Classification of Microbes and Binomial System
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Questions and Answers

Which category do fungi belong to in the classification of microorganisms?

  • Bacteria
  • Viruses
  • Protozoa
  • Fungi (correct)

    • What does the term 'symbiosis' refer to in relation to the human microbiome?

  • A relationship where one organism benefits at the expense of another
  • A mutually beneficial relationship between two different organisms (correct)
  • The presence of harmful pathogens
  • A transient presence of microorganisms

    • Which microorganism is commonly associated with causing peptic ulcer disease?

  • Staphylococcus aureus
  • Streptococcus pneumoniae
  • Escherichia coli
  • Helicobacter pylori (correct)

    • What is the significance of antibiotic resistance in clinical microbiology?

    <p>It poses a challenge in treating infections effectively</p> Signup and view all the answers

    How can the microbiome be disrupted, leading to health complications?

    <p>Through the use of antibiotics</p> Signup and view all the answers

    Which of the following describes a transient microorganism in the human microbiome?

    <p>An organism that only temporarily resides in the body</p> Signup and view all the answers

    What best describes the relationship between biological diversity and the emergence of new pathogens?

    <p>Higher diversity can lead to the emergence of new pathogens</p> Signup and view all the answers

    What is emphasized as necessary for effective patient management in applied microbiology?

    <p>Understanding common pathogens related to specific diseases</p> Signup and view all the answers

    Which of the following is a major component of clinical microbiology that focuses on preventing infection?

    <p>Infection Prevention &amp; Control</p> Signup and view all the answers

    What is the primary feature that differentiates fungi and protozoa from bacteria?

    <p>Presence of a nucleus</p> Signup and view all the answers

    Which of the following organisms is classified as a protozoan?

    <p>Plasmodium falciparum</p> Signup and view all the answers

    What does the term 'genotype' refer to in microbiology?

    <p>Genetic makeup of an organism</p> Signup and view all the answers

    Which of the following pathogens is associated with major skin infections?

    <p>Staphylococcus aureus</p> Signup and view all the answers

    What is one of the key practices involved in antimicrobial stewardship?

    <p>Limiting the use of antibiotics</p> Signup and view all the answers

    Which structure is not typically found in a bacterial cell?

    <p>Nucleus</p> Signup and view all the answers

    What is the definition of colonization in relation to microorganisms?

    <p>The presence of microorganisms on body surfaces without causing harm.</p> Signup and view all the answers

    Which type of symbiotic relationship benefits one organism while leaving the other unaffected?

    <p>Commensal</p> Signup and view all the answers

    What is the primary focus of most microbiome studies?

    <p>Bacteria</p> Signup and view all the answers

    What is one of the main risks associated with the disruption of the microbiome?

    <p>Low resistance to infections</p> Signup and view all the answers

    Which factor is NOT mentioned as affecting the diversity of the microbiome?

    <p>Geographical location</p> Signup and view all the answers

    What is the collective term for genes of the microbes living in and on the human body?

    <p>Microbiome</p> Signup and view all the answers

    Which bacterium is directly associated with increased risk after antibiotic use?

    <p>CLOSTRIDIOIDES DIFFICILE</p> Signup and view all the answers

    Which of the following is NOT a benefit that microorganisms receive from living in the human body?

    <p>Direct communication with human cells</p> Signup and view all the answers

    What is the purpose of a fecal microbiota transplant (FMT)?

    <p>To replace a dysfunctional microbiome</p> Signup and view all the answers

    What term describes the fungal component of the microbiome?

    <p>Human Mycobiome</p> Signup and view all the answers

    What characteristic of CLOSTRIDIOIDES DIFFICILE infection (CDI) makes it a concern?

    <p>It may recur with increased risk each time</p> Signup and view all the answers

    In the context of symbiotic relationships, what characterizes a parasitic relationship?

    <p>One organism is harmed while the other benefits</p> Signup and view all the answers

    What is a necessary step before performing a fecal microbiota transplant?

