Microbiology Introduction - Science and History PDF

**Introduction** A. B. C. D. II. **1.1 What Our Ancestor's Knew** A. B. 1. 2. 3. C. 1. 2. a. Because Ötzi was so well preserved by the ice, researchers discovered that he was infected with the eggs of the parasite *Trichuris trichiura*, which may have caused him to h...

**Introduction** A. B. C. D. II. **1.1 What Our Ancestor's Knew** A. B. 1. 2. 3. C. 1. 2. a. Because Ötzi was so well preserved by the ice, researchers discovered that he was infected with the eggs of the parasite *Trichuris trichiura*, which may have caused him to have abdominal pain and anemia. b. Researchers also found evidence of *Borrelia burgdorferi*, a bacterium that causes Lyme disease. c. Some researchers think Ötzi may have been trying to treat his infections with the woody fruit of the *Piptoporus betulinus* fungus, which was discovered tied to his belongings. This fungus has both laxative and antibiotic properties. d. Ötzi was also covered in tattoos that were made by cutting incisions into his skin, filling them with herbs, and then burning the herbs. There is speculation that this may have been another attempt to treat his health ailments. D. 1. Several ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. 2. The Bible refers to the practice of quarantining people with leprosy and other diseases, suggesting that people understood that diseases could be communicable. 3. The ancient Greeks attributed disease to bad air, mal'aria, which they called "miasmatic odors." They developed hygiene practices that built on this idea. 4. The Romans also believed in the miasma hypothesis and created a complex sanitation infrastructure to deal with sewage. In Rome, they built aqueducts, which brought fresh water into the city, and a giant sewer, the Cloaca Maxima, which carried waste away and into the river Tiber. Some researchers believe that this infrastructure helped protect the Romans from epidemics of waterborne illnesses. 5. Some doctors, philosophers, and scientists made great strides in understanding the invisible forces---what we now know as microbes---that can cause infection, disease, and death. a. The Greek physician **Hippocrates** (460--370 BC) is considered the "father of Western medicine". He dismissed the idea that disease was caused by supernatural forces and theorized that diseases had natural causes from within patients or their environments. Hippocrates and his heirs are believed to have written the Hippocratic Corpus, a collection of texts that make up some of the oldest surviving medical books. Hippocrates is also often credited as the author of the Hippocratic Oath, taken by new physicians to pledge their dedication to diagnosing and treating patients without causing harm. b. The Greek philosopher and historian **Thucydides** (460--395 BC) is considered the "father of scientific history" because he advocated for evidence-based analysis of cause-and-effect reasoning. Among his most important contributions are his observations regarding the Athenian plague that killed one-third of the population of Athens between 430 and 410 BC. Having survived the epidemic himself, Thucydides made the important observation that survivors did not get re-infected with the disease, even when taking care of actively sick people. This observation shows an early understanding of the concept of immunity. c. **Marcus Terentius Varro** (116--27 BC) was a prolific Roman writer who was one of the first people to propose the concept that things we cannot see (what we now call microorganisms) can cause disease. In Res Rusticae (On Farming), published in 36 BC, he said that "precautions must also be taken in neighborhood swamps... because certain minute creatures \[animalia minuta\] grow there which cannot be seen by the eye, which float in the air and enter the body through the mouth and nose and there cause serious diseases." E. 1. A Dutch cloth merchant named **Antonie van Leeuwenhoek** (1632--1723) was the first to develop a lens powerful enough to view microbes. In 1675, using a simple but powerful microscope, Leeuwenhoek was able to observe single-celled organisms, which he described as "animalcules" or "wee little beasties," swimming in a drop of rainwater. From his drawings of these little organisms, we now know he was looking at bacteria and protists. 2. Nearly 200 years later during the "Golden Age of Microbiology" two famous microbiologists, Louis Pasteur and Robert Koch, were especially active in advancing our understanding of the unseen world of microbes. a. **Louis Pasteur**, a French chemist, showed that individual microbial strains had unique properties and demonstrated that fermentation is caused by microorganisms. He also invented pasteurization, a process used to kill microorganisms responsible for spoilage, and developed vaccines for the treatment of diseases, including rabies, in animals and humans. b. **Robert Koch**, a German physician, was the first to demonstrate the connection between a single, isolated microbe and a known human disease. For example, he discovered the bacteria that cause anthrax (*Bacillus anthracis*), cholera (*Vibrio cholera*), and tuberculosis (*Mycobacterium tuberculosis*). 3. Much of what we know about human cells comes from our understanding of microbes, and many of the tools we use today to study cells and their genetics derive from work with microbes. F. 1. 2. 3. 4. 5. 6. 7. III. **1.2 A Systematic Approach.** A. 1. **Taxonomy** - the classification, description, identification, and naming of living organisms. **Classification** is the practice of organizing organisms into different groups based on their shared characteristics. 2. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named **Carolus** **Linnaeus** (1701--1778). a. Linnaeus published *Systema Naturae* an 11-page booklet in which he used a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. b. Linnaeus divided the natural world into three kingdoms: animal, plant, and mineral. Within the animal and plant kingdoms, he grouped organisms using a hierarchy of increasingly specific levels and sublevels based on their similarities. The names of the levels in Linnaeus's original taxonomy were kingdom, class, order, family, genus (plural: genera), and species. B. 1. In the 1800s, there was a growing interest in developing taxonomies that took into account the evolutionary relationships, or **phylogenies**, of all different species of organisms on earth. One way to depict these relationships is via a diagram called a phylogenetic tree (or tree of life). In these diagrams, groups of organisms are arranged by how closely related they are thought to be. In early phylogenetic trees, the relatedness of organisms was inferred by their visible similarities, such as the presence or absence of hair or the number of limbs. Now, the analysis is more complicated. 