Chapter 1: The Microbial World and You PDF

Chapter 1: The Microbial World and You Jason M. Madronero, MEd BIO 313 (Microbiology and Parasitology) Microbes in our Lives The Microbiome Microbiome refers to the collective genomes of the microorganisms (microbiota) that reside in a specific environment, such as the human body. It encompasses al...

Chapter 1: The Microbial World and You Jason M. Madronero, MEd BIO 313 (Microbiology and Parasitology) Microbes in our Lives The Microbiome Microbiome refers to the collective genomes of the microorganisms (microbiota) that reside in a specific environment, such as the human body. It encompasses all the genetic material within a microbiota, including bacteria, fungi, viruses, and archaea. Microbes in our Lives The Microbiome Normal microbiota, also known as normal flora, refers to the microorganisms that are consistently found in specific body sites of healthy individuals. These microorganisms establish a symbiotic relationship with their host, contributing to normal physiological functions. Microbes in our Lives The Microbiome Transient microbiota consists of microorganisms that are temporarily present in or on the body. These microbes do not permanently colonize the host and can be eliminated by the immune system, environmental changes, or competition from resident normal microbiota. Microbes in our Lives Why are microbiota important? Gut Microbiome: Crucial for digestion, vitamin synthesis (e.g., B vitamins, vitamin K), and protecting against pathogens. Dysbiosis (imbalance) is linked to conditions such as inflammatory bowel disease, obesity, diabetes, and mental health disorders. Microbes in our Lives Why are microbiota important? Skin Microbiome: Protects against pathogens, aids in wound healing, and maintains skin health. Includes beneficial bacteria like Staphylococcus epidermidis. Microbes in our Lives Why are microbiota important? Oral Microbiome: Maintains oral health. Dysbiosis can lead to dental caries, periodontal disease, and systemic infections. Microbes in our Lives Why are microbiota important? Immune System Development: Trains the immune system to distinguish between harmful and harmless agents. Germ-free animals have underdeveloped immune systems. Microbes in our Lives Why are microbiota important? Metabolism and Nutrition: Metabolizes complex carbohydrates into short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate, essential for colonic health and energy production. Involved in dietary compound metabolism and xenobiotic biotransformation. Microbes in our Lives Human Microbiome Project (2007) Characterized microbial communities at multiple human body sites and analyzed their role in health and disease. Findings include the uniqueness of individual microbiomes and the conservation of core functions. Naming and Classifying Organisms Nomenclature The system of naming organisms scientifically to ensure each organism has a unique and universally accepted name. This system is essential for accurately identifying and communicating about different species. Naming and Classifying Organisms Binomial Nomenclature Developed by Carl Linnaeus in the 18th century, this system assigns each organism a two-part Latin name consisting of the genus and species. Naming and Classifying Organisms Genus Name: The first part of the name. Always capitalized. Italicized (or underlined if handwritten). Represents a group of closely related species. Example: Homo in Homo sapiens. Naming and Classifying Organisms Species Name: The second part of the name. Not capitalized. Italicized (or underlined if handwritten). Represents a specific organism within the genus. Example: sapiens in Homo sapiens. Example: Escherichia coli (E. coli) o Escherichia (Genus) o coli (Species) Naming and Classifying Organisms Rules for Writing Scientific Names: Both parts of the name are italicized or underlined. The genus name is abbreviated with the first letter (capitalized) after the first full mention, followed by the species name. o Example: Escherichia coli can be abbreviated as E. coli after the first mention. Naming and Classifying Organisms Importance of Binomial Nomenclature: 1. Provides a unique and standardized name for each organism, avoiding confusion caused by common names. 2. Facilitates accurate communication among scientists worldwide. 