BMS2037 Introduction to the module_ Taxonomy 2023 - Copy.pdf

BMS2037 Cellular Microbiology & Virology Introduction to the Module Module organiser: Dr Alison Cottell  Module Aims: Diagnostic techniques To provide an introduction to the principles and techn...

BMS2037 Cellular Microbiology & Virology Introduction to the Module Module organiser: Dr Alison Cottell  Module Aims: Diagnostic techniques To provide an introduction to the principles and techniques of bacteriology in lab practicals & virology To provide an introduction to protozoan evolution and development To provide an introduction to the molecular basis of bacterial phylogeny Next session and the bacterial genome To provide an introduction to modern classification of protozoa & animal viruses, and the major classes of protozoa and viruses Thorough knowledge of To describe structural, physiological, biochemical & genetic characteristics a wide range of of the major groups of bacteria and animal viruses microbes: classification; disease; environment To describe the diseases caused by bacteria and protozoa To examine virulence mechanisms in pathogenic bacteria and protozoa To examine the role and effects of bacteria and protozoa in the environment To understand the nature of viruses and the differences between these Understanding similarities agents and other microbes and differences illustrates your deeper understanding of the subject Module Learning Outcomes: Describe characteristics of major groups of bacteria, protozoa and viruses and recommend tests that could be used to identify and distinguish between species that are most frequently encountered in clinical specimens Understand how the various groups of bacteria and protozoa derive energy and nutrients from their environment and the constraints imposed on viruses by their dependence on the host cell Describe the pathology associated with a number of bacterial and protozoan diseases Understand host-pathogen interactions that lead to disease pathology for a number of model diseases Read and critically analyse research papers on cellular microbiology and virology Describe the principles of diagnosis for selected infectious diseases Perform practical virology techniques Understand the role of bacteria and protozoa in the environment Block 1: Bacteria and Protozoa: you should study short pre-recorded introductions to each topic on SurreyLearn Block 2 topics: virology : you should study short pre-recorded introductions to each topic on SurreyLearn  Module assessment: Two tests – 60 minutes, in-person, invigilated Test 1: Week 6; 1st of November. Block 1 Bacteria / protozoa topics Test 2: Main exam period: – Block 2 Virology topics Each test is worth 50% of module mark – practice tests will be available. Each test will include ~40 Qs Standard MCQs (one correct answer from five options) Target research paper MCQs (one correct answer from five options) Extended matching questions (EMQs; one correct answer from ten options) Short-answer questions  Exam format: examples of different question types Standard MCQ style: Patients with which illness are more at risk from Pseudomonas aeruginosa infection? A. Asthma B. Eczema C. Irritable bowel disease D. Cystic fibrosis E. Atrial fibrillation Target research paper question (example from a previous year): What was suggested as a mechanism by which Giardia duodenalis causes failure to thrive? A. Toxic metabolites In both cases there is only one correct B. Alteration of natural killer cells answer per question. No question will be C. Alteration of CD4:CD8 ratios negatively marked –if you don’t know an D. Duodenal inflammation answer you can make a “best guess”! E. Steatorrhea  Exam format: examples of different question types Extended matching question: Which one of the following lacks a cell wall? A. Gram-positive cell wall B. Gram-negative cell wall C. Mycoplasma D. Fungus E. Malaria F. Plasmodium species G. Photoautotrophs H. Anaerobes I. Trophozoites J. Spore-formers Formative practice tests for all topics will be available on SurreyLearn to give you feedback on your progress  Exam format: examples of different question types Short answer questions: An 81-year old man develops pneumonia in hospital after undergoing treatment for cancer. The same Gram-negative coccobacillus is isolated from his sputum and the air conditioning system of the hospital. What is the most likely pathogen to be responsible for this infection? FAQs Please use the Discussion Board on SurreyLearn to ask any questions about the module. If you email me a question that is of general benefit for all on the module I will address the issue via the Discussion Board.  BMS2037 Cellular Microbiology & Virology Topic 1: Bacterial Classification Understanding taxonomy and phylogeny Dr Alison Cottell  Taxonomy and phylogeny: Bacteria and Archaea Aim / overview of this podcast: Differentiate between Linnaean models of taxonomic classification, and modern phylogenetic methods Understand, concepts of taxonomy and phylogeny Understand how microbiologists refer to microbes using standard protocol Understand taxonomic tests that are used to differentiate and place bacteria into groups Discuss the limitations and benefits associated with genotypic versus phenotypic classification systems Understand the key differences between Bacteria and Archaea Taxonomy and Phylogeny Taxonomy: Classification based on shared characteristics (phenetic; overall similarity) Taxonomy order Us Chimps Seagull Honey bee (hierarchical) Kingdom Animalia Animalia Animalia Animalia Phylum Chordata Chordata Chordata Arthropoda Class Mammalia Mammalia Aves Insecta Order Primates Primates Charadriiformes Hymenoptera Family Hominidae Hominidae Laridae Apidae Genus Homo Pan Larus Apis Species sapiens troglodytes canus dorsata Taxonomy and phylogeny Phylogeny: Measures the evolutionary relationships between organisms Steps in taxonomic classification of microbes 1. Classification: CHAOS!! Ordering organisms into groups, based on shared properties 2. Nomenclature: Naming the classified organisms 3. Identification: Obtaining data on the properties of an unknown organism and determining which species it belongs to, based on direct comparison to