Introduction to Microbiology and Bacteriology, ISM 1

WELCOME TO MICROBIOLOGY Assist. Prof. Dr. Hatice Kübra Akay [email protected]  THIS COURSE INCLUDES.. 1. Overwiev of microbiology, introduction to bacteriology 2. Bacterial metabolism and growth, respiration, energy production 3. Bacterial geneti...

WELCOME TO MICROBIOLOGY Assist. Prof. Dr. Hatice Kübra Akay [email protected]  THIS COURSE INCLUDES.. 1. Overwiev of microbiology, introduction to bacteriology 2. Bacterial metabolism and growth, respiration, energy production 3. Bacterial genetics 4. Bacterial groups differences 5. Host and microbial relationship 6. Eukaryotic microbial groups (fungi, parasites) 7. Antibiotics, antifungals and antibiotic resistance mechanisms 8. Viruses 9. Viruses 2 10. Antimicrobial procedure (sterilization, disinfection) Resources 1. Microbiology (Lippincott's Illustrated Reviews Series), international edition, Richard A Harvey. 2. Jawetz,Melnick &Adelberg’s Medical Microbiology, 28th edition. The microbes within us and a grander view of life What is happening inside us? « this book not only covers the diseases' histories but also addresses public health responses and societal upheavals.» CONTENTS Microbial Life A Brief History of Microbiology Prokaryotic and eukaryotic cells Bacterial cell structure and components Binomial nomenclature  LOOK OUT! THERE ARE MICROBES.. They are everywhere… Microorganism: The organisms most likely can not be seen without microscope. Microscope : It is an instrument to aid observing microobjects/microorganisms that can not be seen with the naked eye. «micros» ► very small «bios» ► life «logos» ► science Microbiology Biohazard caution with cute microbes ☺ Microbial Life Microorganisms live in all parts of the biosphere (soil, hot springs, ocean floor, deep inside rocks and lower parts of the atmosphere…). They are vital to humans and the environment. They participate in the Earth’s element cycles, such as the carbon cycle and the nitrogen cycle. They are used in fermented dairy products and alcoholic beverages. A brief history of microbiology ▪In 1665, Robert Hooke’s study «micrographa» was published. ▪This book contained his observations and drawings he made with the microscope that he built himself. ▪Leeuwenhoek was first to observe microorganisms and called them as «animalcules» protozoa in 1674 bacteria in 1676 Modern light microscope «miasma theory» This theory held that diseases such as cholera, chlamydia, or the Black Death—were caused by a miasma (Ancient Greek for pollution), a noxious form of "bad air». The theory held that epidemics were caused by miasma, emanating from rotting organic matter.  By the early 19th century, smallpox The Germ Theory vaccination was commonplace in Europe, though doctors were unaware of how it worked or how to extend the principle to other diseases. By the end of that decade, the miasma theory was struggling to compete with the germ theory of disease. Edward Jenner applied smallpox vaccination (1749–1823) A transitional period began in the late 1850s with the work of Louis Pasteur. This work was later extended by Robert Koch in the 1880s. The term «microbe» was first used by Charles- Emmanuel Sédillot -a French military physician and surgeon- in 1878. Pasteur He discovered vaccine of Rabies and applied to humans in 1885 He made studies about ✓ Fowl (avian) cholera ✓Anthrax vaccines. He invented the pasteurization method.  Charles Chamberland In 1884, he invented a porcelain filter -for bacteria- with a pore diameter of 0.1 -1 µm. 1892-1902 Dmitry Koch Ivanovsky He discovered the mode of Russian botanist noticed transmission of anthrax and that a disease-causing the causative agent, Bacillus microorganism (TMV) in anthracis, was endospore tobacco could pass forming bacteria (1876). through this bacterial filter. He isolated Mycobacterium tuberculosis and tuberculin (1882) first time. ▪Electron Microscopy technology and imaging of viruses in the 1940s. ❑1953 Watson-Crick-Franklin discovery of DNA double helix structure ❑1977 Fred Sanger, invention of ❑ Discovery of PCR technology by sequencing.. Kary Mullis in 1985.. THREE DOMAINS SYSTEM OF LIFE Phylogenetic classification of living beings. (Huson et al.: Reconstructing the tree of life 2011.  Medically Important Microorganisms UNICELLULAR ACELLULAR MULTICELLULAR Helminths Moulds PROKARYOTES EUKARYOTES Arthropoda (fungi) Bacteria Viruses Prions Yeasts Protozoa (fungi) Viroids prokaryotes eukaryotes  No nucleus, nucleoide. ☺ True nucleus.  