    <p>Rigorous donor screening and testing</p> Signup and view all the answers

    Which microorganisms are predominantly found in the skin?

    <p>Coagulase negative Staphylococci</p> Signup and view all the answers

    What is the predominant environment in the oral cavity for microorganisms?

    <p>Moist with nutrients</p> Signup and view all the answers

    What type of environment does the large intestine primarily provide for microorganisms?

    <p>Anoxic environment</p> Signup and view all the answers

    Which of the following is the predominant microorganism in the female genital tract during reproductive years?

    <p>Lactobacillus</p> Signup and view all the answers

    What is a characteristic of the skin's microbial environment?

    <p>Salt-rich environment supporting salt-tolerant organisms</p> Signup and view all the answers

    Which of the following is a significant health benefit of the microbiome in the GI tract?

    <p>Contributes to fermentation processes</p> Signup and view all the answers

    In what anatomical site would you commonly find anaerobic Bacteroides?

    <p>Large intestine</p> Signup and view all the answers

    Which of the following statements about the upper respiratory tract is correct?

    <p>It usually contains a low number of microorganisms.</p> Signup and view all the answers

    Which of the following protozoans is specifically categorized as a flagellated protozoan?

    <p>Trypanosoma cruzi</p> Signup and view all the answers

    What are the three categories of helminths?

    <p>Nematodes, Trematodes, Cestodes</p> Signup and view all the answers

    Which of the following statements best describes the role of arthropods in relation to infectious diseases?

    <p>They are invertebrate animals that act as vectors.</p> Signup and view all the answers

    Which disease is specifically caused by a prion?

    <p>Creutzfeldt-Jakob disease (CJD)</p> Signup and view all the answers

    Which of the following is NOT a function of the normal flora in the human microbiome?

    <p>Directly causing infections</p> Signup and view all the answers

    What is a primary risk factor for Clostridioides difficile infection (CDI)?

    <p>Long-term antibiotic use</p> Signup and view all the answers

    What procedure is involved in fecal microbiota transplant (FMT)?

    <p>Transfer of donor stool to restore microbiome</p> Signup and view all the answers

    What condition might result from the disruption of the microbiome?

    <p>Decreased nutrient absorption</p> Signup and view all the answers

    Which of the following best describes the relationship between pathogenic microbes and harmless microbes in a healthy microbiome?

    <p>Harmless microbes dominate, keeping pathogenic microbes in check</p> Signup and view all the answers

    What is the goal of donor screening in fecal microbiota transplant (FMT)?

    <p>To guarantee the safety and efficacy of the transplant</p> Signup and view all the answers

    What is one of the primary roles of the human microbiome in relation to health?

    <p>To help train the immune system and protect against pathogens</p> Signup and view all the answers

    How do genotypic characteristics differ from phenotypic characteristics in microorganisms?

    <p>Genotypic characteristics involve genetic sequences, while phenotypic involve physical characteristics</p> Signup and view all the answers

    Which anatomical site is typically associated with the presence of anaerobic bacteria such as Bacteroides?

    <p>Large intestine</p> Signup and view all the answers

    What factor can lead to the disruption of the microbiome?

    <p>Prolonged antibiotic therapy</p> Signup and view all the answers

    What is a transient microorganism in the human microbiome?

    <p>Microorganisms that temporarily inhabit a location without significant impact</p> Signup and view all the answers

    What is one complication that can arise when the microbiome is disrupted?

    <p>Development of antibiotic-resistant infections</p> Signup and view all the answers

    Which term is related to the concept of symbiosis within the human microbiome?

    <p>Mutualism</p> Signup and view all the answers

    What is the significance of studying clinical microbiology for medical students?

    <p>It emphasizes the prevention of infections and patient management</p> Signup and view all the answers

    What is the primary focus of infection prevention in a healthcare setting?

    <p>Standard and transmission-based precautions</p> Signup and view all the answers

    Which of the following best defines the term 'phenotype'?

    <p>The observable characteristics of an organism</p> Signup and view all the answers

    In the classification of microbes, which category encompasses organisms such as Staphylococcus aureus?