2. In 1866, **Ernst Haeckel**, a German biologist, philosopher, and physician, proposed another kingdom, Protista, for unicellular organisms. He later proposed a fourth kingdom, Monera, for unicellular organisms whose cells lack nuclei, like bacteria. 3. Nearly 100 years later, in 1969, American ecologist **Robert Whittaker** (1920--1980) proposed adding another kingdom---Fungi---in his tree of life. a. b. c. d. C. 1. Genetic methods allow for a standardized way to compare all living organisms without relying on observable characteristics that can often be subjective. Modern taxonomy relies heavily on comparing the nucleic acids (deoxyribonucleic acid \[DNA\] or ribonucleic acid \[RNA\]) or proteins from different organisms. The more similar the nucleic acids and proteins are between two organisms, the more closely related they are considered to be. 2. American microbiologists **Carl Woese** and **George Fox** created a genetics-based tree of life based on similarities and differences they observed in the gene sequences coding for small subunit ribosomal RNA (rRNA) of different organisms. Analysis of small subunit rRNA gene sequences suggests archaea, bacteria, and eukaryotes all evolved from a common ancestral cell type. 3. Horizontal gene transfer also complicates the issue of classification 4. Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus), whereas microbes in the domain Eukarya are eukaryotes (their cells have a nucleus). Some microorganisms, such as viruses, do not fall within any of the three domains of life. D. 1. Linnaeus used a system of binomial nomenclature, a two-word naming system for identifying organisms by genus and specific epithet. 2. Ex: modern humans are in the genus *Homo* and have the specific epithet name *sapiens*, so their scientific name in binomial nomenclature is *Homo sapiens*. In binomial nomenclature, the genus part of the name is always capitalized; it is followed by the specific epithet name, which is not capitalized. Both names are italicized. When referring to the species of humans, the binomial nomenclature would be *Homo sapiens*. E. IV. **1.3 Types of Microorganisms** A. Prokaryotic Microorganisms 1. a. Most bacteria are harmless or helpful, but some are **pathogens**, causing disease in humans and other animals. b. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. c. Most bacteria have cell walls that contain peptidoglycan. d. Bacteria are often described in terms of their general shape. Common shapes include spherical (**coccus**), rod-shaped (**bacillus**), or curved (**spirillum**, **spirochete**, or **vibrio**). e. They have a wide range of metabolic capabilities and can grow in a variety of environments, using different combinations of nutrients. i. Some bacteria are photosynthetic, such as oxygenic cyanobacteria and anoxygenic green sulfur and green nonsulfur bacteria; these bacteria use energy derived from sunlight, and fix carbon dioxide for growth. ii. Other types of bacteria are nonphotosynthetic, obtaining their energy from organic or inorganic compounds in their environment. 2. a. Unlike most bacteria, archaeal cell walls do not contain peptidoglycan, but their cell walls are often composed of a similar substance called pseudopeptidoglycan. b. Like bacteria, archaea are found in nearly every habitat on earth, even extreme environments that are very cold, very hot, very basic, or very acidic. Some archaea live in the human body, but none have been shown to be human pathogens. B. Eukaryotic Microorganisms. The domain Eukarya contains all eukaryotes, including uni- or multicellular eukaryotes such as protists, fungi, plants, and animals. The major defining characteristic of eukaryotes is that their cells contain a nucleus. 1. a. i. Their cells are surrounded by cell walls made of cellulose, a type of carbohydrate. ii. Algae are photosynthetic organisms that extract energy from the sun and release oxygen and carbohydrates into their environment therefore they are important parts of many ecosystems. iii. Many consumer products contain ingredients derived from algae, such as carrageenan or alginic acid, which are found in some brands of ice cream, salad dressing, beverages, lipstick, and toothpaste. iv. Agar, a gel derived from algae, can be mixed with various nutrients and used to grow microorganisms in a Petri dish. v. Algae are also being developed as a possible source for biofuels. b. i. Some protozoa move with help from hair-like structures called cilia or whip-like structures called flagella. Others extend part of their cell membrane and cytoplasm to propel themselves forward. These cytoplasmic extensions are called pseudopods ("false feet"). ii. Some protozoa are photosynthetic; others feed on organic material. iii. Some are free-living, whereas others are parasitic, only able to survive by extracting nutrients from a host organism. Most protozoa are harmless, but some are pathogens that can cause disease in animals or humans c. i. ii. iii. C. Helminths are multicellular parasitic worms. 1. 2. D. Viruses. **Viruses** are **acellular** microorganisms, which means they are not composed of cells. Essentially, a virus consists of proteins and genetic material---either DNA or RNA, but never both---that are inert outside of a host organism. However, by incorporating themselves into a host cell, viruses are able to co-opt the host's cellular mechanisms to multiply and infect other hosts. E. Microbiology as a Field of Study. **Microbiology** is a broad term that encompasses the study of all different types of microorganisms. But in practice, microbiologists tend to specialize in one of several subfields. 1. **Bacteriology** is the study of bacteria. 2. **Mycology** is the study of fungi. 3. **Protozoology** is the study of protozoa. 4. **Parasitology** is the study of helminths and other parasites. 5. **Virology** is the study of viruses. 6. **Immunology**, the study of the immune system, is often included in the study of microbiology because host--pathogen interactions are central to our understanding of infectious disease processes. 7. Microbiologists can also specialize in certain areas of microbiology, such as **clinical microbiology, environmental microbiology, applied microbiology,** or **food microbiology**.