to understand that DNA bases were paired in the interior of the double helix.


1.5 The DNA Revolution – 6The discovery of the structure of DNA led to the development of many new techniques and technologies.• A method of DNA sequencing,

developed by Frederick Sanger in 1977, was used to reveal the first genome of a virus.

• The first genome sequence from a cellular microbe (H. influenzae) was obtained in 1995.

• The same strategy was later applied to sequencing the human genome.



20th century microbiology transformed the practice of medicine and generated entire industries of biotechnology and bioremediation.

Antibiotic developmentVaccine developmentBiotechnology for diagnosis of diseaseMicrobial analysis in forensicsBioremediation of wastes and control

pests


Clicker questions – 1

Which of the following is NOT a microbe?

a. Escherichia coli, a bacterium living in the intestinal tract

b. Methanococcus jannaschi, an archaeon living a marsh

c. human immunodeficiency virus (HIV) infecting a patient’swhite blood cells

d. Pelomyxa species, a large ameba, living in a freshwater pond

e. Taenia solium, a parasitic tapeworm found in swine


Clicker question answer – 1

Which of the following is NOT a microbe?

a. Escherichia coli, a bacterium living in the intestinal tract

b. Methanococcus jannaschi, an archaeon living a marsh

c. Human immunodeficiency virus (HIV) infecting a patient’swhite blood cells

d. Pelomyxa species, a large ameba, living in a freshwater pond

e. Taenia solium, a parasitic tapeworm found in swine


Clicker question – 2Antonie van Leeuwenhoek made which contribution to the microbial world?

a. He was the first individual to observe single-celled microbes.b. He was the first microscopist to publish a study of the worldas seen under a microscope.c. He sought to disprove the spontaneous generation of microbes.d. He discovered that fermentation was caused by yeast, a single-celled fungus.e. He was the first to attempt to quantify the role of disease in population mortality.


Clicker question answer – 2Antonie van Leeuwenhoek made which contribution to the microbial world?

a. He was the first individual to observe single-celled microbes.b. He was the first microscopist to publish a study of the worldas seen under a microscope.c. He sought to disprove the spontaneous generation of microbes.d. He discovered that fermentation was caused by yeast, a single-celled fungus.e. He was the first to attempt to quantify the role of disease in population mortality.


Clicker question – 3

Which scientist was the first to develop a set of criteria to establish a causative link between an infectious agent and a disease?

a. Louis Pasteurb. Lazzaro Spallanzanic. Florence Nightingaled. Robert Koche. Robert Hooke



Which scientist was the first to develop a set of criteria to establish a causative link between an infectious agent and a disease?

a. Louis Pasteurb. Lazzaro Spallanzanic. Florence Nightingaled. Robert Koche. Robert Hooke


Clicker question – 4

The first eukaryotic cells are thought to have originated by which of the following processes?

a. symbiosisb. endosymbiosisc. pinocytosisd. exocytosise. exosymbiosis



The first eukaryotic cells are thought to have originated by which of the following processes?

a. symbiosisb. endosymbiosisc. pinocytosisd. exocytosise. exosymbiosis

Microbiology: The Human Experience PowerPoint Lecture ch 1

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