The Microbial World and You
- On this page you have my lecture and also notes
- The little self-check questions give you an idea of what you might find on my quiz
- Watch the lecture, then...
- Read this page and read Chapter 1 of the textbook. These are notes from my lecture and more stuff that you need to know.
- Regarding the self-checks: no, you do not need to turn them in. Self Checks (or Check your understanding) are "hints" of things you find on your actual quizzes. Consider them a sort of study guide. So, definitely know the answers to those questions.
- The theme of this class is to explore the relationship between microbes and our lives
- Microbes – small organisms that usually require a microscope to be seen
- Can be both beneficial (e.g. ecology) and harmful (e.g. disease)
- Microbes – small organisms that usually require a microscope to be seen
Lecture: What is Microbiology?
Lecture Notes
Section 1-1
Microbes in Our Lives
- Microbes/microorganisms – microscopic organisms, including bacteria, fungi (yeasts and molds), viruses, protozoa, helminths, and microscopic algae
- Positive effects of microorganisms:
- Basis of the food chain for marine life
- Decomposition
- Recycling chemical elements between soil and air
- Photosynthesis
- Digestion and synthesis of vitamins
- Microorganisms also have important commercial uses:
- Produce vitamins and chemicals
- Produce pharmaceuticals (antibiotics, purified protein)
- Produce food products (alcohol, pickles, cheese, yogurt)
- Microorganisms can cause disease
- Very few (less than 1%) can cause disease in healthy individuals
- Conversely, sick or injured people (like those found in the hospital) can be susceptible to microbes that are normally harmless.
Check your understanding: Describe three ways in which microbes affect our lives:
- _____________________________________________________________________
- _____________________________________________________________________
- _____________________________________________________________________
Section 1-2
Naming and Classifying Microorganisms – Nomenclature
- Carolus Linnaeus established microorganism nomenclature in 1735, which is still in use today.
- Each microorganism has a two-part name: 1) the genus, which is capitalized; and 2) the species, which is not capitalized.
- The two-part name must be italicized.
- Often you will see the name abbreviated, with only the first initial of the genus and the full species name (e.g. Escherichia coli = E. coli)
- The origin of the names largely fall into three categories:
o Descriptive (e.g. Staphylococcus aureus = Golden clustered spheres)
o Homage to a scientist (e.g. Salmonella typhi = discovered by Daniel E. Salmon)
o Habitat of microorganism (e.g. Helicobacter pylori = microorganism that infects the circular opening leading from the stomach into the duodenum)
Check your understanding: Can you recognize and understand the scientific nomenclature of microorganisms; circle the name with the correct typography:
Salmonella enterica Steptococcus pyogenes Bacillus anthracis Escherichia coli Penicillium chrysogenum Enterobacter Cloacae Saccharomyces cerevisiae Clostridium botulinum Listeria monocytogenes
Can you write the abbreviated form of the following bacteria:
Legionella pneumophila: __________________________________________
Mycobacterium tuberculosis: _______________________________________
Neisseria gonorrhoeae: ___________________________________________
Section 1 - 3
Naming And Classifying Microorganisms – Types of Microorganisms
- There are 7 major types of microorganisms: Bacteria, Archaea, Fungi, Protozoa, Algae, Viruses, and parasitic worms.
From Tortora, Funke and Case, Microbiology, An Introduction, p. 34
Bacteria
- Bacteria – single celled organisms without a nucleus (which makes them prokaryotes)
- Most bacteria are shaped as a bacillus – rod; coccus – sphere; or spiral – corkscrew/curved
- Bacterial cell wall is composed of peptidoglycan (protein-sugar conjugate)
- Bacteria reproduce by binary fission – dividing into two equal cells
- Some bacteria are able to move independently with a flagella
- Some bacteria can generate nutrients by photosynthesis
- Bacteria are known to cause human disease
Archaea
- Archaea = single celled organisms without a nucleus (which makes them prokaryotes)
- Most archaea are shaped as a bacillus = rod or a coccus = sphere
- Archaea cell wall is composed of glycerol-ether lipids, which makes them tougher than bacteria. As a result archaea are able to live in extreme environments: ▪ Extreme halophiles = can live in extreme salt conditions
▪ Extreme thermophiles can live in very hot environments - Archaea reproduce by binary fission = dividing into two equal cells
- Some archaea are able to move independently with a flagella
- Archaea cannot generate nutrients by photosynthesis, but are able to utilize inorganic chemicals for nutrients and perform methanogenesis (producing methane waste during respiration), which is unique to archaea
- Archaea are not known to cause human disease
Viruses
- Viruses - acellular (not cellular), considered to be not living (inert outside of host)
- Viruses fundamentally consist of an icosahedral capsid containing a genome.