    <p>Bacteria</p> Signup and view all the answers

    What is a significant consideration in antimicrobial stewardship?

    <p>Optimizing the use of antibiotics in treatment</p> Signup and view all the answers

    Which of the following components is typically present in a bacterial cell structure?

    <p>Cell wall</p> Signup and view all the answers

    What is the role of vaccination in preventing infections at the community level?

    <p>To promote herd immunity</p> Signup and view all the answers

    Which of the following best describes the unique structure of a prokaryotic cell?

    <p>It has a single chromosome and no organelles.</p> Signup and view all the answers

    Which of these microorganisms is classified as an arthropod?

    <p>Lice</p> Signup and view all the answers

    What is the predominant role of Lactobacillus in the female genital tract?

    <p>To metabolize glycogen and produce lactic acid</p> Signup and view all the answers

    Which anatomical site is characterized by a high diversity of microbial species due to various microenvironments?

    <p>Skin</p> Signup and view all the answers

    What is the primary reason anaerobic bacteria thrive in the large intestine?

    <p>Anoxic environment with minimal oxygen</p> Signup and view all the answers

    Which of the following organisms is predominantly found in the oral cavity?

    <p>Streptococci</p> Signup and view all the answers

    What environmental condition of the skin is most conducive to certain microorganisms?

    <p>Acidic pH between 3 and 5</p> Signup and view all the answers

    What characteristic is particularly important for microorganisms residing in the oral cavity?

    <p>Resistance to mechanical removal</p> Signup and view all the answers

    In which area are coagulase-negative Staphylococci most commonly found?

    <p>Skin</p> Signup and view all the answers

    Which condition primarily increases the risk of opportunistic infections in the female genital tract?

    <p>Presence of Candida albicans</p> Signup and view all the answers

    What type of protozoan is characterized by the use of pseudopods for motility?

    <p>Amoeboid protozoans</p> Signup and view all the answers

    Which category of helminths includes flukes?

    <p>Trematodes</p> Signup and view all the answers

    What is a characteristic of prions that distinguishes them from conventional pathogens?

    <p>They are composed of proteins only.</p> Signup and view all the answers

    Which of the following diseases is specifically associated with prions?

    <p>Bovine Spongiform Encephalopathy (BSE)</p> Signup and view all the answers

    Which of the following organisms is most commonly known to act as a vector for infectious diseases?

    <p>Ixodes species</p> Signup and view all the answers

    What distinguishes the phenotype of an organism from its genotype?

    <p>Phenotype includes observable characteristics.</p> Signup and view all the answers

    Which of the following best describes the role of vaccination in infection prevention?

    <p>Vaccination enhances community immunity against pathogens.</p> Signup and view all the answers

    What component of microbial classification considers both phenotypic and genotypic characteristics?

    <p>Taxonomy</p> Signup and view all the answers

    Which of the following microbes is correctly classified under the genus 'Candida'?

    <p>Candida krusei</p> Signup and view all the answers

    What is one of the primary goals of antimicrobial stewardship?

    <p>To optimize the use of antibiotics to combat resistance.</p> Signup and view all the answers

    Which structure is typically absent in archaea but present in eukaryotic microorganisms?

    <p>Nucleus</p> Signup and view all the answers

    Which infection control practice is considered essential in preventing healthcare-associated infections?

    <p>Standard and transmission-based precautions.</p> Signup and view all the answers

    What is a characteristic feature of the cell wall in bacteria?

    <p>Composed of peptidoglycan.</p> Signup and view all the answers

    What is the main challenge in developing chemotherapy for fungi compared to bacteria?

    <p>Fungi have similar cellular structures to human cells.</p> Signup and view all the answers

    Which characteristic is true about viruses?

    <p>They consist of nucleic acid and a protein coat.</p> Signup and view all the answers

    In which anatomical site does Lactobacillus predominantly reside during reproductive years?

    <p>Vagina</p> Signup and view all the answers

    What is the primary reason anaerobic bacteria are predominant in the large intestine?

