V.Micro 151 Module 5.pdf

V. MICRO 151: GENERAL VETERINARY MICROBIOLOGY MODULE 05: MICROBIAL TAXONOMY 1st Semester | S.Y. 2024-2025 Instructor: Dr. Precy D. Magtoto Program, Yr., and Section: DVM Transcribed By: Harold B. Lac...

V. MICRO 151: GENERAL VETERINARY MICROBIOLOGY MODULE 05: MICROBIAL TAXONOMY 1st Semester | S.Y. 2024-2025 Instructor: Dr. Precy D. Magtoto Program, Yr., and Section: DVM Transcribed By: Harold B. Lacumbes CLASSIFICATION SYSTEMS - Encompasses a broader scope, including taxonomy Taxonomy as well as the study of the evolutionary relationships - Science of classification and naming of organisms between organisms (Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern) - Thus, systematics encompasses disciplines such - Aids in categorizing organisms not yet studied in as morphology, ecology, epidemiology, detail biochemistry, genetics, molecular biology, and - Aids in identifying already classified organisms physiology. - Provides common frame of reference when TAXONOMY organisms are discussed Science of classification of organisms - Taxon: A group or “level” within the classification Aids in categorizing organisms not yet studied in system detail Phylogenetic/Phyletic Classification System: Aids in identifying already classified organisms – - Groups reflect genetic similarity and evolutionary Provides common frame of reference when relatedness organisms are discussed - phylogeny (Greek phylon, tribe or race, and Taxon: A group or “level” of classification genesis, generation or origin) refers to the Three Parts or Components: evolutionary development of a species. 1. Classification - is the orderly arrangement of - evolutionary history of an organism organisms into groups, preferably in a format that Phenetic Classification System: Groups are based shows evolutionary relationships on convenient, observable characteristics. 2. Nomenclature - is the process of assigning names Polyphasic taxonomy- This approach includes to the various taxonomic rankings of each microbial phenotypic, phylogenetic, and genotypic features species Genotypic Classification 3. Identification - is the process of discovering and - seeks to compare the genetic similarity between recording the traits of organisms so that they may organisms. be placed in an overall taxonomic scheme. - Individual genes or whole genomes can be compared TIMELINE International Journal of Systematic and 1735 Plant & Animal Kingdoms Evolutionary Microbiology (IJSEM)- To be 1857 Bacteria & fungi put in the Plant Kingdom recognized as a new species, genomic, metabolic, 1866 Kingdom Protista proposed for bacteria, morphological, reproductive, and ecological data protozoa, algae, and fungi must be accepted and published in the IJSEM; until 1937 Prokaryote introduced for cells "without a that time, the new species name will appear in nucleus” quotation marks 1961 Prokaryote = cells in which nucleoplasm is not surrounded by a nuclear membrane Taxonomy is consists of 3 parts or components 1959 Kingdom Fungi 1. Classification - is the orderly arrangement of 1968 Kingdom Prokaryotae proposed by Murray, is organisms into groups, preferably in a format that accepted as fourth Kingdom. shows evolutionary relationships. 2 1978 Two types of prokaryotic cells found. 2. Nomenclature - is the process of assigning names CLASSIFICATION SYSTEMS to the various taxonomic rankings of each microbial Two Kingdom System species - Plantae/Animalia - bacteria, fungi, and algae 3. Identification - is the process of discovering and were classified as plants; - protozoa were recording the traits of organisms so that they may classified as animals be placed in an overall taxonomic scheme Three Kingdom System (Haeckel, 1866) : Systematics animals, plants and protist - infers a more general scientific study of organisms Five Kingdom System (Whittaker, 1969) with the ultimate objective of arranging them in an - Animalia, Plantae, Fungi, Protista, Prokaryotae orderly manner - Bacteria were separated into the Kingdom  Three Domain System of Carl Woese (1978) - The classification in Bergey’s Manual is accepted - Based on comparison