3. Reflects the organism's taxonomic relationships. Types of Microorganisms Bacteria Prokaryotic, unicellular organisms. Cell walls contain peptidoglycan. Reproduce by binary fission. Diverse shapes (cocci, bacilli, spirilla) and metabolisms. Examples: Escherichia coli, Staphylococcus aureus Types of Microorganisms Archaea Prokaryotic, unicellular organisms. Cell walls do not contain peptidoglycan. Often found in extreme environments (extremophiles). Methanogens, extreme halophiles, and extreme thermophiles. Not known to cause disease in humans Types of Microorganisms Fungi Eukaryotic organisms. Cell walls contain chitin. Include yeasts (unicellular) and molds (multicellular). Reproduce sexually and asexually. Decomposers in ecosystems. Examples: Saccharomyces cerevisiae (yeast), Aspergillus (mold) Types of Microorganisms Protozoa Eukaryotic, unicellular organisms. Lack cell walls. Motile via pseudopods, cilia, or flagella Free-living or parasitic. Examples: Amoeba, Paramecium Types of Microorganisms Algae Eukaryotic, photosynthetic organisms. Cell walls contain cellulose. Found in freshwater, saltwater, and soil. Produce oxygen and carbohydrates through photosynthesis. Examples: Chlamydomonas, Spirogyra Types of Microorganisms Viruses Acellular entities. Consist of DNA or RNA core surrounded by a protein coat (capsid), sometimes with a lipid envelope. Obligate intracellular parasites. Infect all forms of life (bacteria, archaea, eukaryotes). Examples: Influenza virus, HIV Classification of Microorganisms Three Domains Based on genetic analysis, particularly rRNA sequences. 1. Bacteria: True bacteria, prokaryotic cells with peptidoglycan in their cell walls. 2. Archaea: Prokaryotic cells without peptidoglycan, often extremophiles. 3. Eukarya: Eukaryotic cells, including protists, fungi, plants, and animals. Classification of Microorganisms Taxonomic Hierarchy Domain Kingdom Phylum Class Order Family Genus Species Classification of Microorganisms Five-Kingdom System Prior to the three-domain system, organisms were classified into five kingdoms: Monera (prokaryotes) Protista (unicellular eukaryotes) Fungi Plantae Animalia A Brief History of Microbiology The First Observations Robert Hooke (1635-1703) In 1665, Robert Hooke published "Micrographia," where he described the microscopic structure of cork and coined the term "cell." Hooke's work marked the beginning of the study of cell biology, laying the groundwork for cell theory, which states that all living things are composed of cells. A Brief History of Microbiology The First Observations Anton van Leeuwenhoek (1632-1723) Between 1673 and 1723, Anton van Leeuwenhoek used simple microscopes he designed himself to observe and describe live microorganisms, which he called "animalcules." Van Leeuwenhoek's meticulous observations and detailed sketches provided the first glimpse into the microbial world, significantly advancing the field of microbiology. A Brief History of Microbiology The Debate over Spontaneous Generation Spontaneous Generation: The theory that living organisms could arise from nonliving matter. Biogenesis: The hypothesis that living organisms arise from preexisting life. A Brief History of Microbiology The Debate over Spontaneous Generation Francesco Redi (1626-1697) Conducted experiments in 1668 that showed maggots on decaying meat were the offspring of flies, not products of spontaneous generation. His work provided crucial early evidence supporting biogenesis, challenging the prevailing belief in spontaneous generation. A Brief History of Microbiology A Brief History of Microbiology The Debate over Spontaneous Generation John Needham (1713-1781) In the mid-1700s, Needham boiled broth, sealed it, and observed microbial growth, which he interpreted as evidence for spontaneous generation. Needham’s experiments supported the theory of spontaneous generation at the time. A Brief History of Microbiology A Brief History of Microbiology The Debate over Spontaneous Generation Lazzaro Spallanzani (1729-1799) Spallanzani conducted experiments by boiling broth in sealed flasks and observed no microbial growth unless the flasks were opened to the air. His work suggested that microorganisms from the air contaminated Needham’s solutions, supporting the theory of biogenesis. A Brief History of Microbiolog y A Brief History of Microbiology The Theory of Biogenesis Rudolf Virchow (1821-1902) In 1858, Virchow proposed the concept of biogenesis, stating that all cells arise from preexisting cells. Virchow’s concept was critical in challenging the theory of spontaneous generation A Brief History of Microbiology The Theory of Biogenesis Louis Pasteur (1822-1895) In 1861, Pasteur’s swan-neck flask experiment demonstrated that boiled broth remained