    <p>Anoxic environment</p> Signup and view all the answers

    Which of the following methods is primarily used for genotypic characterization in microorganisms?

    <p>PCR</p> Signup and view all the answers

    What differentiates protozoans from other microorganisms?

    <p>They are primarily single-celled eukaryotic organisms.</p> Signup and view all the answers

    Which microbial group is most commonly found in the skin of healthy adults?

    <p>Coagulase negative Staphylococci</p> Signup and view all the answers

    Which of the following statements accurately reflects the classification of fungi?

    <p>Fungi are eukaryotic organisms with a complex structure.</p> Signup and view all the answers

    What is a significant factor influencing the microbial diversity in the GI tract?

    <p>Diet</p> Signup and view all the answers

    How do antibiotics affect fungal infections compared to bacterial infections?

    <p>Fungi often show high resistance to commonly used antibiotics.</p> Signup and view all the answers

    Which of the following organisms is considered an opportunistic pathogen that may be present in the vaginal environment?

    <p>Candida albicans</p> Signup and view all the answers

    Which anatomical site supports a population of diverse microorganisms, with quantities up to 10^10 organisms?

    <p>Oral Cavity</p> Signup and view all the answers

    Which typing method specifically assesses the susceptibility of microorganisms to phages?

    <p>Phage typing</p> Signup and view all the answers

    What is a key characteristic of parasitic protozoans compared to free-living protozoans?

    <p>They require a host for survival and reproduction.</p> Signup and view all the answers

    What characteristic of the skin contributes to the predominance of salt-tolerant organisms?

    <p>Presence of sweat</p> Signup and view all the answers

    Which type of organism is favored in the aerobic regions of the oral cavity?

    <p>Strict aerobes</p> Signup and view all the answers

    What is the primary role of the human microbiome in relation to its host?

    <p>It provides nutritional benefits and stimulates immunity.</p> Signup and view all the answers

    Which of the following factors does NOT affect the content and diversity of the microbiome?

    <p>Environmental pollution</p> Signup and view all the answers

    What distinguishes a commensal relationship from a mutualistic relationship in microbiomes?

    <p>In a commensal relationship, one organism benefits while the other is unaffected.</p> Signup and view all the answers

    Which statement best describes the characteristics of the human virome?

    <p>It encompasses bacteriophages along with human viruses.</p> Signup and view all the answers

    What does the term 'antagonistic' refer to in microbial symbiosis?

    <p>An interaction that is detrimental to both organisms involved.</p> Signup and view all the answers

    What role do transient microorganisms typically play in the human microbiome?

    <p>They appear temporarily and do not establish long-term residence.</p> Signup and view all the answers

    How does the presence of Staphylococcus epidermidis benefit the human host?

    <p>Through competition with pathogenic organisms to prevent overgrowth.</p> Signup and view all the answers

    Which statement accurately reflects the composition of the human microbiome?

    <p>It includes a variety of microbes including bacteria, fungi, viruses, and protozoa.</p> Signup and view all the answers

    Study Notes

    Classification of Microbes

    • Microorganisms can be classified into five main categories: bacteria, viruses, fungi, protozoa, and arthropods.
    • To differentiate microorganisms, phenotypic and genotypic characteristics are used.
    • Phenotype refers to the observable characteristics of an organism, while genotype refers to the organism’s genetic makeup.

    The Binomial System

    • The binomial system uses two words to classify organisms; the genus and species.
    • The genus is like a surname and the species is like a first name.
    • Examples include: Homo sapiens, Staphylococcus aureus, Candida albicans and Plasmodium falciparum.
    • Individuals within the same species are similar and can interbreed.

    Microorganisms

    • Bacteria and archaea differ from fungi and protozoa in their cell structures.
    • Bacteria and archaea have a single chromosome and no cell organelles.
    • Fungi and protozoa include a nucleus, mitochondria, Golgi apparatus, and endoplasmic reticulum.