No membranous organelles ☺ Membranous organelles ☺ Cell wall(peptidoglycan) and cell  Only cell membrane. membrane. ☺ Eukaryotic flagellum ☺ Pili and prokaryotic flagella ☺ Size, 10 times of a prokaryotic ☺ Size, very tiny (0,3-5 µm). cell (10-100µm). ☺ 16S rRNA conserved region in ☺ 18S rRNA conserved region in ribosome small subunit ribosome small subunit  No cholesterol, (with exceptions) ☺ Cholesterol in cell membrane in cell membrane Pro: primitive Eu: true Karyon: nucleus the largest prokaryotes http://www.whoi.edu/page.do?pid=14958&tid=282&cid=46727 http://news.softpedia.com/news/The-Secret-of-the-World-039-s-Largest- Bacterium-Revealed-85149.shtml Which one of the following is a prokaryotic? A. Viruses B. Fungi C. Prions D. Bacteria E. Protozoa BINOMIAL NOMENCLATURE Genus name Species name As used for other organisms binomial Escherichia coli nomenclature is used to Vibrio cholerae identify microorganisms. or Vibrio cholerae How? Vibrio parahaemolyticus I. The genus name is capitalized, the species name is lower case. Virus families named with a suffix–viridae II. Both genus and Virus genus have the suffix –virus species name are For example always italicized or underlined Poxvirus. INTRODUCTION TO BACTERIOLOGY BACTERIA They are single celled prokaryotic microorganisms, They have no nuclei, prokaryotic DNA is found in a part of the cell called the nucleoid. They may carry plasmids which have some genetic material related to antibiotic resistancy They have mostly a cell wall and are mainly classified according to their wall structure They have no membrane-bound organelles, they have only ribosomes. Bacterial cell components Interior structure Sheath Appendages Outer membrane(GN) Peptidoglycan wall Periplasma(GN) Cytoplasmic membrane INTERIOR STRUCTURE CYTOSOL ▪Protein synthesis is done in ribosomes in cytosol, ▪The enzymes that are used for protein synthesis and other metabolic enzymes are here (because there aren’t any organelles). ▪Nucleoid and plasmids and inclusions are also in cytosol.  BACTERIAL DNA Chromosome: double-stranded DNA is coated with histone-like proteins. (haploid) Plasmid: a small, extrachromosomal DNA molecule which can replicate independently. Bacterial chromosomes and plasmids are double- stranded circular DNA molecules and are often referred to as covalently closed circular DNA, or cccDNA. Bacterial DNA is 1000 times longer than the cell that contains it. The DNA must be supercoiled in order to fit into the cell. DNA gyrase puts negative supercoils into a bacterial chromosome. Genomes and DNA David P. Clark, Nanette J. Pazdernik, in Molecular Biology (Second Edition), 2013  Although supercoiling reduces the size of the DNA, the chromosome still will not fit into the bacterial cell. The second level of compaction occurs when approximately 50 giant loops of supercoiled DNA are arranged around a protein scaffold. These two levels of compaction are essential and actually keep the bacterial chromosomal DNA compacted into a small area called the nucleoid. This structure contains the chromosome and its associated proteins. Genomes and DNA David P. Clark, Nanette J. Pazdernik, in Molecular Biology (Second Edition), 2013  Bacteria can live without plasmid as all the essential genes are found on its chromosomal DNA. Plasmids contain just a few genes, and these genes are usually not essential for the bacterium’s survival – instead, they help the bacterium to overcome occasional stressful situations. Many plasmids contain genes that, when expressed, make the bacterium resistant to an antibiotic. Bacteria can pick up new plasmids from other bacterial cells or from the environment. They can also lose them – for instance, when a bacterium divides in two, one of the daughter cells might miss out on getting a plasmid. https://www.sciencelearn.org.nz/resources/1900-bacterial-dna-the-role-of-plasmids Bacterial Ribosome A bacterial ribosome consists of the small (30S) and large (50S) subunits, which together form the 70S particle. Cytoplasmic Granules Cytoplasmic granules or inclusion bodies are nutrient storage regions. Polysaccharide granules contain either glycogen or starch as an energy or carbon reserve. Volutin granules are high-energy reserves held in the form of polymerized metaphosphate.  SHEATH PLASMA MEMBRANE Bacterial membranes are negatively charged due to the presence of highly electronegative groups on their constituent phospholipids and lipopolysaccharides. It performs many functions, including transport, biosynthesis, energy transduction and detection of environmental signals. Lack sterols except Mycoplasmataceae family members (Mycoplasma and Ureaplasma species). https://youtu.be/W5soSpVWMT8?si=DoqmRwdJujcMB9c1  Mesosome Mesosome is a structure formed by the invagination of the plasma membrane. Mesosomes are involved in DNA replication and guide distribution of duplicated bacterial chromosomes into the two daughter cells during cell division. PEPTIDOGLYCAN WALL Peptidoglycan is the major structural polymer in most bacterial cell walls and consists of glycan chains of repeating N -acetylglucosamine and N - acetylmuramic acid residues cross-linked via peptide side chains. It determines the cell shape. It has a cross-linked polymeric network structure. Glycan structure It consists of