sterile unless exposed to air, proving that microorganisms came from the environment. Pasteur’s work definitively disproved spontaneous generation, established biogenesis, and led to the development of aseptic techniques. A Brief History of Microbiology A Brief History of Microbiology The First Golden Age of Microbiology Louis Pasteur (1822-1895) Pasteur’s work on fermentation, pasteurization, and germ theory established the role of microorganisms in disease and food spoilage. He developed vaccines for rabies and anthrax. Pasteur's discoveries laid the foundation for microbiology and immunology. A Brief History of Microbiology The First Golden Age of Microbiology Joseph Lister (1827-1912) Inspired by Pasteur’s germ theory, Lister introduced antiseptic surgery using carbolic acid to disinfect wounds and surgical instruments. Lister’s antiseptic methods significantly reduced surgical infections and mortality, validating the application of the germ theory in medical practice. A Brief History of Microbiology The Germ Theory of Disease Agostino Bassi (1773-1856) In 1835, Bassi proved that a fungus was the cause of a silkworm disease, marking the first demonstration of a microorganism causing an animal disease. His work provided early evidence supporting the germ theory of disease, paving the way for future discoveries in microbiology. A Brief History of Microbiology The Germ Theory of Disease Ignaz Semmelweis (1818-1865) Discovered in the 1840s that handwashing with a chlorinated lime solution drastically reduced the incidence of puerperal (childbirth) fever in maternity wards. His findings laid the foundation for antiseptic practices, emphasizing the role of hygiene in preventing disease transmission. A Brief History of Microbiology The First Golden Age of Microbiology Robert Koch (1843-1910) Koch developed Koch’s postulates, a set of criteria for linking specific microbes to specific diseases. He identified the causative agents of anthrax, tuberculosis, and cholera. Koch’s postulates became essential for establishing the microbial cause of diseases, solidifying the germ theory of disease. A Brief History of Microbiology The First Golden Age of Microbiology Koch’s Postulates 1. The microorganism must be found in abundance in all organisms suffering from the disease but should not be found in healthy organisms. 2. The microorganism must be isolated from a diseased organism and grown in pure culture. A Brief History of Microbiology The First Golden Age of Microbiology Koch’s Postulates 3. The cultured microorganism should cause disease when introduced into a healthy, susceptible host. 4. The microorganism must be re-isolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent. A Brief History of Microbiology A Brief History of Microbiology The First Golden Age of Microbiology Edward Jenner (1749-1823) In 1796, Jenner developed the first successful vaccine by using material from cowpox lesions to immunize against smallpox. Jenner’s work laid the foundation for immunology and vaccination. A Brief History of Microbiology The Second Golden Age of Microbiology Paul Ehrlich (1854-1915) Ehrlich developed the concept of chemotherapy, using chemicals to treat diseases. He discovered Salvarsan, an arsenic-based compound effective against syphilis. Ehrlich’s work marked the beginning of antimicrobial chemotherapy. A Brief History of Microbiology The Second Golden Age of Microbiology Alexander Fleming (1881-1955) In 1928, Fleming discovered penicillin, the first antibiotic, produced by the mold Penicillium notatum. Penicillin revolutionized the treatment of bacterial infections and led to the development of numerous other antibiotics. A Brief History of Microbiology Bacteriology, the study of bacteria, began with van Leeuwenhoek’s first examination of tooth scrapings. New pathogenic bacteria are still discovered regularly. Many bacteriologists, like Pasteur, look at the roles of bacteria in food and the environment. A Brief History of Microbiology One intriguing discovery came in 1997, when Heide Schulz discovered a bacterium large enough to be seen with the unaided eye (0.2 mm wide). This bacterium, named Thiomargarita namibiensis lives in mud on the African coast. Thiomargarita is unusual because of its size and its ecological niche. The bacterium consumes hydrogen sulfide, which would be toxic to mud-dwelling animals. A Brief History of Microbiology Mycology is the study of fungi, including yeasts, molds, and mushrooms, with a focus on their taxonomy, physiology, and their roles as