    The Bacterial Cell

    • The bacterial cell contains a single chromosome, plasmids, cytoplasm, ribosomes, a cytoplasmic membrane, a cell wall, flagellae, and pili/fimbriae.

    Symbiosis

    • Symbiosis is an association between two or more species.
    • Commensalism: One species benefits, and the other is neither harmed nor helped.
    • Mutualism: Both species benefit from each other.
    • Parasitism: The host is harmed, and the symbiant benefits.
    • Antagonism: The relationship harms both symbiants.

    The Human Microbiome

    • The human microbiome encompasses the collective genomes of microbes, including bacteria, bacteriophages, fungi, protozoa, and viruses, that live inside and on the human body.
    • The human body has about 10 times as many microbial cells as human cells.
    • The human microbiome is composed of a diverse range of microorganisms, including bacteria, fungi, and viruses.
    • Most microbiome studies focus on the bacterial component, but researchers are increasingly investigating the roles of fungi and viruses.

    Factors Influencing the Microbiome

    • Age, sex, genetics, diet, and other factors such as stress, antibiotics, and immunosuppression can affect the composition and diversity of the microbiome.

    Benefits of the Microbiome

    • Microorganisms benefit from a supply of nutrients and a stable environment.
    • The human host benefits from the microbiome's role in nutrition, immunity, and preventing the overgrowth of pathogens.
    • The microbiome can prevent pathogen overgrowth.
    • The microbiome may contribute to nutrient absorption.
    • The microbiome helps to stimulate the body’s immune response.

    Anatomical Sites of Microbiome

    • Anatomical sites where microorganisms are most prevalent include the skin, oral cavity, gastrointestinal tract, upper respiratory tract, and vagina.

    Skin Microbiome

    • The skin of an adult human is about 2 square meters and contains approximately 10^12 bacteria.
    • The skin is a diverse environment that supports a variety of bacterial species.
    • Moist areas, such as the axilla, groin, and between the toes, are more densely populated than dry areas.
    • Sweat is salt-rich, favoring salt-tolerant organisms.
    • The skin's pH is acidic, ranging from 3 to 5.
    • The skin contains both resident and transient microbes.
    • Coagulase-negative staphylococci comprise up to 90% of the skin's microflora.
    • Other less common skin microbes include Staphylococcus aureus, Corynebacterium, Micrococcus, and Cutibacterium acnes.

    Oral Cavity Microbiome

    • The oral cavity harbors approximately 10^10 organisms.
    • The oral environment includes diverse microenvironments, such as the tooth surface, mucosa, and gingival crevices.
    • Organisms that can resist mechanical removal are favored.
    • Individuals differ in the efficiency of their salivary flow.
    • Aerobic organisms reside on the tooth surface, while anaerobic organisms typically populate gingival crevices.
    • The oral cavity provides a favorable environment with nutrients, moisture, and temperature.
    • Oral biofilms, such as dental plaque on the tooth surface, require regular physical removal to prevent disease.
    • Predominant microbes in the oral cavity include streptococci, lactobacilli, neisseria, staphylococci, and corynebacteria.

    Large Intestine Microbiome

    • The large intestine is the most densely populated site, with approximately 10^12 organisms per gram of wet weight.
    • The large intestine's anaerobic environment supports diverse anaerobic bacteria.
    • Predominant species in the large intestine include anaerobic Bacteroides and anaerobic lactic acid bacteria, such as Bifidobacterium bifidum.
    • Aerobic and anaerobic Escherichia coli, Klebsiella aerogenes, and Proteus species are also present.
    • The population in the large intestine closely resembles that found in feces.
    • Dietary variations influence the proportions of different species within the large intestine.

    Genitourinary Tract Microbiome

    • The upper genitourinary tract (kidney, bladder, ureters) is typically sterile.
    • The female genital tract has a low pH environment due to glycogen metabolism by lactic acid bacteria.
    • Lactobacillus predominates during reproductive years.
    • Candida albicans, an opportunistic organism, may be present.