N-acetyl glucose amine(NAG) and N- acetylmuramic acid. It is a linear polymer formed by connecting (NAM) and (NAG) to each other respectively by by aa sequence varies β-1,4 glycosidic bonds. between species. https://doi.org/10.1128/ecosalplus.ESP-0010-2020 Peptide structure It consists of AA chains connected to each other. A peptide chain is attached to MurNAc In Gram-positive bacteria, the peptides can cross-linked through an additional bridging peptide (pentaglycine). It prevents explosion in hypotonic solutions where osmotic pressure is high. BACTERIA LACK PEPTIDOGLYCAN Cell wall–deficient bacteria (CWDB), also known as L-phase or L- form bacteria, are bacterial variants that lack a cell wall. Mycoplasmataceae L-forms are able to grow as spheroplasts or protoplasts. family members L-form bacteria are distinct from mycoplasmas, because Mycoplasma spp. do not originate from bacteria that normally (Mycoplasma possess a cell wall. and Ureaplasma A huge variety of bacterial species may become CWDB when species). exposed to certain stressors in the laboratory (such as antimicrobial drugs). CWDB assume a spherical or pleomorphic shape, and are susceptible to osmotic lysis. However, they resist β-lactam drugs such as penicillin. In human patients, L-form bacteria have been implicated as causes of a variety of clinical syndromes that include culture-negative endocarditis, bacteremia, uveitis, pneumonia, osteomyelitis and arthritis, recurrent UTIs, soft tissue infections, and meningitis. Classification Bacteria Depending on GRAM STAINING In 1884, Christian Gram first developed the Gram staining method. No outer membrane Outer membrane %70-80 mürein %10-20 murein (peptidoglycan) (peptidoglycan) lipid content %20-30 Very limited No teichoic acid molecules Teichoic acid molecules Lipopolysaccharides No lipopolysaccharides (LPS) Teichoic acid Wall teichoic acids are a major and integral component of the Gram-positive cell wall. These structures serve important roles in colonization, coordination of peptidoglycan synthesis and resistance to β-lactam antibiotics. Colonization: The establishment of bacteria in a new environment. https://doi.org/10.1038/ja.2013.100 Outer Membrane Outer membrane (OM) is found in the Gram-negative bacteria. The periplasm is a concentrated gel-like matrix in the space between the plasma membrane and the outer membrane called the periplasmic space. OM porin proteins form channels to allow the entry of substances. Lipopolysaccharide (LPS) is the major component of the outer membrane. Outer Membrane Lipopolysaccharide (LPS) LPS consists of lipid A, core polysaccharide, and O-polysaccharide or O antigen. Lipid A domain is responsible for much of the toxicity of Gram-negative bacteria. When bacterial cells are lysed, fragments of membrane containing lipid A are released into the circulation, causing fever. O antigen can be strain specific. It is exposed on the very outer surface of the bacterial cell, and, as a consequence, is a target for recognition by host antibodies.  CAPSULE It is a slimy, gelatinous material, composed of polysaccharide, protein or rarely polypeptide It is tightly attached to the cell membrane and has an organized structure Protects the bacteria from phagocytes Blocks the antibiotics to penetrate the cell Protective to cold and dryness Capsule has roles in the virulence and Under the light microscope, the colonisation of a number of pathogenic capsules are bacteria unstained, although the gram positive cocci ara purple. Slime layer If the material is loosely bound and amorphous, it is called a slime layer, or glycocalyx. 1 Capsule 2 Slime layer Biofilm 3 Biofilm If the microorganisms are embedded in exopolysaccharide matrix, it is called biofilm. Colonies of Pseudomonas aeruginosa on the sheep blood agar Colony morphology of Bacillus anthracis CELLULAR APPENDAGES Pilus or Fimbrium / Pili (pl.) or Fimbriae (pl.) The pilus is a hair-like structure associated with bacterial adhesion and related to bacterial colonization and infection. Conjugative pilus (sex pilus) is a special pilus allows the transfer of DNA between bacteria, in the process of bacterial conjugation. Flagellum / Flagella (pl.) A flagellum is a hairlike appendage involved in motility. Flagellin is a structural protein of the flagellum. Endospore An endospore is a dormant, and non- reproductive structure produced by certain bacteria (Bacillus and Clostridium genus). It consists of the chromosomal DNA and a small portion of cytoplasm. It has a thick and tough outer coat. Endospore formation is usually triggered A. Types of endospores according to their position in parent by lack of nutrients. cells, B. C. Germination of endospores Endospores enable bacteria to lie dormant for extended periods, even centuries. When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state. Endospore staining under the light microscope BACTERIAL MORPHOLOGY