of sequences of Rrna by most microbiologists as the best consensus for Ernst Haeckel (1866)- 3-kingdom system: animals, prokaryotic taxonomy plants and protist - In 1984, a more detailed work entitled Bergey’s - proposed a third Kingdom of Life: The Protista. Manual of Systematic Bacteriology was published, FIVE KINGDOM SYSTEM OF ROBERT H. - The Manual serves as a primary reference for WHITTAKER (1969) prokaryotic taxonomy Proposes the five-kingdom system with the - Taxonomic Structure: Bacteria are classified into 26 addition of the Kingdom Fungi. phyla, while Archaea are divided into two phyla. This classification is based on phylogenetic KINGDOM PROKARYOTAE/MONERA relationships, particularly utilizing nucleic acid Eubacteria (true bacteria) (Binary fission; Energy sequences such as 16S rRNA. source: organic chemicals, inorganic chemicals, or - Volumes: The second edition consists of five photosynthesis) volumes, each focusing on different groups of Archaebacteria/archaea bacteria and archaea: - Unusual metabolism - Volume I: Covers Archaea and deeply branching - Extreme living conditions bacteria. No peptidoglycan in cell walls - Volume II: Focuses on Proteobacteria. Examples: Methanogens; Halophiles; - Volume III: Discusses Firmicutes. thermoacidophiles - Volume IV: Includes Spirochaetes, Bacteroidetes, and other groups. KINGDOM PROTISTA - Volume V: Addresses Actinobacteria Primarily unicellular eukaryotes 2. Domains Protozoa, algae, slime molds, water molds - Based on the research of Carl Woese and others in the 1980s and 1990s, most biologists divide all KINGDOM FUNGI living organisms into 3 domains: Unicellular yeasts - Domain Archaea Multicellular molds - Domain Bacteria Mushrooms - Domain Eucarya Saprophytes with hyphae - rRNA sequence data suggests that Archaea & Eucarya may share a more recent common KINGDOM PLANTAE ancestor with each other than with Bacteria 3. Three Domain System of Carl Woese (1978) Some alga, mosses, ferns, conifers, flowering - Based on molecular biology and recognition that plants ribosomal differences suggest two types of Multicellular prokaryotes Photosynthetic (autotrophs - Based on comparison of sequences of rRNA - Sometimes organized as empires or domains = a KINGDOM ANIMALIA category above kingdom. Sponges, worms, insects, chordates Domain (cont.) Heterotrophic - Many microbiologists reject the “kingdom” Multicellular designation. MICROBIAL PHYLOGENY - Each domain is divided into phyla, phyla into 1. Bergey's Manual of Systematic Bacteriology classes. etc. - In 1923, David H. Bergey & colleagues published - There is often great metabolic and ecological Bergey’s Manual of Determinative Bacteriology, a diversity among the members of a group, perhaps manual that grouped bacteria into phenetic groups, reflecting parallel evolution of such things as used in identification of unknowns. It is now in its 9th fermentation pathways, photosynthetic pathways, edition. etc. - In 1984, a more detailed work entitled Bergey’s - New classification scheme Manual of Systematic Bacteriology was published, ▪ Domain Bacteria - Unicellular prokaryotes still primarily phenetic in its classification with cell wall containing peptidoglycan - Publication of the second edition of Bergey’s ▪ Domain Archaea- prokaryotes Manual of Systematic Bacteriology begun in 2001. - Lack peptidoglycan - The 2nd edition gives the most up-to-date - Often live in extreme environments phylogenic classification of prokaryotic organisms, - Not known to cause disease in humans or including both eubacteria and archaea. animals - When it is completed, it will consist of 5 volumes.  - Had been considered bacteria until examination of their unique rRNA sequences. Methanogens, Extreme halophiles, Extreme thermophiles ▪ Domain Eukarya - all eukaryotes - Kingdom Animalia - Kingdom Plantae - Kingdom Fungi - Kingdom Protista Domain Bacteria - Kingdom: Bacteria - Phylum: Firmicutes - Class: Bacilli - Order: Lactobacillales - Family: Lactobacillaceae - Genus: Lactobacillus - Species: L. delbrueckii - Subspecies: L. d. bulgaricus Genus a taxonomic category that groups together species that share common characteristics and are closely related. TAXONOMICAL GROUPS Species Linnaeus defined the biological classification - most basic unit of biological classification; single system unique organism group Levels in the hierarchy were as follows: - collection of strains that share many stable - Domain properties and differ significantly from other groups - Kingdom of strain - Phylum SPECIES IN MICROBIOLOGY - Class A group of microorganisms (bacteria, archaea, fungi, or - Order protists) that share a set of distinctive characteristics, - Family exhibit similar phenotypic traits, and can interbreed or - Genus exchange genetic material through horizontal gene - Species transfer, leading to viable offspring or progeny under natural conditions. DEFINITION OF “SPECIES” - Classic definition: A collection of microbial strains that share many properties and differ significantly from other groups of strains - Species are identified by comparison with known “type strains”: well-characterized pure cultures; references for the identification of unknowns - There are several collections of type strains, including the American Type Culture Collection (ATCC) Strain: - A population of microbes descended from a single individual or pure culture - Different strains represent genetic variability within a species Biovars: Strains that differ in biochemical or physiological differences Morphovars: Strains that vary in morphology Serovars: Strains that vary in their antigenic properties  PHYLOGENY OF DOMAIN ARCHAEA 5. Epsilonproteobacteria – e.g., Helicobacter pylori Based primarily on rRNA sequence data, domain Archaea is divided into two phyla (previously, but has Significant groups and genera include: evolved with updates in bacterial taxonomy and - Photosynthetic genera such as Rhodospirillum (a advances in molecular techniques : purple non-sulfur bacterium) and Chromatium (a 1. Phylum Thermoproteota (formerly known as purple sulfur bacterium) Crenarchaeota) Originally containing thermophilic - Sulfur chemolithotrophs, genera Thiobacillus and and hyperthermophilic sulfur-metabolizing archaea Beggiatoa Recently discovered Crenarchaeota are inhibited - Nitrogen chemolithotrophs (nitrifying bacteria), by sulfur & grow at lower temperatures genera Nitrobacter and Nitrosomonas 2. Phylum Euryarchaeota Contains primarily - Other chemolithotrophs, genera Alcaligenes, methanogenic archaea, halophilic archaea, and Methylobacilllus, Burkholderia thermophilic, sulfur-reducing archaea - The family Enterobacteriaceae, the “gram-negative 3. Phylum Korarchaeota A relatively small phylum enteric bacteria,” which includes genera that are often found in hot springs and geothermal Escherichia, Proteus, Enterobacter, Klebsiella, areas Salmonella, Shigella, Serratia, and others 4. Phylum Nanoarchaeota This phylum is - The family Pseudomonadaceae, which includes characterized by its extremely small size and genus Pseudomonas and related genera parasitic lifestyle. The only known member of this - Other medically important Proteobacteria include phylum is Nanoarchaeum equitans genera Haemophilus, Vibrio, Campylobacter, 5. Phylum Thaumarchaeota This phylum includes Helicobacter, Rickettsia, Brucella organisms that are important for nitrogen cycling in 5. Phylum Firmicutes “Low G + C gram-positive” the environment. They are often found in soil and bacteria aquatic environments Divided into 3 classes PHYLOGENY OF DOMAIN BACTERIA ▪ Class I – Clostridia; includes genera The 2nd edition of Bergey’s Manual of Systematic Clostridium and Desulfotomaculatum, and Bacteriology divides domain Bacteria into 23 phyla (in others the 4th edition there are 26 or more phyla recognized). ▪ Class II – Mollicutes; bacteria in this class Nine of the more notable phyla are described here. cannot make peptidoglycan and lack cell walls; 1. Phylum Aquiflexa/Aquifex The earliest “deepest” includes genera Mycoplasma, Ureaplasma, branch of the Bacteria. Contains genera Aquifex and others 9e.g., A. aeolicus) and Hydrogenobacter that can ▪ Class III – Bacilli; includes genera Bacillus, obtain energy from hydrogen via chemolithotrophic