    Consequences of Microbiome Disruption

    • Pathogenic microbes are typically outnumbered by harmless microbes, maintaining a balanced state.
    • However, under certain circumstances, the balance can shift, leading to opportunistic infections.
    • Factors that can disrupt the balance include breaches of mucosal surfaces, impaired host defenses, and prolonged antibiotic use.
    • Compromised hosts with weakened immune systems are at increased risk of infections.
    • Common factors contributing to compromised host immunity include malnutrition, cancer, diabetes, immunosuppression, trauma from surgery, and prolonged antibiotic use.

    Clostridioides difficile Infection (CDI)

    • Clostridioides difficile is a spore-forming, toxin-producing anaerobic bacterium carried asymptomatically by many individuals.
    • It is a common healthcare-associated infection (HAI) in Europe, affecting about one in twenty HAIs, accounting for 48% of gastrointestinal HAIs.
    • Antibiotics are the main risk factor for CDI.
    • CDI is a toxin-mediated disease characterized by diarrhea, ranging from mild to severe colitis.
    • Recurrent CDI is common, with the risk increasing with each recurrence.

    Faecal Microbiota Transplant (FMT)

    • FMT is a well-established, accepted, and potentially life-saving therapeutic strategy for managing recurrent CDI.
    • FMT involves transferring carefully screened donor stool via colonoscopy, enema, or a pill to replace a dysfunctional microbiome.
    • Rigorous donor screening and testing are essential.

    Summary

    • The human microbiome plays a crucial role in maintaining health.
    • Different anatomical sites support distinct microbiome compositions.
    • Disruptions to the microbiome can create conditions that favor opportunistic pathogens, leading to infections, such as CDI.

    Microbes and The Microbiome

    • Microorganisms are classified as bacteria, viruses, fungi, protozoa, or arthropods.
    • The Binomial System uses genus and species names to identify organisms, e.g., Homo sapiens, Staphylococcus aureus.
    • Bacteria and Archaea have a single chromosome and no cell organelles.
    • Fungi and Protozoa have a nucleus, mitochondria, Golgi apparatus, and endoplasmic reticulum.
    • The bacterial cell has a single chromosome, plasmids, cytoplasm, ribosomes, a cytoplasmic membrane, a cell wall, flagellae, and pili/fimbriae.
    • Microorganisms are classified using phenotypic and genotypic characteristics.
    • Phenotype refers to the observable features of an organism, while genotype refers to its genetic makeup.
    • Examples of protozoans include Amoeboid protozoans (like Entamoeba histolytica), Ciliated protozoans (like Balantidium coli), Flagellated protozoans (like Trypanosoma cruzi), and Sporozoans (like Plasmodium falciparum).
    • Parasites include helminths (parasitic worms) and arthropods (invertebrate animals), which often act as vectors for infectious agents.
    • Prions are small hydrophobic glycoproteins that are closely related to human proteins and lack nucleic acid.
    • Prions cause spongiform encephalopathies, which are rare but fatal neurodegenerative diseases.
    • The human microbiome refers to the mixture of organisms regularly present at any anatomical site.
    • The human microbiome is diverse, with different anatomical sites harboring specific microbial communities.
    • The most densely populated area is the large intestine, with 10^12 organisms per gram of wet weight.
    • Disruption of the microbiome can lead to infection, as pathogenic microbes are normally outnumbered by harmless microbes.
    • Disruption of the microbiome can occur due to various factors: breach of mucosal surfaces, impaired host defenses, prolonged antibiotic use, or underlying conditions.
    • Clostridioides difficile is a spore-forming, toxin-producing bacterium that can cause infection, commonly in healthcare settings.
    • C. difficile infection (CDI) is a toxin-mediated disease that can range from mild diarrhea to colitis, and is associated with prolonged antibiotic use.
    • Fecal microbiota transplant (FMT) is a therapeutic strategy for recurrent CDI, replacing the dysfunctional microbiome with carefully screened donor stool.