- Some viruses can surround their capsid by a membrane, which make them a sphere.
- If a virus has a membrane envelope, then it is derived from host animal cells, and thus contains glycerol-ester lipids
- Viruses reproduce by hijacking a host cell and creating an assembly factory
- Viruses are not able to move independently
- Viruses do not require nutrients
- Viruses can cause disease in all living organisms, including other microbes
Protozoa
- Protozoa = Single-celled organisms with a nucleus (which makes them Eukaryotes)
- Protozoa have very diverse shapes
- Protozoa do not have a cell wall, only a cell membrane composed of glycerol-ester lipids
- Protozoa reproduce both asexually and sexually by mitosis
- Protozoa are able to move independently with various appendages, including cilia, flagella, and pseudopods
- Protozoa eat other microorganisms for nutrients,
- and some perform photosynthesis, such as Euglena
- Protozoa are known to cause human disease
Fungi
- Fungi – Single-celled or multi-celled organisms with a nucleus (which makes them Eukaryotes)
- Most unicellular fungi are shaped as an oval (e.g. yeast); multicellular fungi can be complex in shape (e.g. mushroom)
- Fungi cell wall is composed of chitin = a fibrous substance consisting of polysaccharides. When combined with calcium carbonate, chitin forms the hard substance that makes exoskeletons for insects and crustaceans.
- Fungi reproduce both asexually and sexually by spore production
- Fungi are not able to move independently
- Fungi cannot generate nutrients by photosynthesis
- Fungi are known to cause human disease
Algae
- Algae – single- or multi-celled organisms with a nucleus (which makes them Eukaryotes)
- Algae have very diverse shapes
- Algae cell wall is composed of cellulose (like plants)
- Algae reproduce both asexually and sexually by mitosis or spore production
- Algae are not able to move independently
- Algae can only produce nutrients by photosynthesis
- Algae are only harmful to humans if they produce a toxin, which most algae do not
Parasitic Worms
- Parasitic worms - multi-celled organisms with a nucleus (which makes them Eukaryotes)
- Parasitic worms have diverse shapes and sizes, but mainly look like thin worms
- Parasitic worms do not have a cell wall, only a cell membrane composed of glycerol-ester lipids
- Parasitic worms reproduce sexually via egg laying
- Parasitic worms move like large worms or snakes move, called lateral undulation
- Parasitic worms acquire nutrient from organic material
- Parasitic worms are known to cause human disease
Table 1: Types of Microorganisms
Prokaryote |
Eukaryotes |
Other | |||||
Bacteria | Archaea | Fungi | Protozoa | Algae | Parasitic Worms | Viruses | |
Shapes |
Rod/sphere/ spiral | rod/sphere | oval and complex | Various | Various | worms | sphere, icosahedral |
Cell wall/membrane |
Peptido- Glycan |
glycerol-ether lipids | chitin | Glycerol-ester lipids | cellulose | Glycerol-ester lipids | Glycerol-ester lipids |
Reproduction |
Asexual Binary fission |
Asexual binary fission |
asexual and sexual through spore production | Asexually and sexually by mitosis | Asexually and sexually by mitosis or spore production | Sexually by egg laying | Assembly factory |
movement |
flagella | flagella | no | cilia, flagella, pseudopods | no | lateral undulation | no |
nutrients |
Various, including organic chemicals and photosynthesis | Various, including inorganic chemicals and methano-genesis | Various, including organic chemicals |
Various, including eating other micro- Organisms |
photosynthesis |
organic material |
does not require nutrients |
can cause human disease |
yes | no | yes | yes | no | yes | yes |
Self Check: Differentiate the major characteristics of each group of microorganisms (memorize Table above)
Section 1 - 4
Naming and Classifying Microorganisms – Classification of Microorganisms