Lactobacillus, Streptococcus, Lactococcus, pathway. Geobacillus, Enterococcus, Listeria, 2. Phylum Cyanobacteria Oxygenic photosynthetic Staphylococcus, and other bacteria. Also known as blue-green algae 6. Phylum Actinobacteria “High G + C gram- 3. Phylum Chlorobi The “green sulfur bacteria”. positive” bacteria. Includes genera Actinomyces, Anoxygenic photosynthesis. Includes genus Streptomyces, Corynebacterium, Micrococcus, Chlorobium Mycobacterium, Propionibacterium 4. Phylum Proteobacteria 7. Phylum Chlamydiae Small phylum containing the - The largest group of gram-negative bacteria genus Chlamydia - Extremely complex group, with over 400 genera 8. Phylum Spirochaetes The spirochaetes and 1300 named species - Characterized by flexible, helical cells with a - All major nutritional types are represented: modified outer membrane (the outer sheath) and phototrophy, heterotrophy, and several types of modified flagella (axial filaments) located within the chemolithotrophy outer sheath - Sometimes called the “purple bacteria,” although - Important pathogenic genera include Treponema, very few are purple; the term refers to a hypothetical Borrelia, and Leptospira purple photosynthetic bacterium from which the 9. Phylum Bacteroidetes Includes genera group is believed to have evolved Bacteroides, Flavobacterium, Flexibacter, and Divided into 5 classes: Cytophaga; Flexibacter and Cytophaga are motile 1. Alphaproteobacteria – e.g., Rickettsia, Brucella, by means of “gliding motility Rhizobium 2. Betaproteobacteria – e.g., Nitrosomonas, Neisseria, Burkholderia 3. Gammaproteobacteria – e.g., Escherichia coli and Salmonella, Pseudomonas. 4. Deltaproteobacteria – e.g., Campylobacter.\  PHYLOGENY OF DOMAIN EUCARYA - Francisella tularensis (Tulare County, The domain Eucarya is divided into four kingdoms by California) most biologists - Pseudomonas fairmontensis (Fairmount 1. Kingdom Protista, including the protozoa and Park, Pennsylvania) algae - Mycobacterium genavense (Geneva, 2. Kingdom Fungi, the fungi (molds, yeast, and fleshy Switzerland) fungi) - Blastomyces brasiliensis (Brazil) 3. Kingdom Animalia, the multicellular animal - ` spp. (Brown University, Providence, RI) 4. Kingdom Plantae, the multicellular plants 4. ORGANIZATIONS NOMENCLATURE OF MICROORGANISMS - Legionella (American Legion) The Origin of Names - Afipia felis (Air Force Institute of Aristotle: Pathology) - Greek philosopher, attempted to classify all living - Cedecea spp. (Centers for Disease things as either Plant or Animal. He grouped Control) animals into Land Dwellers, Water Dwellers, and Air - Bilophila wadsworthia (VA Wadsworth Dwellers Medical Center in Los Angeles). - Subsequent scientists later tried to classify living RULES OF NOMENCLATURE creatures 1. USE BINARY NAMES - by means of locomotion Binary names (invented by Linnaeus), consisting of - grouping butterflies and bats (flying) a generic name and a species epithet (e.g., - This system of classification was obviously flawed Escherichia coli), must be used for all as well. microorganisms. Carl Linnaeus: Names of categories at or above the genus level - a Swedish botanist. He developed his naming may be used alone, but species and subspecies system in the middle 1700’s, which essentially the names (species names) may not. In other same one we use today words…never use a species name alone. - He attempted to name all known plants, animals, 2. WHEN TO CAPITALIZE – The genus name (and and minerals using Latin and Greek names above) is always capitalized, the species name is never - Systema Naturae, meaning “The Natural capitalized, e.g., Bacillus anthracis Classification", was published in 1735/ 3. WHEN TO ITALICIZE - Known as the “Father of Modern Taxonomy” Names of all taxa (kingdoms, phyla, classes, - was the first to consistently name plants and orders, families, genera, species, and subspecies) animals using the binomial system of Latin names are printed in italics and should be underlined if for genus and species handwritten; strain designations and numbers are MICROORGANISM NAMES ORIGINATE FROM not FOUR DIFFERENT SOURCES If all the surrounding text is italic, then the binary 1. DESCRIPTIVE name would be non-italic (Roman typeface) or - Staphylococcus aureus (grape-like cluster of underlined (e.g., A common cause of diarrhea is E. spheres, golden in color) coli O157, a gram-negative bacillus). - Streptococcus viridans (chains of spheres, 4. WHEN TO USE INITIALS green in colony color) - Proteus vulgaris (first and common) A specific epithet must be preceded by a generic - Helicobacter pylori (spiral shaped rod at the name, written out in full the first time it is used in a entrance to the duodenum) paper. 