    Clinical Microbiology

    • Clinical microbiology focuses on microbes causing human diseases.
    • Key aspects include understanding bacterial pathogenicity, antibiotic resistance, clinically relevant pathogens, major infections by system, and preventing infection through community-based vaccinations and healthcare-associated infection (HAI) control.
    • Clinical microbiology teaching incorporates scientific concepts, clinically relevant pathogens, major infections by system, and infection prevention strategies.
    • Professionalism in clinical microbiology involves infection prevention and control (e.g., hand hygiene) and antimicrobial stewardship.

    What are the Categories of Microbes?

    • Microbes are classified into five categories: bacteria, viruses, fungi, protozoa and arthropods.
    • Microorganisms are differentiated by their phenotypic and genotypic characteristics.

    What is the Binomial System?

    • The Binomial System is a naming system that uses two names to identify an organism, the genus and species name.
    • The genus name is always capitalized, while the species name is not.
    • Both names are written in italics or underlined, e.g. Homo sapiens or Staphylococcus aureus.

    Bacteria and Archaea

    • Bacteria and Archaea are single-celled organisms that contain a single chromosome (genome) and lack cell organelles.

    Fungi and Protozoa

    • Fungi and Protozoa are eukaryotic organisms, meaning they have a nucleus that contains chromosomes.
    • Fungi and Protozoa have other cell organelles, such as mitochondria, Golgi apparatus, and endoplasmic reticulum.

    The Bacterial Cell

    • The bacterial cell has a number of key structures, including a single chromosome, plasmids (extrachromosomal DNA), cytoplasm, ribosomes, cytoplasmic membrane, cell wall, flagellae, and pili/fimbriae.

    Classification of Microbes

    • Classification can be based on both phenotypic and genotypic characteristics.
    • Genotype: The genetic make-up of an organism.
    • Phenotype: The observable (micro and macroscopic) features of an organism.

    Analysis of Phenotypic Characteristics

    • Phenotypic characteristics are used to separate one microbial strain from another (typing) or confirm the identification of an isolate.
    • Biotyping: Biochemical testing
    • Serotyping: Surface antigens
    • Antibiograms: Antibiotic susceptibility
    • Phage typing: Susceptibility to viruses

    Analysis of Genotypic or Proteomic Characteristics

    • Genotypic characterisation can be achieved by techniques such as polymerase chain reaction (PCR) and whole genome sequencing.
    • Proteotypical characterisation can be done using techniques like MALDI-TOF.

    Fungi

    • Fungi are eukaryotic organisms, more closely related to human cells than bacteria.
    • Treatment options for fungal infections are more limited than those for bacterial infections because it is difficult to develop drugs that selectively target fungal cells without harming human cells.

    Viruses

    • Viruses are not strictly cells, because they cannot produce their own metabolic energy or replicate on their own.
    • Viruses are obligate intracellular parasites, meaning they must infect a host cell to replicate.
    • Viruses have a simple structure consisting of nucleic acid and a capsid (nucleocapsid).
    • Some viruses also have an envelope derived from the host cell.

    Parasites

    • Parasites include protozoans, helminths, and arthropods.
    • Protozoa are single-celled eukaryotic microorganisms that can be free-living or parasitic.
    • Most protozoa are free-living, but all higher animal species are infected with one or more species of protozoa.
    • Helminths are parasitic worms, which are divided into three categories: nematodes (roundworms), trematodes (flukes), and cestodes (tapeworms).
    • Arthropods are invertebrate animals such as arachnids and insects. They usually act as vectors for infectious agents, but they are not direct human pathogens.

    Prions

    • Prions are small, hydrophobic glycoproteins that are closely related to human proteins.
    • Prions do not contain nucleic acid.
    • Prion diseases are characterized by spongiform encephalopathies, which are degenerative brain diseases.
    • Examples of prion diseases include Creutzfeldt-Jakob disease (CJD), Kuru, Scrapie, and Bovine Spongiform Encephalopathy (BSE).

