Microbial Diversity: Bacteria, Session 1 PDF

MIRCOBIAL DIVERSITY BACTERIA Session 1 -- 2/12/2024 BACTERIAL NOMENCLATURE - Bacteria can be both beneficial and harmful -- we need to think the environment it's in, what animal it's in -- bacteria have relationships with the environments, determining whether they are pathogenic or...

MIRCOBIAL DIVERSITY BACTERIA Session 1 -- 2/12/2024 BACTERIAL NOMENCLATURE - Bacteria can be both beneficial and harmful -- we need to think the environment it's in, what animal it's in -- bacteria have relationships with the environments, determining whether they are pathogenic or not - We benefit from having *E. coli* in our intestines - Bacteria often diverge from adaptations to the environment - *Genus* and *species* - Etymology of bacterial names can vary - Named after scientists, places, food, shapes, colors, other examples Bacterial Taxonomy/Nomenclature - *Genus* and *species* - Etymology of bacterial names can vary - Named after scientists, places, food, shapes, colors, other examples - If you look at *staphylococcus aureus* under a microscope, they look like a bunch of grapes - Very diverse and different ways of naming bacteria - There are number of ways to classify bacteria - In phenotypic classifications, we have: - Cell morphology -- how does it look under a microscope, how they move - Pleiomorphic bacteria -- morphology can change, depending on what environment they are in - Metabolic activity -- do they have the ability to undergo anaerobic respiration, can they metabolize lactose, or they need some other C source, how they metabolize certain chemicals - Staining -- what the cell wall/membrane is made of, using Gram staining - Pathogenicity -- is It resistant to antibiotics, does it have genes that enable it to resist heavy metals (Mercury, for example), does it produce toxins, what are these toxins are, what harm can they bring? - Nutritional needs - In genotypic classifications, we have: - DNA based - G-C content of the genome - 16S RNA sequencing -- very important method to classify archaea and bacteria -- 16s is present in eukaryotes too, but it is used as a classification method for archaea and bacteria because it's a way they have diversified. 16S gene has many different regions that will be sequenced to be able to classify bacteria - 18s RNA sequencing for eukaryotes - Metagenomics of whole sample of bacteria, sequence the sample, get an idea of the variation of the whole sample, not an isolated organism - No reliance on culture of the organisms -- there are many organisms that have been identified through 16S sequencing and metagenomics, which has allowed us to see that there are other organisms in that sample, we don't have to culture it A diagram of a tree Description automatically generated  Why Study Microbial Diversity? - Just from interest -- bacteria are very interesting and diverse - Gain and organize knowledge of organisms and their characteristics - Make predictions and frame hypothesis based on knowledge of related or similar organisms - Communicate between other scientists -- if people didn't know what e. coli is, they wouldn't be able to identify it as a causative agent - If you have one name for an organism, this means that you can share information about that organism with other people in your field - Even in environments we think are sterile and clean, there are actually an awful lot of bacterial diversity present there - Accurate identification -- important for correct treatment - There are 2 sections of the genomic approach: - Phylogenetic -- based on 16s RNA sequencing of housekeeping genes (for example, in *e. coli* there are 7 housekeeping genes, found in pretty much every *e. coli*, but there is some variation in them), sequence genes and that gives an idea of the variation, based on the alleles of these different housekeeping genes - Housekeeping genes -- set of genes that are constitutively expressed in cells and are essential for basic cellular functions. - Functional -- what genes are present or absent from that organism? -- gives an idea of some of the functional mechanisms and metabolic pathways present in the organism (resistance genes, enzymes, involved in a particular metabolic pathway) - Look at these 2 things together because we can get a lot of information about the ways organisms are related to each other on a general whole genome scale, but it is also important to understand what kind of genes are present in it and how they might have obtained those genes Function and Phylogenetic Correlation - Often correlate, but not always - There's not always a strong correlation - Reasons for this: - Gene loss -- at some point, some genes have been present in the organisms, but through evolution, they have lost them - Convergent evolution -- independently obtained genes that might have enabled them to produce an antibiotic, or are involved in a metabolic process - Gram-positive and Gram-negative bacteria have developed methods to become resistant to Penicillin, but they are both very different - Gram-negatives use an enzyme to break down the antibiotic - Gram-positives have mutated to produce a binding protein that no longer recognizes the antibiotic - Two very different mechanisms that address the same issue, but very different organisms - Horizontal gene transfer -- lots of resistance genes can be found in lots of unrelated organisms of bacteria through movement of plasmids, or other chunks of the bacteria - Different clades of bacteria share similarities, even if they are not related A diagram of different types of bacteria Description automatically generated Functional Diversity - Can be: - Physiological -- Metabolism and biochemistry - We could do biochemical testing to look for certain metabolites, what processes do they undergo? - Morphological - Look at them on a plate, under a microscope, how do they stain? - Ecological - What environment do they inhibit? - What other organisms are