- In 1978, Carl Woese defined the three domains of organisms
- Bacteria – has cell walls that contain peptidoglycan, no nucleus
- Archaea – has cell walls that do not contain peptidoglycan, no nucleus
- Eukarya – contains a nucleus
- Protists = protozoa and algae
- Fungi = yeasts, molds, and mushrooms
- Plants = trees, shrubs, herbs, grasses, ferns, and mosses
- Animals = vertebrates, arthropods, mollusks, and annelids
Self-check: What are the three domains of organisms? What domain contains viruses (trick question)? _______________________
Section 1 – 5
A Brief History Of Microbiology – The First Observations
- Using handcrafted microscopes, Anton van Leeuwenhoek was the first person to observe and describe single celled organisms. He is often called “the father of microbiology”, and is credited with inventing the microscope.
- However, Anton van Leeuwenhoek did not invent the microscope. That honor goes to Zacharias Jansen, who had invented microscopes in 1590, almost 40 years before Anton van Leeuwenhoek was born. But Jansen’s microscopes only had a magnification of 20-30x, which is not enough to see microorganisms.
- Anton van Leeuwenhoek designed a superior microscope that could achieve magnification over 200x. The trick was in the lens crafting, which van Leeuwenhoek perfected.
- Compared to a modern microscope, van Leeuwenhoek's design is extremely simple, using a single lens mounted in a tiny hole in a brass plate that makes up the body of the instrument. The entire instrument was only 3-4 inches long, and had to be held up close to the eye, requiring good lighting and great patience to use.
- Robert Hooke coined the term cells to describe small microorganisms, and invented the “cell theory”—the theory that all living things are composed of cells.
- Hooke used microscopes to observe thin slices of cork, describing the pores, or "cells" he viewed. Hooke had discovered plant cells, or more precisely, Hooke had been viewing the cell walls in cork tissue.
From Tortora, Funke and Case, Microbiology, An Introduction, p. 7
Self-check: Explain the microbiology contributions of:
Zacharias Jansen__________________________________________________________
Anton van Leeuwenhoek____________________________________________________ Robert Hooke ____________________________________________________________
What is the “cell theory”? ______________________________________________________________________________ ______________________________________________________________________________
Section 1 - 6/7
A Brief History Of Microbiology – Debate over spontaneous generation
- Spontaneous Generation = the theory that microorganisms could arise spontaneously from nonliving matter.
- This theory was supported by John Needham in 1745, when he showed that even heated broth put into covered flasks could still generate microorganisms.
- In 1765, Lazzaro Spallanzani tried to disprove Needham’s results by showing the microbes are floating in the air, and broth exposed to air will generate microorganisms regardless of prior heating. No one was interested in this theory at the time.
- In 1858, Rudolf Virchow invented the theory of biogenesis = living cells arise only form preexisting living cells.
- The theory of biogenesis was not widely accepted until 1861, when Louis Pasteur demonstrated that microorganisms are present in the air and can contaminate sterile solutions, but that air itself does not create microbes.
- Pasteur’s experiment: He created long neck flasks bent into an S-shape, such that air could enter the tube, but microorganisms would be stuck at the first loop of the “S”. He put broth in the flask, and boiled it. After sitting—exposed to air for months—no signs of life were found in the flask.
- Louis Pasteur’s experiment formed the basis for “aseptic technique” = standard laboratory procedures that prevent contamination by unwanted microorganisms.