    The Microbiome/Normal Flora

    • The microbiome is the mixture of organisms regularly present at any anatomical site in the human body.
    • Microorganisms usually form relationships with their host, called symbiosis.
    • Colonization is the presence of microorganisms on a body surface (eg skin, mucosal membranes) without causing damage to the host.
    • Resident colonizers live on the body permanently, while transient colonizers come and go.
    • Infection occurs when a microorganism invades body tissue.

    Symbiosis

    • Symbiosis refers to the association between two or more species.
    • Different types of symbiotic relationships are defined by their mutual effects on each other:
      • Commensal: One symbiont benefits while the other is neither harmed nor helped.
      • Mutualistic: Both organisms benefit from each other.
      • Parasitic: The host is harmed while the symbiont benefits.
      • Antagonistic: The relationship harms both symbiants.

    The Microbiome

    • The microbiome is composed of the collective genomes of microbes that live inside and on the human body.
    • The components of the microbiome include bacteria, bacteriophage, fungi, protozoa, and viruses.
    • The human body has about 10 times more microbial cells than human cells.
    • Most studies of the microbiome focus on the bacterial component, but learning more about the role of fungi and viruses is also important.
    • Human Virome is made up of human viruses (e.g.Enteroviruses) + bacteriophages.
    • Human Mycobiome is the fungal component of microbiome.

    Factors that Affect the Microbiome

    • Factors that affect the content and diversity of the microbiome include age, sex, genetics, diet, and other factors such as stress, antibiotics, and immunocompromised state.

    Benefits of the Microbiome to the Micro-Organisms

    • The microbiome provides microorganisms with a supply of nutrients and a stable environment (constant temperature, protection).

    Benefits of the Microbiome to the Human Host

    • The microbiome provides human hosts with a number of benefits:
      • Nutritional benefits
      • Stimulates immunity
      • Prevents overgrowth of pathogens

    Anatomical Sites

    • Anatomical sites with exposure to the outside environment are typically colonized with microorganisms.
    • The most densely populated sites include:
      • Skin (10^12 organisms)
      • Oral cavity (10^10 organisms)
      • GI tract (10^14 organisms)
      • Upper respiratory tract
      • Vagina

    Skin

    • The skin of adult humans is about 2m2 and is home to 10^12 bacteria.
    • The moist environment of occluded sites (eg. axilla, groin, between toes) is more densely populated.
    • Sweat is salt-rich, so salt-tolerant organisms are favored.
    • The pH of the skin is acidic (pH 3 to 5).
    • Resident and transient microbes are supported on the skin, including coagulase-negative staphylococci (up to 90%), S. aureus, corynebacteria, micrococci, and Cutibacterium acnes.

    Oral Cavity

    • The oral cavity has about 10^10 organisms.
    • Diverse microenvironments support diverse species of microorganisms. The tooth surface, mucosa, and gingival crevices are all home to different microorganisms.
    • Organizations that resist mechanical removal are favored. Individuals differ in the efficiency of salivary flow.
    • Predominant microbes include streptococci, lactobacilli, neisseria, staphylococci, and corynebacteria.
    • Oral biofilms (dental plaque) develop on the tooth surface and require physical removal to avoid disease.

    Large Intestine

    • The large intestine is the site of the densest population of microorganisms (with 10^12 organisms per gram of wet weight).
    • The large intestine plays an important role in human health.
    • The anoxic (oxygen-deprived) environment supports a vast population of anaerobic microorganisms.
    • There are many anaerobic Gram-negative and Gram-positive bacteria.
    • Predominant species include anaerobic Bacteroides and anaerobic lactic acid bacteria (eg. Bifidobacterium bifidum).
    • The population in the intestine is very similar to that in the feces. The proportions of different species are related to diet.

    Genitourinary Tract

    • The upper genitourinary tract (including the kidneys, bladder, and ureters) is usually free of microorganisms.
    • The low pH environment of the vagina is a result of glycogen metabolism by lactic acid bacteria.
    • During reproductive years Lactobacillus species predominate.
    • Candida albicans is an opportunistic organism that may be present in the vagina.

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