present in their environment -- gives an idea how they work with other bacteria to be able to survive Microbial Habitats - Microbes are EVERYWHERE! - Range if environments they can live in is enormous -- can be found in ice caps, in the sea/ocean, acidic environments, alkaliphiles, deep down in the ocean with high pressure - Thermophiles -- love high/hot temperatures - Psychrophiles -- love low/cold temperatures - Halophiles -- live in high salinity - Acidophiles -- live in acidic environments - Alkaliphiles -- live in alkali/basic environments - Barophiles -- live in high-pressure environments - Reasons why they are there -- they have managed to find ways to adapt to their environment, but it has come to the point that they need these environments to live in - You'll struggle to culture a hydrothermal organism, using normal culture techniques - Microbial populations can also vary with different niches of the same environment - Soil types - pH, water, organic content may all impact the type of organism you find there - Fresh water -- zones, flow rates, oxygen levels, pH, a flowing stream or a lake - Marine environments -- pressure, light levels, oxygen levels, salinity - There are so many ways, in which we can classify bacteria, below is a summary. - We tend to use many of those to classify bacteria that we find  DIVERISTY OF BACTERIA - Largest taxon of the prokaryote domain - 55 bacterial phyla currently with cultured representatives listed in LPSN - Many more have a Candidatus status -- identified, but not fully approved, not similar enough to some of the taxa we already have, so a new name is proposed, lots of time takes to approve everything - More bacteria are identified, and we know of them because of 16s sequencing -- this is always increasing, we are finding more and more species and taxa we haven't been aware of - Almost all (90%) of those characterized are only from 4 phyla - Proteobacteria, Acinetobacteria, Firmicutes, Bacteroides - We've focused on the ones we can culture, and we can work with - Bacterial names change quite often A close-up of a chart Description automatically generated Thermophilic phyla -- Aquificae/Aquificota - One of the earlier ones to branch off from the other domains - Gram-negative - Have a flagella that enables them to be motile - Don't produce spores -- no ability to survive in desiccation (very dry) - Hyperthermophiles (up to 95 C) -- very warm optimal temperatures - Most are chemolitoautotrophs -- produce their own energy, mostly using sulphur oxidation, chemical way of producing energy - Many of them need absence of oxygen in order to survive - Includes both microaerophilic and anaerobic bacteria - Harsh environments -- hot springs, sulphur pools, thermal ocean vents Thermophilic phyla -- Thermotogae/Thermotogota - Deep branching - Gram-negative, sheathed -- have an extra layer outside of the cell for protection - Hyperthermophiles (up to 95 C) - All are chemoorganotrophs -- use organic chemicals to produce their energy - Anaerobic - Live in harsh environments -- hot springs, sulphur pools, thermal ocean vents  Thermophilic phyla - Deinococcota - Another one of the deep branching organisms - Very thick cell wall, two membranes -- very thick layer of peptidoglycan - Heterotrophic - Strictly aerobic - One of the *deinococcus* species is world's toughest bacteria (Guiness world record) because is hyper resistant to ionizing and UV radiation - Withstand very harsh environments Thermophilic phyla -- Chloroflexi/ Chloroflexota - The final of the deep branching organisms - Tend to look green because of some of the proteins/chemicals inside them - They don't have an outer membrane polysaccharide membrane is easier to access you'd expect them to stain Gram-positive - HOWEVER, they mostly stain Gram-negative - Found in hot conditions -- moderate thermophiles (around 80 C) - Long and filamentous morphology - They are photoheterotrophic -- use light to get their energy, but don't photosynthesize, they use it in other ways, without producing oxygen - Use light energy to convert chemicals present in their environment into usable energy - NOT photosynthetic  Cyanobacteria - Photosynthetic - Often a green color because of the presence of chlorophyl - Chlorophyl is present in the carboxysomes -- small membrane-enclosed parts of the cytoplasm, where CO2 fixation happens, where photosynthesis takes place - Responsible for creation of free oxygen in the atmosphere -- enabled evolution to occur - Found in many aquatic and land environments A green cell with black dots Description automatically generated with medium confidence Proteobacteria  - Very diverse metabolically - ALL Gram-negative - Six classes -- phylogeny based on rRNA sequencing 1. Alpha proteobacteria - Comprised of 10 orders - Most of them are anaerobes - Majority prefer low-nutrient environments - *Rhizobiales* -- the largest order, contain phototrophs, chemolithotrophs, nitrogen fixers, methylotrophs - *Rickettsiales* -- obligate intracellular parasites of mutualists, could be human pathogens - Some of the organisms we know causes diseases are present -- typhus, cat scratch disease 2. Beta proteobacteria - Has 6 orders - *Burkholderia* -- nitrogen fixer, really useful for farmers and agriculture - *Neisseriales* -- causes of meningitis and gonorrhea - *Nitrosomondales* -- important in agriculture and wastewater treatment - *Hydrogenophilales* -- live extreme environments - *Rhodocyclales* -- versatile metabolic capabilities - *Methylophiales* -- use one-Carbon molecules to create energy 3. Gamma proteobacteria - Largest group of proteobacteria - Use different sources of energy, very different metabolically -- may use S, or H, or C - *Enterobacteriales* -- salmonella, *e. coli*, hemophilis, influenza; all of them are human pathogens, we know much more about them, they can survive without oxygen, but prefer to have oxygen, a lot are found in intestines and soil. We know much more about