known groups Leeuwenhoek’s drawing of Carl Linnaeus – founder of bacteria; viewed through an modern taxonomy 1708 - 1778 early microscope  Classification of bacteria Traditional properties used in classification Molecular and genetic methods Microscopy / Morphology Choose appropriate molecular markers for a gene family Response to oxygen Amplify and sequence Mode of energy synthesis / source of carbon Create evolutionary model Biochemical, enzymatic tests Phylogenetic tree analysis and construction  Phylogeny: Evolutionary relationships between organisms Basis of phylogeny: All living things have genes which mutate randomly (base changes) at low frequency All progeny will carry the mutation (base changes) Organisms differing by a few DNA base changes have diverged more recently in evolutionary time than organisms that differ by more bases Steps in taxonomic classification of microbes 1. Classification: Ordering organisms into groups, based on shared properties 2. Nomenclature: Naming the classified organisms 3. Identification: Obtaining data on the properties of an unknown organism and determining which species it belongs to, based on direct comparison to known groups The work of a microbial taxonomist is never done!! The universal phylogenetic tree based on 16S sRNA analysis: the three domains of life They were first grouped together in the Monera, despite Archaea being more phylogenetically related to Eukarya than bacteria https://bio.libretexts.org Extremophiles: Methanogens Anaerobic CH4 producers Hyperthermophiles 113 – 200oC Psychrophiles -15oC Acidophiles pH 1.0 Barophiles 1200 atm Phylogenetic tree of major lineages of bacteria based on 16S rRNA  Linnaean classification system: Example for Shigella Sub-species / strain classification: Biovar: biochemical / physiological variant Morphovar: differ morphologically Serovar / serotype: antigenic differences Source: McGraw-Hill Companies Bacterial classification in context: Example for Salmonella Distinct from other S. enterica: e.g. differences in host range; absence of flagella Bacterial taxonomy discussion topics 1. What phenotypic and chemotaxonomic methods could you use to help with classification of a previously unrecorded microbe? 2. Genotypic and phenotypic systems for classifying primates were shown in the pre-recording. What are the relative benefits of each type of system? 3. Since Woese, Archaea are accepted as a separate domain of life in the “Three Domain” model. Why may Woese have experienced resistance to his proposal for reclassification in this way? Focus on differences and similarities between archaea and bacteria. Discussion topic 1 - What phenotypic and chemotaxonomic methods could you use to help with classification of a previously unrecorded microbe? You are carrying out biological assessments of a previously undiscovered cave. You collect samples of fresh bat droppings, which culture in the lab. You attempt to genotype these bacteria, but nothing matches the database. You seem to have discovered a new microbe! Genotypic – classification on the basis of genetic similarities Phenotypic – physical; structural, or metabolic features Chemotaxonomic – phenotypic classification which measures degree of similarity of biochemical composition of organisms, e.g. Raman spectroscopy -RNA / DNA / GC -Fatty acids Classification of bacteria Microscopy / Morphology Spore-forming bacteria Response to Oxygen Aerobes Thrive in the presence of O2 (e.g. Bacillus) Microaerophiles Require O2 but cannot tolerate 21%. Campylobacter grows at ~5% O2 Anaerobes Cannot tolerate O2 (e.g. Clostridia) Facultative anaerobes Prefer O2 but will grow without (e.g. E. coli) Biochemical & enzymatic tests used in classification: Examples The urease test Some bacteria possess a urease enzyme: by-product of urea metabolism is ammonia The pH change alters the colour of the media following incubation: pink = urease positive Analytical profile index – multiple biochemical and enzymatic tests Microbes that produce cytochrome c can oxidise a test reagent. A by-product of the reaction is a blue/purple pigment Genotypic Phenotypic Chemotaxonomic Discussion topic 2 Genotypic and phenotypic systems for classifying primates were shown in the pre-recording. What are the relative benefits of each type of system? N.B. Primate classification is an intuitive example, but this appraisal of classification applies to all organisms Taxonomy and Phylogeny Taxonomy: Classification based on shared characteristics (phenetic; overall similarity) Taxonomy order Us Gorillas Macaques Lemurs (hierarchical) Kingdom Animalia Animalia Animalia Animalia Phylum Chordata Chordata Chordata Chordata Class Mammalia Mammalia Mammalia Mammalia Order Primates Primates Primates Primates Family Hominidae Hominidae Cercopithecidae Lemuridae Genus Homo Gorilla Macaca Lemur Species sapiens beringei sylvanus catta Taxonomy and phylogeny Phylogeny: Measures the evolutionary relationships between organisms Discussion topic 3 Since Woese, Archaea are accepted as a separate domain of life in the “Three Domain” model. Why may Woese have experienced resistance to his proposal for reclassification in this way? Focus on differences and similarities between archaea and bacteria  Bacteria and Archaea compared Similarities: The two types generally share shape, size, and microscopic appearance (rods, cocci, spirals, coiled etc.) Differentiation difficult with just a microscope (although some are distinguished by their square-edged appearance) Like bacteria, Archaea multiply by binary fission and if motile move primarily by means of flagella. Most archaea are similar in microscopic appearance to bacteria, but can also be more square-shaped / angular  Bacteria and Archaea compared Differences: Despite morphological similarities some Archaea are more angular / square shaped than bacteria Archaea do not have peptidoglycan – - some have no cell wall - may have protein S-layers - may have polysaccharide walls - may have pseudopeptidoglycan Archaea genes are more similar to eukaryotes than bacteria NAG: shared by both; NAM: only in bacteria. Archaea have N- Different 70S ribosome and more complex RNA acetytalosaminuronic acid (NAT) polymerase