Self-check:
What is the difference between the theories of “Spontaneous generation” and “biogenesis”? ____________________________________________________________________________________________________________________________________________________ __________________________________________________________________
Identify the major contributions of the following people:
John Needham________________________________________________________________
Lazzaro Spallanzani______________________________________________________________
Rudolf Virchow_________________________________________________________________
Louis Pasteur__________________________________________________________________
Section 1 - 8/9/10
A Brief History Of Microbiology – The Golden Age of Microbiology
- The Golden Age of Microbiology is a period from 1857-1914, when Louis Pasteur and Robert Koch inspired rapid advances in our understanding of microorganisms, resulting in the establishment of Microbiology as a field of science.
- Some key findings that occurred during the Golden Age:
- Louis Pasteur discovered that yeast are capable of fermentation = converting sugar into alcohol in the absence of air. He then discovered that bacteria are also capable of fermentation; converting alcohol into acetic acid (making vinegar).
- Louis Pasteur solves the problem of spoiled wine by inventing pasteurization = using heat to kill microorganisms to prevent spoilage.
- In the 1860s, Joseph Lister started using phenol solution to clean wounds during surgery. This was the invention of aseptic surgery = cleaning hands and wounds to prevent infection and death during surgery.
- In 1876, Robert Koch proved that bacteria can cause disease. He isolated bacteria from the blood of a cow sick with anthrax, and injected the bacteria into a healthy cow. Once the injected cow became sick with anthrax, Robert Koch isolated the blood and found that the same bacteria were present. This experiment established Koch’s Postulates = a sequence of experimental steps for directly relating a specific microbe to a specific disease.
- Koch’s Postulates validated the recently invented Germ Theory = disease can be caused by microorganisms.
- In 1880, Louis Pasteur discovered why vaccinations are effective. Though Edward Jenner was the first to discover that people treated with cowpox were protected from getting small pox in 1798, no one knew how it worked. Louis Pasteur demonstrated that a bacteria that became avirulent (cannot cause disease), could be used to prevent others from getting the disease. This process became known as vaccinations = exposing a person to a treatment that will prevent future infection by a microorganism.
- Vaccination work validated the theory of immunity = the protection from acquiring a specific disease in the future, by having prior exposure to that specific disease.
Self-check: What is the germ theory? _____________________________________________________________________________________________________
Koch’s Postulates (memorize)
- The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.
- The microorganism must be isolated from a diseased organism and grown in pure culture.
- The cultured microorganism should cause disease when introduced into a healthy organism.
- The microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.
Why is Edward Jenner’s work significant? _____________________________________________________________________________________________________
Section 1-11
A Brief History of Microbiology – The Birth of Modern Chemotherapy
- Chemotherapy – treatment of disease by using chemical substances
- Synthetic Drugs – chemotherapy chemicals prepared in a laboratory
- In 1910, Paul Erlich discovered the first synthetic drug, salvarsan, a chemical that was effective against syphilis.
- Antibiotics – chemicals produced by bacteria or fungi to antagonize microorganisms
- The first antibiotic was discovered in 1928 by Alexander Fleming. It was called penicillin, and was discovered by accident when Alexander Fleming realized that Penicillium chrysogenum mold inhibited nearby bacterial growth.
- Though many antibiotics exist today, they are becoming less effective due to antibiotic resistance – genetic changes in microorganisms that enable them to be resistant to antibiotic exposures that would normally cause inhibition.
Self-check: What significant contributions to medicine did the following people make?
Paul Erlich ____________________________________________________________________
Alexander Fleming _____________________________________________________________
Section 1 – 12/13
A Brief History of Microbiology – Modern Developments in Microbiology
- After the Golden Age, many new sub-fields of Microbiology were developed:
- Bacteriology – the identification, classification, and characterization of bacterial species
- Virology – Virology is the study of viruses and virus-like agents, including (but not limited to) their taxonomy, disease-producing properties, cultivation and genetics.
- Parasitology – the study of parsites (protozoa and parasitic worms), their hosts, and the relationship between them.
- Mycology – the study of fungi, including their genetic and biochemical properties, their taxonomy and their use to humans as a source for tinder, medicine, food and entheogens, as well as their dangers, such as toxicity or infection.