enterobacteria - MOST IMPORTANT ENTEROBACTERIALES: *Salmonella, E. coli, Shigella, Proteus, Enterobacter* - There are different media to identify them -- on agar plates, spreading, culturing, we can also use agar plates that may have a certain C source that only 1 type of bacteria can use, but others can't - They are similar under a microscope, that's why we need different ways to identify them 4. Delta proteobacteria - Tend to use sulphur or sulphate compounds to get their energy (reduce the sulphur) - *Myxococcales* and *Bdellovibrionales* -- predators to other bacteria, one of their energy sources are to predate other bacteria within their niche - *Syntrophobacterales* -- often work in symbiotic relationships with other organisms within their niche, produce H2 gas, but it can be toxic for them in high levels Live in niches with other organisms, which can consume this H2 gas as an energy source -- they work together with other bacteria to maintain their environment 5. Epsilon proteobacteria - *Campylobacterales* -- key class, sulphur oxidizers, many of them are only known by RNA sequencing, below are examples - *Helicobacter pylori* -- form stomach ulcers - *Campylobacter* -- food borne pathogens 6. Zeta proteobacteria - Less is known for these organisms, they've only recently been discovered - Tend to use iron sources for their energy - Microaerobic -- don't need a lot of oxygen - Commonly found in sea and marine environments A diagram of bacteria Description automatically generated  Spirochaetota - Spiral/helical shape -- how get their name - ALL are Gram-negative - Majority are anaerobes or facultative anaerobes (can survive with oxygen) - They have endo flagella -- have a flagella that starts inside them, but protrudes out, helping them have the corkscrew motion and swim in their environment - *Treponema pallidum* -- causes syphilis and other diseases like yaws and bejel - *Borrelia burgdorferi* -- responsible for Lyme disease A close-up of a microscope Description automatically generated Chlamydiota - Required to live in a host, have to be intracellular - Reasons: - Very small genomes -- don't have the ability to produce all of their key components - Intracellularity gives access to things they can't produce themselves - Diverse phylum - Stain Gram-negative - Unique life cycles -- 2 life stages - Elementary body -- contain a number of the bacteria, free-living state, they will start to infect other state, then will develop into: - Inclusion bodies -- the second stage of the life cycle, they will reproduce and continue the cycle - *Chlamydia* human pathogen (STI chlamydia and eye disease)  Firmicutes - Gram-positive - Very low GC content in genomes - Includes the cocci bacteria -- *Staphylococcus*, *Streptococcus* - Many are facultative anaerobes -- can do both aerobic respiration and anaerobic - Some, like lactic acid bacteria, specialize in fermentation processes - Genera, such as *Bacillus* and *Clostridium* produce endospores, allowing survival in harsh conditions -- endospores don't get killed, while cooking -- a way for food poisoning - Can survive in very harsh environments Blue bacteria shaped like a cross Description automatically generated Actinobacteria - Gram-positive - High GC content in genomeр, contrary to cutecutes - Majority are spore-forming - Often thrive in soil environments, but can be found in aquatic environments too - They are able to break down cellulose, lectin and chitin -- have access to other energy sources - Examples: - *Streptomyces* -- a lot of antibiotics have been produces from this bacteria, very important - *Mycobacterium* -- waxy cell walls, slow growing, some human pathogens (tuberculosis and leprosy) - *Propionibacterium --* produce cheese from the milk  Bacteroidetes - Gram-negative - Many can break down complex polysaccharides - Most of them are obligate anaerobes -- need to have complete absence of oxygen - Found in animal intestines, but are commensal -- don't cause any problems A close-up of a petri dish Description automatically generated DIVERSITY OF ARCHAEA - Until recently, the archaea haven't been that studied - Now we are starting to know more and more about these organisms, and learning to potentially culture them  General Characteristics - They have different membrane structure than prokaryotes and bacteria -- they can produce a monolayer structure, not a bilayer - Lack of peptidoglycan in the cell wall -- they have pseudopeptidoglycan - RNA polymerase is more similar to the eukaryotic one - They are very diverse in terms of how they look and how they get their energy source - Some of them are able to produce methane -- unique quality - No evidence of pathogenicity Archaeal Phyla - Most are grouped into 2 major phyla -- Crenarchaeota and Euryarchaeota - 3 others are currently recognized/present -- Korarchaeota, Nanoarchaeota, Thaumarchaeota Euryarchaeota - Live high-salt environments -- halophilic - Some of them can produce CH4 -- methane, contribute to global warming - Some of them are acidophilic - *Methanobacterium* - Thermococcales and Methanopyrus -- found in thermal water, can move with a flagella - Nanoarchaeum -- one of the smallest organisms identified that isn't a virus, has the smallest genomes A close-up of several bacteria Description automatically generated Crenarchaeota - The most ancient archaea in terms of when and where they have diverged in the phylogenetic tree - Found in extreme temperatures -- either very hot or very cold temperatures (Antarctic) FUNGI AND PARASITES FUNGI: - Eukaryotes -- have a nucleus, mitochondria, a lot of eukaryote features - Diverged from their common ancestor to other eukarya about 500 MYA - Around 70 000 identified species, but there are a lot more, which are unidentified -- same as with bacteria - Mycology -- study of fungi - WE CAN'T EXIST WITHOUT FUNGI! - Yeast, alcohol wouldn't be a thing, no good soil... The Fungi - A sister group to animals -- diverged from