2. SCIENTIST’S NAMES Thereafter, the generic name should be abbreviated - Escherichia coli (Theodor Esherich) to the initial capital letter (e.g., E. coli), provided - Ehrlichia (Paul Ehrlich) there can be no confusion with other genera used - Nessieria (Albert Neisser) in the paper. - Listeria (Joseph Lister) Be careful with the “S” words; Salmonella, Shigella, - Pasturella (Louis Pasteur) Serratia, Staphylococcus, Streptococcus, etc - Yersinia (AlexandreYersin) 5. COMMON NAMES - Vernacular (common) names - Bartonella (Alberto Barton) should be in lowercase roman type, non-italic (e.g., - Morganella (H. de R. Morgan) streptococcus, brucella). However, when referring to the - Edwardsiella (P. R. Edwards) actual genus name (or above) always capitalize and 3. GEOGRAPHIC PLACES italicize i.e., Streptococcus, Brucella. - Legionella longbeachiae (Long Beach, 6. SUBSPECIES AND SEROVARS California) For Salmonella, genus, species, and subspecies names should be rendered in standard form: Salmonella enterica at first use, S. enterica  thereafter; Salmonella enterica subsp. arizonae at COMMON LATIN AND GREEK ROOTS USED IN first use, S. enterica subsp. arizonae thereafter. MICROBIOLOGY Names of serovars should be in roman type with the a-, an- not, without bac- rod-shaped first letter capitalized: Salmonella enterica serovar ab-, a-, abs- away baro- weight, pressure Typhimurium. acr-, acro- height, basi- at the bottom After the first use, the serovar may also be given summit, tip without a species name: Salmonella serovar aer-, aero- air, bi- two Typhimurium or Salmonella Typhimurium. atmosphere 7. ABBREVIATIONS FOR SPECIES albus- white bio- life use “sp.” for a particular species ambi- both, on both blast- germ, embryo, “spp.” for several species (“spp” stands for “species sides bud, cell with nucleus plural”). ampulla- bottle, flask bon(i)- good These abbreviations are not italicized; e.g., ana- again, against, bor- north Clostridium sp. or Clostridium spp. back meaning 'for example' (it comes from the Latin, angeion - vessel brach- short exempli gratia) ant-, anti- against, brachi-, brachio- arm i.e. meaning 'that is' (from the Latin id est). Note that opposed to, preventive 'i.e.' specifies particular things, whereas 'e.g.' gives ante-, anti- before, in brachys, brachy - short examples. front of, prior to etc. meaning 'and so forth' (from the Latin et cetera) anth-, antho- flower brev(i)- brief, short (time) [Some people, wrongly, write ect.] aqu- water brevis - short et al. meaning 'and others' (from the Latin et alia). archaeo-, archeo- bronch- windpipe You would use this only when citing references ancient 8. PLURAL FORMS arthr- , arthro- joint bucc- cheek, mouth, Plural of genus is genera cavity species (sp.) is species (spp.) astr-, astro- star, star- aur- relating to gold, or medium is media (never say “this culture media”) shaped gold-colored fungus is fungi aureus - golden, gold avi- bird streptococcus is streptococci (staphylococcus - coin staphylococci; enterococcus - enterococci, etc) bacillus is bacilli MAJOR CHARACTERISTICS OF BACTERIA bacterium is bacteria 1. Morphological alga is algae characteristics protozoan is protozoa 2. Chemical 9. Listing References composition Always use the “Journal of Clinical Microbiology” as 3. Cultural a guideline. List the authors (in bold), publication characteristics date, name of article, name of journal, volume (in 4. Metabolic bold), then pages. For example: characteristics Angot, P., M. Vergnaud, M. Auzou, R. Leclercq, 5. Antigenic and Observatoire de Normandie du characteristics Pneumocoque. 