Fundamentals of Microbiology Lecture 1 PDF

Fundamentals of Microbiology Dr Leighann Sherry  AIMS Symbiotic relationships Commensalism, mutualism, parasitism Commensals, opportunistic pathogens, primary pathogens Koch’s postulates ‘The father of modern Tr...

Fundamentals of Microbiology Dr Leighann Sherry  AIMS Symbiotic relationships Commensalism, mutualism, parasitism Commensals, opportunistic pathogens, primary pathogens Koch’s postulates ‘The father of modern Traditional and microbiology’ modern Virulence Identification tools  SYMBIOSIS Symbiotic relationships involve the association of 2 or more partners Microorganisms, animals, surfaces May rely on each other for survival One organism benefits while the other remains unchanged One species benefits at the expense of the other  HUMAN-MICROBE RELATIONSHIP Viruse Fung s i Adenoviruses Candida Retroviruses Aspergillus Microbial Papillomaviru Malassezia population exceeds ses us in terms abundance and Parasi Bacter diversity Entamoeba tes ia Streptococcus Cryptosporidi Staphylococc um us Giardia Clostridium A lot remains unknown about Methanobrevibac Archa ter these relationships, ea Methanosphaera specifically in  HUMAN-MICROBE RELATIONSHIP These interactions are not new! Egyptian mummies and TB (600 BC) Black Death – up to 200 million deaths (mid 1300s) Irish potato famine - Phytophthora infestans Our relationship continues to change (1840s) HIV pandemic - First cases early 1980s Zika epidemic in the Americas - 2015-2016 - Mosquito-borne viral infection Ebola in West Africa - First recognised 1976 - First case of 2014 outbreak; 2 yr old died in 2013 in Guinea Microbes are rarely found in isolation or pure culture  THE MICROBIOME Bacterial Mycobiome Virome Cho & Blaser (2012) Underhill & Iliev (2014) Liang & Bushman (2021) Nat  THE MICROBIOME Genome wide study of gut microbes revealed Ottman et al (2012) Front Cell Infect Micr  MUTUALISM Both organisms benefit Colonic bacteria provided with a niche in the host Organisms synthesise vitamin K and folate, metabolised by host Ruminococcus spp. can be found in high numbers in the gut and involved in cellulose breakdown. Mycorrhizae (myco = fungi, rhiza = root) Fungal mycelium associated with plant roots Fungi attach to the roots and allow root extension In exchange, the plant provides sugars to the fungi MYCORRHIZAE  MYCORRHIZAE Over >80% of plants are associated with mycorrhizae e.g. trees, crops, plants, highlighting how important they are, but there are other advantages to plants Obtain immobilised nutrients e.g. phosphate, iron Speed up decomposition of organic matter Increased resistance to disease Remove heavy metal toxicity Ferrol et al., (2016) J  COMMENSALISM One organism benefits, other neither benefits or is harmed A product produced by one organism can be beneficial to the other organism Bacteroides (and other obligate anaerobes) benefit from Escherichia coli Staphylococcus epidermidis utilises dead skin cells without causing harm  COMMENSALISM One organism benefits, other neither benefits or is harmed We’re reliant on many gut microbes e.g. Bifidobacterium, Bacteroides - breakdown or generation of metabolites Low gut Dietary fibre inflammation intake ↓ risk of some ↑ SCFA infections production ↑ antioxidant production Improved lipid Adapted from Valdes et al.,  PARASITISM One organism (parasite) benefits at the expense of the other Parasitic microbe live or multiply within/on the host, causing damage in Plasmodium Bacillus Histoplasma Ebola virus the process falciparum anthracis capsulatum (Ebola virus (Malaria) (Anthrax) (Histoplasmosis) disease)  PATHOGENS Opportunistic pathogens - Do not normally cause disease Candida albicans (candidiasis) Pseudomonas aeruginosa (burn-related infection) Toxoplasma gondii (toxoplasmosis) Herpes simplex virus (cold sores)  ZOONOSIS Zoonosis - an infectious disease transmitted to humans from animals The Germ Theory  KOCH’S POSTULATES 3. The pathogen 4. The same organism must cause the must be re-isolated same disease if from the inoculated used to inoculate diseased host the healthy host 1. The suspected pathogen must be 2. The pathogen absent in all healthy must be isolated and individuals but present grown in pure in all diseased hosts culture from all diseased patients  MOLECULAR KOCH’S POSTULATES Stanley Falkow (1988) – ‘father of molecular microbial pathogenesis’ o Isolation of genetic material enables pathogen identification o Specific genes correlate with disease o Knockouts linked with disease reduction D  VIRULENCE FACTORS Pathogenicity – the ability to cause disease Virulence – the degree of pathogenicity of an organism e.g. infectivity/ intensity Clostridium tetani Made from chemically detoxified tetanus toxin Antibodies raised –  OTHER VIRULENCE FACTORS BUDDING YEAST TRUE PSEUDOHYP HYPHAE HAE Phenotypic switching - increased adherence - biofilm development - invasion  IDENTIFICATION Classical Microbiology How do we identify this? Extract all DNA from the population and digested into smaller fragments. Restricts growth - Does not cater for organisms found in all environments - Laboratory environment is far removed from reality Time consuming - Some organisms can take weeks to grow (Mycobacterium spp.) Data analysis to identify organisms. Cloned in to plasmid vectors before sequencing. Only 1% of microbial population is known!  OMICS Biomolecule Technology Information DNA Genomics What genes are present? Organism identification. Which parts of the DNA Transcriptomics have been expressed to RNA allow protein production? Protein Proteomics What proteins are being produced and to what level? All metabolites produced by Metabolite Metabolomics a population living together.  MICROARRAY TECHNOLOGY Insert single stranded DNA in to each square of the grid  target gene Extract mRNA from samples and synthesise cDNA Combine the samples together and add to the microarray Measure fluorescence and determine what genes are expressed within each population  MICROBIOMES MICROBIOME Large and mixed population of microorganisms coexisting together under many circumstances. SEA EARTH HUMAN Samples taken across the globe with the Starting to understand the microbial The Human Microbiome Project majority of organisms identified being novel. interactions in this environment.  SUMMARY Symbiotic relationships Define and provide examples of each Commensals v opportunistic pathogens v primary pathogens Koch’s postulates Traditional and modern Virulence factors Identification tools Culture v molecular OMICS