plants, and diverged from animals a little bit later - They can be unicellular (yeast/*saccharomyces*), multicellular (mushrooms), dimorphic (can live both as single-celled organisms, but can multiply and live in a community) - There are 2 stages fungi will go through -- vegetative (surviving and growing in search of food) and reproductive (produce spores, helping them spread and find another nutrient-rich environment) - Like moist and slightly acidic environments -- soil - They are able to grow both with and without oxygen and with or without light - They can get their nutrients in 3 ways: - Saprophytic -- take their nutrients from dead material, decompose that material - Parasitic -- will get their energy from living organisms and parasitise these organisms - Symbiotic -- with other organisms in the environment, they will provide nutrients for that organism and will receive nutrients - As of 2019, there are 9 phyla that are agreed on with 5 major phyla that we see regularly and are involved in infections, or have agricultural impacts...  Chytridiomycota - Found mostly in aquatic environments - Have a unique way of producing spores -- spores have flagellum, can swim - Different ways for nutrition: - They do parasitize -- mostly on amphibians - Decomposers - saprophytic - Have both sexual and asexual reproduction Zygomycota - Primarily terrestrial, you wouldn't see them in water - Include molds like *Rhizopus* -- black bread mold - Decomposers or symbionts - Have sexual reproduction -- have to have 2 opposing mating strains - A positive and a negative strain - When these two strains come together, they will undergo sexual reproduction and produce spores - Quite resistant to harsh conditions -- spores spread and can be propagated - If they land in an environment, where they can't germinate, without enough nutrients, they will just stay as a spore for a very long time, until the conditions are good for them to germinate A close up of a plant Description automatically generated Ascomycota - Largest phylum -- 75% of all fungi identified are in this phylum - Live on land, can be also aquatic - Truffles, morels, molds, yeasts - Their reproductive organs are the asci -- sac-like structures that contain haploid ascospores - They can be decomposers, pathogens or symbionts - Dutch elm disease -- fungal disease, which is destroying elm trees - Aspergillosis, Valley fever -- human diseases - Have both sexual and asexual reproduction  Basidiomycota - Field mushrooms -- the ones we know, puffballs, rusts and mirror yeasts - External spores are produced on club-shaped structures called basidia, then they would be released - They decompose wood (lignin) - Can be pathogenic -- if you inhale some spores, they could cause a mycosis infection, they are opportunistically pathogenic - Have primarily sexual reproduction - Important agriculturally and ecologically -- lots of different types and form they can take A group of mushrooms in the moss Description automatically generated Glomeromycota - They HAVE to live in symbiosis with another organism -- plants mostly - The fungi is associating with the roots of different plants, forming a symbiotic relationship (endomycorrhiza), fungi will get nutrients from the plant, the plant will make use of any nutrients, produced by the saprophytic activity in the fungus - Without this symbiotic relationship, many plants will struggle to thrive, they need to have the symbiotic relationship with the fungi, so that they can grow sufficiently - It has become important for farmers to make sure that glomeromycota are incorporated into the soil and don't disturb it too much, so that it helps their crops to grow - The fungi's hyphae invade the roots, while growing, allowing them go gain access to the nutrients in the roots -- grow into the plant roots - They produce large, thick-walled spores that germinate when plant root are present - Help plants thrive and improve survival in nutrient-poor soils  Fungal Taxonomy is in flux - Classical fungal taxonomy defines fungal groups based on morphological characteristics and reproductive structures - Different organisms may be reclassified because we've carried out sequencing, and discovered new things about them - Supplemented and revised by novel discoveries via phylogenetic analysis and the whole genome sequencing projects - Classifying of fungi is mostly based on how they reproduce -- do they have motile spores or they sporulate through the basidium or the ascs - Sequencing is starting to complement our understanding of categorization - It can get very complicated very quickly -- not focus on details, look at the general situation/case of the phyla is - We are focused on the ones that are classified - 1753 was the time the first fungus was identified, and ever since then, a lot has happened -- different orders come and go, different phyla come and go, phyla split up Applications - Very important -- we can't live without them, can do lots of things for us - We've taken advantage of their properties - Agriculture -- work in symbiotic relationships, decomposing dead plant matter to get the nutrients back into the soil, control pests (fungi infect insect pests and reduce their number, allowing the plant to thrive and not be destroyed), plant and food spoilage (bread mold...) - Industry -- many cheeses are produced as a result of fungi, biofuels and biogas (*saccharomyces* produce ethanol, which we can use as a biofuel), enzymes and vitamins -- supplements for our nutrient intake, many antibiotics have come from fungi (Penicillin) - Environment -- they decompose and recycle nutrients, work with plants, mushrooms (tasty) Fungal Anatomy and Structures - Hypha -- filaments that comprise the mycelium, basic unit, underneath a mushroom is a vast network of hyphae - Mycelium -- vegetative body of the fungus (has different shapes and forms), network of many hyphae - Fruiting body -- reproductive structure is usually above