pathogens, decomposers, and sources of antibiotics. In medical mycology, the focus is on fungal infections in humans, such as those caused by Candida, Aspergillus, and dermatophytes, as well as the development of antifungal therapies and the impact of fungi on human health. A Brief History of Microbiology Parasitology is the study of protozoa and parasitic worms. Because many parasitic worms are large enough to be seen with the unaided eye, they have been known for thousands of years. Key topics in parasitology include the life cycles of parasites, the diseases they cause (e.g., malaria, schistosomiasis), methods of transmission, and strategies for prevention and control, including antiparasitic drugs and public health measures. A Brief History of Microbiology Immunology is the study of immunity. Vaccines and interferons are being investigated to prevent and cure viral diseases. The use of immunology to identify some bacteria according to serotypes (variants within a species) was proposed by Rebecca Lancefield in 1933. A Brief History of Microbiology Lancefield proposed that streptococci be classified according to serotypes (variants within a species) based on certain components in the cell walls of the bacteria. Streptococci are responsible for a variety of diseases, such as sore throat (strep throat), streptococcal toxic shock, and septicemia (blood poisoning). A Brief History of Microbiology The study of viruses, virology, originated during the First Golden Age of Microbiology. In 1892, Dmitri Iwanowski reported that the organism that caused mosaic disease of tobacco was so small that it passed through filters fine enough to stop all known bacteria. At the time, Iwanowski was not aware that the organism in question was a virus. A Brief History of Microbiology In 1935, Wendell Stanley demonstrated that the organism, called tobacco mosaic virus (TMV), was fundamentally different from other microbes and so simple and homogeneous that it could be crystallized like a chemical compound. Stanley’s work facilitated the study of viral structure and chemistry. A Brief History of Microbiology Molecular genetics made significant strides through the study of unicellular organisms, particularly bacteria. A Brief History of Microbiology George W. Beadle and Edward L. Tatum (1940s) Demonstrated the relationship between genes and enzymes, establishing the connection between genetic material and biochemical processes. A Brief History of Microbiology Oswald Avery, Colin MacLeod, and Maclyn McCarty (1940s) Identified DNA as the hereditary material, a foundational discovery in genetics. A Brief History of Microbiology Joshua Lederberg and Edward L. Tatum Discovered bacterial conjugation, the process by which genetic material can be transferred between bacteria, furthering understanding of genetic exchange. A Brief History of Microbiology James Watson and Francis Crick (1950s) Proposed the double-helix model of DNA structure and explained DNA replication, a pivotal moment in molecular biology. A Brief History of Microbiology François Jacob and Jacques Monod (1960s) Discovered messenger RNA (mRNA) and uncovered the mechanisms of gene regulation in bacteria, advancing the understanding of protein synthesis. A Brief History of Microbiology François Jacob and Jacques Monod (1960s) Discovered messenger RNA (mRNA) and uncovered the mechanisms of gene regulation in bacteria, advancing the understanding of protein synthesis. A Brief History of Microbiology Third Golden Age of Microbiology Stephen Jay Gould termed the current era as the "age of bacteria," emphasizing the newfound understanding of bacteria's importance to Earth and human health.  Third Golden Age of Microbiology Advances in DNA sequencing and computing enable scientists to study and identify genes and their A Brief functions in organisms. History of Genomics, the study of an organism’s entire set of genes, Microbiology allows scientists to classify bacteria, fungi, and protozoa based on genetic relationships rather than just visible characteristics.  