Lecture 1 Classifying and Identifying Bacteria

Classifying and Identifying Bacteria Microorganisms They are very diverse which include bacteria, fungi, algae, and protozoa; microscopic plants, and animals. Single-celled microorganisms were the first forms of life to develop on earth, approximately 3 billion–4 billion years ago....

Classifying and Identifying Bacteria Microorganisms They are very diverse which include bacteria, fungi, algae, and protozoa; microscopic plants, and animals. Single-celled microorganisms were the first forms of life to develop on earth, approximately 3 billion–4 billion years ago. Bacteria are one of the more well studied microorganisms… They live in soil, seawater, and deep within the earth’s crust. Some bacteria have been reported even to live in radioactive waste. ~ 30 phyla shown here Only a few key organisms or lineages are shown in each domain. The branch lengths in this tree are arbitrary, and nodes have been collapsed to reflect phylogenetic uncertainty. At least 84 phyla of Bacteria have now been identified, although many of these have not yet been cultured. LUCA, last universal common ancestor (Figure 13.4). The procedures used to generate phylogenetic trees are discussed in There are the 3 domain shown. At least 84 phyla of Bacteria have now been identified, although many of these have not yet been cultured. Section LUCA, 13.11. last universal common ancestor (Figure 13.4). The procedures used to generate phylogenetic trees are discussed in Section 13.11. Yellowstone National Park Microorganisms Many bacteria live on and in the bodies of people and animals—on the skin and in the airways, mouth, and digestive, reproductive, and urinary tracts—without causing any harm. Such bacteria are called resident flora, or the microbiome. There are at least as many bacteria in our resident flora as there are cells in the body. Ex an ave human 70kg has 30 trillion cells and apprx. 39 trillion bacteria (Nature 2016; https://doi.org/10.1038/nature.2016.19136) Many resident flora are actually helpful to people—for example, by helping them digest food or by preventing the growth of other, more dangerous bacteria. However, under certain conditions, the resident bacterial flora can cause disease by producing harmful substances (toxins), invading tissues, trigger inflammation that may affect the heart, nervous system, kidneys, or gastrointestinal tract. Some bacteria can (such as Helicobacter pylori) increase the risk of cancer. Bacterial Infections Gram Gram Spirochete Anaerobic Negative Positive infection infection Infection Infection Pertussis Anthrax Lyme disease Botulism (Bordetella (Bacillus (Borrelia (Clostridium pertussis) anthracis) burgdorferi) botulinum) Cholera Listeriosis Syphilis Tetanus (Vibrio Staphylococc (Treponema Actinomycosi cholera) al infections pallidum) s E coli Streptococcal (Actinomyces infection infection israelii) Legionella infection (Legionella pneumophila) Plague (Yersinia pestis) Microorganisms The most widely used initial method to differentiate bacteria from all other microorganism….Gram staining. This distinction is important because treatment of the two types may require different types of antibiotics. Gram staining characterizes bacteria based on the structural characteristics of their cell walls. By combining morphology and Gram-staining, most bacteria can be classified as belonging to one of 4 groups (Gram-positive cocci, Gram- positive bacilli, Gram-negative cocci, and Gram-negative bacilli) Microorganisms One of the fundamental tasks of a microbiology laboratory is to fully identify the microorganisms involved in processes associated with infection related to humans. It is important to understand their etiopathogenic (disease causing) nature, their clinical evolution, as well as applying an efficient antimicrobial therapy. Identification and Typing methods Traditionally identification and characterization of bacteria in the past have based on diverse phenotypic methods however, in the last decades, genotypic methods have been represent a better alternative to establish the identity of bacteria and their etiopathogenic nature. Phenotypic vs Genotypic identification…. Phenotypic Identification It is based on combination of methods to get to the answer, such as staining and morphology (shape) of the cells. The sample must come from the site where the microorganism is causing the damage Some samples used in clinical microbiology are: feces, urine, pharyngeal exudate, cerebrospinal fluid, tears, semen, vaginal fluid, tissues, and/or biopsies. Some methods require a pure isolation and growing of the microorganism from the sample. It is based fundamentally on the comparison of phenotypic characteristics of unknown bacteria to those of known standard culture. Ex: If we suspect that an UNKNOWN bacteria is either Staph or Strep…a Catalase test is performed, if it shows that catalase is present than it is Staphylococcus spp because we know that Staph are Catalase positive. 2H2O2 2H2O + O2 catalase Staph infections, such as MRSA, often require different, more powerful antibiotics and while Strep infections are generally more sensitive to penicillin Mnemonic for Catalase Positive Organisms CATs Need PLACES to Belch their Hairballs Cat =catalase positive N=Nocardia P =Pseudomonas L =Listeria A =Aspergillus C =Candida E =E coli S =Staphylococcus and Serratia B =Burkholderia cepacia H =Helicobacter Genotypic (molecular) Identification In recent years, there has been a lot of advancement in molecular methods which provided great advances in the diagnosis of clinically significant bacteria and viruses (SARS-COVID 2) Ex: ribosomal RNA detection of the clinical sample through hybridization with a DNA probe and nucleic acids amplification…PCR. Types of Identification Phenotypic vs Genotypic Phenotypic methods Genotypic methods Biochemical reactions (ex Gram Hybridization staining) Serological reactions Plasmids profile Susceptibility to anti-microbial Analysis of plasmids agents polymorphism Susceptibility to phages Restriction enzymes digestion Susceptibility to bacteriocins Reaction and separation by Pulsed-Field Gel Electrophoresis (PFGE) Profile of cell proteins Ribotyping Polymerase Chain Reaction (PCR) and its variants Ligase Chain Reaction (LCR) The three DOMAINS The relationship between the three domains ( Bacteria, Archaea, and Eukarya) is of central importance for understanding the origin of life  Scale of things… tps://courses.lumenlearning.com/boundless-microbiology/chapter/methods-of-classifying-and-identifying-microorganisms/ Gram Positive vs Gram Negative Important Groups of Bacteria Gram Gram Gram Gram Positive Positive Negative Negative Cocci Bacilli Cocci Bacilli Staphylococcus Corynebacteri Neisseria Escherichia Streptococcus um Moraxella coli Enterococcus Bacillus Veillonella Klebsiella Peptococcus Clostridium Proteus Peptostreptococ Actinomyces Shigella Gram cus Listeria Salmonella Ruminococcus Lactobacilli Negative Cocco-Bacilli Vibrio Viridans Nocardium Yersinia Haemophilus Bordetella Legionella Francisella Pasteurella Aeromonas Mycobacterium Tuberculosis Pseudomonas Acinetobacter Bacteroides Fusobacterium Campylobacter Helicobacter pylori THE END