- Immunology = the study of the immune system, which is responsible for protecting the body from microorganisms.
- Recombinant DNA Technology = discovered in 1960s by Paul Berg, recombinant DNA technology inserts fragments of DNA from one organism, into a different organism to enable the new organism to make large quantities of a desired protein.
Self-check: Define...
Bacteriology________________________________________________________________
Mycology__________________________________________________________________
Parasitology____________________________________________________________________
Immunology___________________________________________________________________
Virology______________________________________________________________________
What is a major commercial application of recombinant DNA technology? (hint: think about Pharmaceutical companies, farms, or human genetics)? _____________________________________________________________________________________________________
Section 1 - 14/15
Microbes And Human Welfare
- Only a small minority of microorganisms can cause human disease.
- The vast majority of microbes actually benefit humans, other animals, and plants in a variety of ways.
- Recycling vital Elements = In the 1880s, Martinus Beijerinck and Sergei Winogradsky were the first to show that microorganism have an important impact on the biosphere, specifically in recycling elements between the soil and the atmosphere. This finding started the field of Microbial Ecology, which studies the role of microorganisms in converting carbon, nitrogen, oxygen, sulfur, and phosphorus to forms that are useful by earth’s ecosystem.
- Sewage Treatment = microbes are being used to remove harmful chemicals from contaminated water supplies, in an effort to preserve the precious resource of drinkable water.
- Bioremediation = waste management technique that uses microorganisms to break down hazardous substances into less toxic or non-toxic substances in order to neutralize pollutants from a contaminated site.
- Pest Control = microbes can be used for their natural ability to cause fatal disease in pests like insects.
- Biotechnology and Recombinant DNA technology = microorganisms can be repurposed to make useful products. Whether modifying a virus to kill only cancer cells, or adding a human gene to a bacteria to produce mass quantities of lactase to produce the product Lactaid (to help lactose intolerant people digest dairy products), microorganisms have a very important commercial value in modern society. Recombinant DNA technology has paved the way for the next big leap in medicine, gene therapy, in which the human genome can be modified to correct the genetic birth defects that cause serious disease (e.g. Severe Combined Immunodeficiency Disease (SCID) = “bubble boy” disease.)
Section 1 - 16/17/18
Microbes And Human Disease
- All animals have microorganisms that live in their body. This is called “Normal Microbiota”.
- Microbiota can be both beneficial (prevent pathogens from gaining access, produce useful substances like vitamins, and digest substances vertebrates can’t like cellulose), and harmful (cause ulcers, diarrhea, and other disease).
- The difference of when a microbiota can cause disease is related to two factors: 1) immune system resistance, 2) location of microorganism. For example:
- If you have a bacteria in your intestine that is kept in check by white blood cells, the bacteria can become pathogenic if your white blood cell count is lowered for any reason
- If a microorganism from your intestine, makes its way to your bladder, it could cause a Urinary tract infection (UTI) due to being in a new and unfamiliar location.
- For survival, some microorganisms form a biofilm = when microorganisms (usually bacteria) adhere to a surface and excrete a slimy, glue-like substance called exopolysaccharide matrix, which allows the microbes to aggregate in a protective layer. Biofilms tend to be resistant to anti- microbials (e.g. antibiotics), the immune system, and physical stress.
- Infectious Disease - a disease in which a pathogen invades a susceptible host, such as humans, and causes undesirable conditions for the host.
- Emerging Infectious Disease = disease that are new or changing and are increasing or have the potential to increase in incidence in the near future. The increase in Emerging diseases is due to a number of factors:
1) evolution of the pathogen
2) new modes of transportation that allow long distance travel
3) exposure of humans to new environments (including new plants and new animals).
Self-check: What is Normal Microbiota, and how is it beneficial to animals? _____________________________________________________________________________________________________
Define biofilm in your own words _____________________________________________________________________________________________________
There are three factors that contribute to the presence of emerging infectious diseases; pick two and describe how they contribute?
- ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
- __________________________________________________________________________________________________________________________________________________________________________________________________