Third Golden Age of Microbiology Genomic tools help identify new microbes in various environments, including the ocean, leaves, and the A Brief human body, many of which have not History of been grown in laboratories. Microbiology Genetic modification of microorganisms now enables the production of large quantities of human hormones and other essential medical substances. A Brief History of Microbiology Third Golden Age of Microbiology Paul Berg pioneered recombinant DNA technology in the late 1960s by combining human or animal DNA fragments with bacterial DNA, creating the first hybrid DNA. Recombinant DNA (rDNA) technology involves inserting recombinant DNA into bacteria or other microbes to produce large amounts of a desired protein, revolutionizing microbiology research and applications. Microbes and Human Welfare Recycling Vital Elements Role of Microbes in Nutrient Cycling Microorganisms play a crucial role in the biogeochemical cycles of essential elements such as carbon, nitrogen, sulfur, and phosphorus. Microbes and Human Welfare Recycling Vital Elements Carbon Cycle Microbes decompose organic matter, releasing carbon dioxide (CO₂) back into the atmosphere through respiration. Photosynthetic microorganisms (cyanobacteria, algae) fix CO₂ into organic compounds, supporting the food web. Microbes and Human Welfare Recycling Vital Elements Nitrogen Cycle Nitrogen-fixing bacteria (e.g., Rhizobium) convert atmospheric nitrogen (N₂) into ammonia (NH₃), which plants can use. Nitrifying bacteria convert ammonia into nitrites (NO₂⁻) and then into nitrates (NO₃⁻), further used by plants. Denitrifying bacteria convert nitrates back into N₂, completing the cycle. Microbes and Human Welfare Recycling Vital Elements Sulfur Cycle Sulfur-oxidizing bacteria convert hydrogen sulfide (H₂S) into sulfur and sulfate (SO₄²⁻), which are used by plants and other organisms. Sulfate-reducing bacteria convert sulfate back into H₂S under anaerobic conditions. Microbes and Human Welfare Recycling Vital Elements Phosphorus Cycle Microbes decompose organic matter, releasing phosphate (PO₄³⁻) into the soil, which plants absorb. Microbes and Human Welfare Sewage Treatment: Using Microbes to Recycle Water Growing environmental awareness emphasizes the need to recycle water and prevent pollution of rivers and oceans. Sewage, a major pollutant, includes human excrement, wastewater, industrial wastes, and surface runoff, consisting of 99.9% water and a small amount of suspended solids and dissolved materials. Microbes and Human Welfare Sewage Treatment: Using Microbes to Recycle Water Sewage treatment plants remove undesirable materials and harmful microorganisms using a combination of physical processes and beneficial microbes. Large solids (e.g., paper, wood, glass, gravel, plastic) are removed from sewage, leaving behind liquid and organic materials. Microbes and Human Welfare Sewage Treatment: Using Microbes to Recycle Water Bacteria in the treatment process convert these organic materials into by-products like carbon dioxide, nitrates, phosphates, sulfates, ammonia, hydrogen sulfide, and methane. Microbes and Human Welfare Bioremediation: Using Microbes to Clean Up Pollutants In 1988, scientists began using microbes to clean up pollutants and toxic wastes from industrial processes, a process known as bioremediation. Certain bacteria can use pollutants as energy sources, while others produce enzymes that break down toxins into less harmful substances. Microbes and Human Welfare Bioremediation: Using Microbes to Clean Up Pollutants Bioremediation is employed to remove toxins from underground wells, chemical spills, toxic waste sites, and oil spills, such as the 2010 British Petroleum oil spill in the Gulf of Mexico. Bacterial enzymes are also used in drain cleaners to remove clogs without harmful chemicals. Microbes and Human Welfare Bioremediation: Using Microbes to Clean Up Pollutants Microorganisms used in bioremediation can be either indigenous to the environment or genetically modified. Commonly used microbes in bioremediation include species from the genera Pseudomonas and Bacillus. Bacillus enzymes are additionally used in household detergents to remove spots from clothing. Microbes and Human Welfare Insect Pest Control by Microorganisms Fungal Pathogens Entomopathogenic fungi (e.g., Beauveria bassiana, Metarhizium anisopliae) infect and kill insect pests. Used in integrated pest management (IPM) to reduce reliance on chemical pesticides. Microbes and Human Welfare Insect Pest Control by Microorganisms Nematodes Beneficial nematodes (e.g., Steinernema, Heterorhabditis) infect and kill soil- dwelling insect pests. Nematodes release symbiotic bacteria that produce toxins, killing the host insect. Microbes and Human Welfare Biotechnology and Recombinant DNA Technology Biotechnology refers to the commercial use of microorganisms to produce foods, chemicals, and other products, a practice that has evolved significantly with advancements in technology. Recombinant DNA technology has revolutionized