ground, the part of the mushroom we see is the reproductive organ - Sporangium -- parts of fungus that contains the spores -- could be gills, could be contained in a tiny sphere on top of the mycelium stock - Fungi can reproduce: - Sexually -- spore form via meiosis, if they are fungi of the opposite class - Asexually -- spores form via mitosis, create spores by duplicating themselves Fungi Cell Wall -- An Important Difference Between Fungi and Other Eukaryotes - Contains chitin -- a polymer, forming a layer next to the cell membrane, enables structure and rigidity, and allows flexibility - Mannoproteins -- sugars that surround the chitin, important for evading the host immune system, it's a target for some anti-fungals - Ergosterol -- regulates permeability and fluidity of the cell membrane - One of the biggest differences -- in animal cell membranes, we have cholesterol, giving membrane fluidity and permeability  The Hyphal Tip - The way that a non-sexually active fungal organism will grow - Move using the tip on the hyphae, they will grow away from where they started, to look for more nutrients - There are many septa -- small pores in between all components, which allow nutrients and water and everything that they need to extend and to grow, moving from compartment to compartment - Nutrients will be moved in vesicles - In the end, they will come to the rightmost area, the area of the hyphal tip will traffic those vesicles to the right places so that the hyphae will continue to grow - Spitzenkorper -- the organizing center of the hyphae -- directs the vesicles, leads the growth - The hyphae tend to extend straight up, but for any reason, they can create branches, as they move along - The hyphal tip has a concentration of nutrients - This is how fungi expand -- cytoplasm moves and flows through, the hyphal tip is leading A close-up of a green and red object Description automatically generated  Mycelium - The branching of the hyphae, will grow in all directions - Hyphae grows and creates the mycelium - Diameter -- around 2 -- 30 - They exhibit autotropism -- self avoidance - Hyphae avoid each other, they are able to sense other hyphae, so that each hyphae doesn't block the growth of another hyphae produced - The center dies off because as the mycelium is branching, nutrients flow more and more and leave their starting point -- the center A white circle with lines on it Description automatically generated with medium confidence Yeast Form - Fungi, in their single-celled form - Not all fungi will exist as hyphae, some take the single-celled form - Generally, single celled, can form hyphae, but only in very specific conditions - *Saccharomyces cerevisiae* -- baker's yeast - *Histoplasma, Blastomyces* -- fungi that can cause serious infections in animals and people, skin and lung infections How Do They Propagate and Disseminate? - Where fungi grow, they always form a mycelial network - Sexually, or asexually - Asexual -- mycelium undergoes mitosis and divides, enables development of spores, which are then dispersed and spread, when in the right environment, they will germinate and produce their own environment there, they tend to do that in low-nutrient areas -- they need to start thinking of how to preserve themselves - Sexual -- introduces genetic variation and mutations into the population, involves the mycelium (if there are 2 forms of mycelium in the same environment, they will fuse and split into spores, after they've undergone meiosis, then spread and germinate in the same way as in asexual reproduction) Yeast Forms - Asexual: - Budding -- duplicating to the nucleus, moving it to a smaller part of the membrane, starting to create a septum, then they will slowly bud off and break off to create its own identical copy of the parent cell - Binary fission -- the same way as in bacteria - Sexual: - 2 diploid cells, 2 copies of the chromosomes, spores fuse, DNA recombinates, they but, split into 4 haploid ascospores, which are later dispersed and grow - Mating between one of each mating type Sporulation - Once they've produced the spores, they undergo sporulation -- they could disperse, spread and grow, or they could remain in a dormant state, if the conditions are good enough, can be dispersed either by being knocked by animals or wind - Sizes and shapes of spores can be very different -- spores in mushrooms are on the underside, on the gills - The way they produce their spores, is the way we use to characterize them  Many Ascomycetes are Dimorphic - They can take both the hyphal form and the yeast form - Happens as a response to changes in the environmental conditions, BUT - There is no clear individual environmental change, which drives the transition to the yeast form -- we don't understand the specifics of how this environmental changes drive the transition - Could be change in temperature, light.... Summary - Fungal taxonomy covers a diverse kingdom and it's in a flux -- we know there are lots of changes in terms of how we identify and classify fungi - They adapt very well to different environments -- we see them in aquatic, terrestrial, as parasites or symbionts - They take advantage of the fact that they can reproduce both asexually and sexually, depending on the situation - If they need to just propagate themselves, they will undergo asexual reproduction - If they are able to, they will undertake sexual reproduction, if they are in the right environment and have other compatible organisms - The fungal kingdom is still being discovered and understood, and is of pressing importance within the antimicrobial resistance paradigm - Fungi can be explored more deeply and help identify other antibiotics fungi produce PARASITES Parasitism -- a Way of Life - Living together always happens with organisms -- we live in symbiotic relationships with many microorganisms within us - Symbiosis may be (whether it is living inside or outside of the organism, the interactions