2000. Macrolide resistance 6. Genetic phenotypes and genotypes in French clinical characteristics isolates of Streptococcus pneumoniae. Eur. J. Clin. 7. Pathogenicity Microbiol. Infect. Dis. 19:755-758 8. Ecological characteristics Additional rules: List your sources in an alphabetical USEFUL PROPERTIES IN CLASSIFICATION order according to the author's last name. Colony morphology If no author is listed, begin with the main word of the Cell shape & arrangement article or book title (ignoring A, An, or The). Cell wall structure (Gram staining) Underline or italicize the title of books or magazines. Special cellular structures 10. O vs. 0 – Mind your “O’s” and zeros. It is E. coli O157, Biochemical characteristics not E. coli 0157 IDENTIFICATION OF MICROORGANISMS Classification into taxonomic hierarchy based on morphological characteristics, DNA hybridization, and rRNA sequencing  Identification of an unknown (but previously Serology: Study of serum and its immune discovered and classified) microbe requires more response. specific and often combined methods Combine known antiserum + unknown bacterium 1. Morphological characteristics -size, shape, Slide agglutination cellular characteristics (capsule, flagella, ELISAp288, 514 endospores, etc.) Western blotp289 - Useful for identifying eukaryotes Southern Blot p292 2. Differential staining e.g., Gram stain, Acid fast DNA chip p293 stain Advantages: - Gram staining, acid-fast staining - Highly specific 3. Biochemical tests- Determines presence of - Does not usually require the organism to be bacterial enzymes isolated into pure culture - probe for specific enzyme activities: - Can be used to identify organisms that can’t be ▪ carbohydrate fermentation grown on medium ▪ nitrogen fixation Molecular Characteristics – Genetics ▪ sulfur oxidation - DNA base composition Guanine + cytosine ▪ gas production moles% (GC) ▪ Acid production - DNA fingerprinting Electrophoresis of restriction ▪ Nitrate reduction enzyme digest - rRNA sequencing - Polymerase Chain Reaction (PCR)p251 2. Nucleic Acid Base Composition G + C content Estimated by determining the melting temperature of the DNA Higher G + C gives a higher melting temperature 3. Nucleic acid hybridization A.k.a DNA-DNA hybridization (DDH) By mixing ssDNA from two different species and determining the percentage of the DNA that can form dsDNA hybrids IDENTIFYING A GRAM – NEGATIVE, OXIDASE – The greater the percent hybridization, the closer NEGATIVE ROD the species Design a rapid test for a Staphylococcus aureus. 10-14 USEFUL PROPERTIES IN CLASSIFICATION 1. Serological Tests Use group specific antiserum isolated from the plasma of animals that have been sensitized to the 4. Nucleic acid sequencing organism Genes for specific enzymes - The antiserum contains antibody proteins that The nucleic acid sequence for the complete react with antigens on the unknown organism. genome of several species is now available - The reaction can be detected by examining 5S and 16S rRNA (ribosomal RNA) sequences; agglutination or by using sera labeled with comparison of these sequences has been colorimetric or fluorescent labels extensively used to determine the phylogenetic relationships of microbial groups.  BERGEY’S MANUAL OF SYSTEMATIC FISH BACTERIOLOGY - Fluorescent in situ hybridization- Add DNA Morphological characteristics probe for S. aureus Presence of various enzymes Serological tests Phage typing- Determining a strains suceptability to certain phage or bacterial viruses Fatty acid profiles DNA finger printing Is still very difficult Sequence of ribosomal RNA- Is still very difficult Phage Typing - Determining a strains suceptability to certain phage or bacterial viruses - Flow Cytometry- Uses differences in electrical conductivity between species - Fluorescence of some species - Cells selectively stained with antibody plus fluorescent dye FLOW CYTOMETRY Uses differences in electrical conductivity between species Fluorescence of some species Cells selectively stained with antibody plus fluorescent dye. Differentiate between classification and identification