biotechnology, enabling bacteria, viruses, yeast, and other organisms to act as biochemical factories for producing natural proteins, vaccines, and enzymes with medical applications. Microbes and Human Welfare Biotechnology and Recombinant DNA Technology Gene therapy is a significant outcome of recombinant DNA technology, involving the insertion or replacement of genes in human cells to treat genetic disorders such as SCID, Duchenne's muscular dystrophy, cystic fibrosis, and LDL- receptor deficiency. Gene therapy utilizes harmless viruses to deliver missing or new genes into host cells, where they integrate into the chromosomes. Microbes and Human Welfare Biotechnology and Recombinant DNA Technology Agricultural applications of recombinant DNA technology include genetically modifying bacteria to protect crops from frost damage and insects, and improving the appearance, flavor, and shelf life of fruits and vegetables. Future agricultural uses of recombinant DNA could enhance crop resistance to drought, insects, microbial diseases, and increase temperature tolerance. Microbes The balance between a healthy human and disease is determined by the interaction and between the body's natural defenses and the disease-causing properties of Human microorganisms. Disease Resistance is the body's ability to ward off diseases and is crucial in determining whether a microbe is harmful or harmless. Key resistance factors include the skin, mucous membranes, cilia, stomach acid, and antimicrobial chemicals like interferons. Microbes Microbes can be destroyed by the body's natural defenses, including white blood and cells, the inflammatory response, fever, Human and the immune system. Disease When natural defenses are insufficient, antibiotics or other drugs may be needed to combat microbial invaders. Microbes and Human Disease Biofilms Microorganisms can exist as single cells or form complex aggregations known as biofilms on solid surfaces. Biofilms are common in nature, such as the slime on rocks in lakes or the biofilm on teeth. Beneficial roles of biofilms include protecting mucous membranes from harmful microbes and serving as an important food source for aquatic animals. Microbes and Human Disease Biofilms Beneficial roles of biofilms include protecting mucous membranes from harmful microbes and serving as an important food source for aquatic animals. Harmful aspects of biofilms include clogging water pipes and causing infections on medical implants, such as joint prostheses and catheters. Microbes and Human Disease Infectious Diseases Infectious diseases occur when pathogens invade a susceptible host, such as a human or animal, and carry out part of their life cycle within the host, often causing disease. Microbes and Human Disease Infectious Diseases Malaria was not eliminated; it still infects over 200 million people worldwide Pertussis (whooping cough) is not eradicated, but vaccination has significantly reduced annual cases from 200,000 to 12,000. Cholera outbreaks continue to occur, particularly in less-developed regions of the world. Microbes and Human Disease Emerging Infectious Diseases Emerging Infectious Diseases are infectious diseases that have newly appeared in a population or have existed but are rapidly increasing in incidence or geographic range. Microbes and Human Disease Emerging Infectious Diseases Factors contributing to EIDs include evolutionary changes in existing organisms (e.g., Vibrio cholerae) and the spread of known diseases to new regions or populations through modern transportation. Increased human exposure to new or unusual infectious agents in ecologically changing areas (e.g., deforestation, construction) has led to new EIDs (e.g., Venezuelan hemorrhagic virus). Changes in a pathogen's ecology can result in new EIDs, such as Powassan virus shifting to deer ticks that also transmit Lyme disease. Microbes and Human Disease Emerging Infectious Diseases 1. Zika Virus: Spread by Aedes mosquitoes, associated with birth defects and neurological complications. 2. Ebola Virus Disease: Severe hemorrhagic fever with high mortality rates, outbreaks primarily in Africa. Microbes and Human Disease Emerging Infectious Diseases 4. Severe Acute Respiratory Syndrome (SARS): Caused by SARS coronavirus (SARS-CoV), resulting in severe respiratory illness. 5. Middle East Respiratory Syndrome (MERS): Caused by MERS coronavirus (MERS-CoV), associated with severe respiratory illness. 6. COVID-19: Caused by SARS-CoV-2, leading to a global pandemic with significant morbidity and mortality.