matter): - Commensalism -- sharing the table, one partner benefits, but the other is not hurt, could be just sharing the same environment, not necessarily taking advantage of one another - Mutualism -- both organisms benefit -- protection, nutrients, or any other important aspects of living in this association - Parasitism -- one partner harms or lives on the expense of the other -- parasite and host Parasitism - Facultative parasitism -- when an organism can live in a free form, but it may establish a parasitic existence, if it comes across the right host, or the right environment - Obligatory parasitism -- when an organism establishes a permanent parasitic existence and is completely dependent on the host -- plasmodium, part of its reproductive cycle HAS to take place in the mosquito and within an erythrocyte in a blood cell, HAS to have those 2 parts of its life cycle, so that it can reproduce. Parasite HAS to associate with its host in order to be able to reproduce and survive -- this is how it gets its nutrients. - Accidental or incidental parasitism -- occasionally an organism parasitizes a species other than its usual host -- rat tape worm in men, some fleas that normally reside on a cat/dog, but have gone in humans. The parasite is taking up residence in a host that is not normally associated with that parasite Types of Parasites - Endoparasites -- live within the host, causing infection -- tapeworms, malaria plasmodium - Ectoparasites -- live on the external surface of the host, causing infection -- ticks, lice, ringworms - Temporary parasite -- only visits the host to get its meal/needs, then it will drop off and survive in the environment as a free-living organism, until they need to feed again. Mosquitoes and ticks - Permanent parasites -- always fixed on host, live there all the time - Opportunistic parasites -- produce diseases only in immunodeficient hosts because hosts may not be able to protect themselves well enough to continue with the symbiotic relationship with the parasite, and therefore, it could cause disease. Demodex, which is a mite that everybody has on their skin and in some individuals, it could be causing an inflammation on their face, as a result of the demodex starting to become parasitic Types of Hosts - Definitive host -- in which the adult or sexually reproducing form of the parasite lives. For nematodes, the definitive host would be sheep - Intermediate host -- in which the parasite lives during its larval stage or asexually reproducing form. Smaller animals -- a snail, fish, where the larval stages of the parasite develop, then they would be released and find their definitive host - Reservoir host -- Animals that carry these parasites, but they don't necessarily cause disease on these animals. If they represent a potential source of infection for men, they would be considered a zoonotic host. Reservoir hosts represent a potential source of infection to man. - Vectors -- organisms that are used by the parasites to transmit from one organism to another. Plasmodium uses the mosquito not only as a host, but also a vector to introduce plasmodium into the blood of people Habitat - Gastrointestinal tract of many animals-- round worms - Blood vessels -- plasmodium needs to be in erythrocytes, so that it can undergo a part of its life cycle - Organs -- liver, lung, heart (worms mainly) - Muscles -- tiny worms present in a muscle of pigs - Lymphatics -- worm resides in the lymphatic system - Reticuloendothelial system -- liver, bloodstream - Pathogens can be found in lots of different places Sources of parasitic infections - Water -- amoeba dysentery - Soil -- toxoplasma, other parasites - Raw vegetables and fruits -- parasite may have grown in the soil - Animals -- cats carry toxoplasma, it still be found in their feces and if a person comes in contact with them, when handling, they will become infected with toxoplasma (Can cause miscarriage in the fetus). - There is a recommendation that if you are pregnant, you should avoid litter trays - Fish -- parasites in fish meat, could be spread by vectors, and could be found - Arthropods -- they are mainly vectors - Blood -- infected blood Model of infection - Parasites have many different innovative ways to find themselves in the right environment A diagram of different types of transfusion Description automatically generated How can a parasite harm its host? - Having a large number of parasites, causing blockages - The actual site of parasitism -- can become infected and damaged, as a result of the activity of the parasite - Feeding habits of the parasite -- injuries or wounds, as a result of the way the parasite feeds - Competition of nutrients -- hosts receive nutrient deficiency, if you find a dog, covered in ticks, it could have anemia because these ticks are taking blood from the animal, causing the host to have anemia Life Cycles of Parasites - Takes 1 of 2 forms: - Direct -- involves 1 definitive host (1 host in total), may have some larva stages, or stages where they are not parasitic -- they are free living organisms - Nematodes -- released as eggs from the feces of the host, then they will hatch, and the larval stages will develop on pasture, then will be reintroduced into a host through the animals eating that pasture - Indirect -- involves at least 2 hosts, there is the definitive host (where the adult parasite develops), eggs are released into the environment, they may find themselves in an intermediate host (snail/fish/others), then they will develop into larval stages, which may be released as a free-living organism into pasture, or be directly consumed by consumption of the intermediate host, - Could involve a number of intermediate hosts before it reaches the adult form, OR it could have just one intermediate host and one definitive host Taxonomic Classification of Parasites - The medically important ones are classified into 2 kingdoms: - Protozoa -- microscopic organisms, unicellular - Malaria, giardia - Classified according to morphology and means of locomotion - Metazoa -- multicellular - Helminths (worms, cestodes, flukes) - Arthropods -- have an external skeleton, fleas, tics (ectoparasites) Protozoa - Single-celled eukaryotic organisms, microscopic - Sub-group of Protista (eukaryotic organisms that are nor-plants, nor-fungi, haven't been easily classified, they've created this group of organisms, which isn't easily classified) - Heterotrophic (this is why they are parasites -- they need to get their nutrients from someone else), motile (have a flagella), no cell wall - Most are free living in moist environments, protists have no involvement in parasitism at all - Many can be symbionts - Some of them will be parasitic -- amoeba, *plasmodium*, - Motile, single-celled, eukaryotic - Examples of parasitic protozoa: - Intestinal protozoa -- *entamoeba histolytica*, *Giardia*, *Cryptosporidium.* Site of parasitism is in the intestines - Vaginal protozoa *-- trichomonas vaginalis* - Systemic infections -- *Plasmodium falciparum, Trypanosoma brucei* Helminths - There are 3 different groups within the helminths - Nematodes -- found in guts, intestines and trachea of animals, cause very serious problems (breathing, stomach issues) - *Syngamus trachea* - *Haemonchus contortus* - Trematodes -- liver fluke - Cestodes -- tapeworm, found in intestines Classification of Arthropods - Invertebrate animals with an exoskeleton, segmented body, jointed appendages - Acari -- ticks - Have 4 pairs of legs, larval stages have 3, 2 body regions - Insecta -- insects - 3 pairs of legs, 3 body regions - Arthropods can be classified into: - Diptera -- flies - Phthiraptera -- lice - Siphonaptera -- fleas - Acarina -- ticks Vectors and Zoonoses - Parasites aren't important by themselves, they can also act as vectors for other diseases, zoonotic diseases - Lyme disease -- *Borrelia burghdoferi.* - Spread by ticks - We get sore regions around the bite sites - Ticks are a vector for Lyme disease - Cat scratch disease -- *Bartonella henselae* - Spread by fleas - Tapeworm -- *Dipylidium caninum* - The tapeworm is spread by fleas and lice - Tapeworms are released into the blood and find their way into the intestines - Heartworm -- *Dirofilaria immitis* - Spread by mosquitoes - An infection in dogs - Louping ill -- flavivirus - Caused by a virus, spread by ticks - An infection in sheep VIRUSES Week 1 -- Session 3 6/12/2024 Viruses Can Influence Human Behaviours - Thermal cameras in airports -- checked whether people had an illness before leaving the country - More and more masks being worn to try and reduce infection - Animal losses -- cost farmers a lot of money - Political issues -- Egypt government decided to kill all pigs in the country because of swine flu (Egypt is a Muslim country, a lot of the Christians in the country felt they were deprived of their food source, pigs weren't the issue -- it spread from person to person from the origin, pigs weren't affected) - Travel behaviours -- airport detection of people having an illness, wearing masks Swine Flu - Just part of the normal flu circulating nowadays - In 2010/2011, H1N1 (scientific name for swine flu) is still present, but in a normal circulation. If we've had a flu vaccine, one of the antigens in the vaccine may've been against the swine flu - Eventually, it starts to become normal - WHO have a phase approach in how they deal with pandemics. They thought the flu is going to be the next big pandemic - So, they came up with a plan that meant that everybody knew what was happening. - Start with animal-human infections, phase 4 goes to human-human infections, the pandemic stage starts when there are a lot of countries being affected internationally - Finally, the virus becomes seasonal with peaks and lows, people know how to deal with it - It was a pandemic, it caused a lot of problems, but it just started to become normal HIV - Ebola is a good example of what can we do when we have a lot of research and develop vaccines to fight - There are still cases of HIV, but there are ways to treat it now, it's not a death sentence - There are ways to treat the virus - You can still live a long and happy life, communication is needed - Spread through drug use (needles and other people using the same needle), from same sex intercourse Smallpox - We've never had to actually deal with it - When Europe started to explore other countries, with travelling, they introduced smallpox everywhere - It ended up killing many of the natives -- Europeans had immunity - Many countries in SA speak Spanish because smallpox killed the natives -- all people left were the colonizers - 300 million individuals in the 20^th^ century Ebola - Discovered near the Ebola River - It's deadly, mortality rates depend on the strain of the virus - Previously, there was no way to treat it -- it all depended on whether your body could fight it - Patients had infected blood coming out of everywhere - Lots of volunteers got infected themselves and passed away - Patients were handled badly -- people who treated them felt scared and lots and lots of caution was needed to not get infected - There has been a vaccine developed - 2020 wasn't the first instance of coronaviruses causing an outbreak - It was suggested that it came from a web market in China - We had to self-isolate to reduce the spread - Bats carry many different strains of Coronavirus, considered as a source for lots of pandemic strains - There are cases, where cave explorers tried to find bats, who carry these viruses, so that they can try to get ahead and already set ways to combat them, before they start a pandemic - In 2002, there was another pandemic in China, but it was dealt with and stopped before it became global Rabies - Virus looks a bit like a bullet - Still one of the ones, where if you get rabies, you won't survive - 55 000+ people die every year because of rabies - Spread through affected dog bites -- quite common in dogs - Once the signs and symptoms start to appear, it's almost fatal - The closer the bite is to the head -- the less time they have to get viral medication - The way to prevent it is by getting rid of rabies in the dogs -- vaccinating the dogs, there are lots of vaccination programs in high-rabies countries - There is also a human vaccine developed - Rabies in the UK -- in bats, 2003 was the last time there was rabies in the UK - Generally, rabies is in wild animals, bats (don't touch them) Foot and Mouth Disease - Animal virus - In 2001, there was a very bi g outbreak in the UK, resulting in the slaughter of 4 million animals - There are ways we can try and control it -- sadly, one of the ways is by euthanizing the affected animals Discovery - In 1898, the virus was said was smaller than bacteria, named "virus" - The discovery was made after leaves developed the tobacco mosaic disease, even though the infected leaves were filtered there is something we can't get rid of, which causes the disease Virus Definition - Metabolically inert, replicates only within living cells, with some kind of genome (RNA/DNA, some protein code), sometimes having an envelope  What is a Virus? - Obligate intracellular pathogens - They are so small, that they can't carry the needed proteins to replicate themselves - Some may carry enzymes, but need ribosomes they need a host, which provide these ribosomes - VIRUSES NEED RIBOSOMES, THEY ARE PARASITISING OUR RIBOSOMES - Relative Sizes - Bacteria -- 1-10 [µm]{.math.inline} - 1µm = 10\^-3 mm - Viruses -- 20-300 nm - 1 nm = 10\^-9 m - 10\^-9 m = 10\^-6 mm - Viruses are very very much smaller, we need an electron microscope to see them Viral Taxonomy - There was no easy way to characterize and identify them - Uses the same Linnaeus structure -- subgenus is called a "virus", the genus is the\_\_ - Genus could be the animal it affects, or where it was first identified -- Human Papilloma virus, ebolavirus Structure of Viruses - Genetic material is inside - There is a capsid -- structural proteins, which are part of the genome, requires the host ribosome to create these capsids, capsid enclose the genetic material - Viruses can be naked -- no envelope - Viruses can be covered in a lipid envelope -- enveloped - The viral glycoproteins are on the surface, they are involved in recognition, so that they can attach to a surface, or be a target of vaccines A diagram of a cell structure Description automatically generated The Capsid - Can look in many different ways - Icosahedral/spherical - HIV - Helical -- rabies, tobacco virus, - Complex -- Ebola virus - Bacteriophages are viruses that infect bacteria, genome is contained in the head, the tail is used to attach to and injected the genome into the host cell - There are a lot of different ways to characterize a virus' capsid - The Anomaly: - There are viruses, where there is no symmetry, it's very complex, lots of proteins outside, strange internal organization  Nucleic Acid - We can characterize viruses, based on what they have in their genome -- RNA or DNA - Linear or segmented - You can have a genome, made up of short segments - If you were to isolate the DNA or RNA from a virus, which has a segmented genome, then run it on electrophoresis gel, you would see the different lengths of the genes/segments of the genome. These genes could encode for different functions -- structural proteins, glycoproteins on the outside... - You can have one long genome - Single stranded or double stranded - Positive or negative sense - Positive sense -- 5' 3' - Negative sense 3' 5' Viral Genome Nucleic Acids - The way this genome is organized, is one of the ways we use to classify them - Viruses can be put into 1 out of 7 groups, depending on what type of DNA they have - Called the Baltimore organization method - Group 1 -- Double-stranded DNA, it could use ribosomes and RNA polymerase present in the host cell - Group 2 -- single stranded DNA, positive sense DNA, 5' 3' stranded, they need to convert the DNA to double stranded, so that the host convert that to proteins made - Each group may need certain proteins or enzymes to be packaged with it to enable it to get its genome to a point, where it can have the mRNA produced - We are focusing on 2 MAIN GROUPS of viruses -- positive sense RNA and negative sense RNA Positive Sense RNA - Viruses that have a single RNA strand, which is 5' 3' -- directly codes for proteins - In the host cell, the + sense strand is directly translated into proteins by the host ribosome - It enters the host cell, immediately starts making use of ribosomes, present in the host, to create the proteins they need - Production of proteins is necessary for viral progeny, it starts right away - No need for functional proteins, such as an enzyme, packaged in a capsid with it, because it can make use of all enzymes the host cell has - Quick to infect other host cells -- within 25 minutes we can have the host cell ready to burst the RNA out and spread - It doesn't have to change the structure of its genome before starting to use the proteins - Examples -- calicivirus, foot and mouth disease Negative Sense RNA - Some viruses needs extra things packaged within their genome - They have 3' 5' RNA, which is NOT readable by the host ribosome - First, the strand must be converted into positive sense RNA by virus RNA dependent RNA polymerase, which is made in the previous host and packaged with the genomic content - The virus has to package the enzyme "RNA-dependent RNA polymerase" into the capsid of its genome, so that once it gets to the host cell, it can use that enzyme to create a complementary strand to its genome to allow it to produce the proteins it needs - The virus needs to make sure it includes this enzyme in its virions to allow them to convert their strand in their host cells - Examples: influenza, rabies Virus Classification - What type of nucleic acid does it have? - What is the shape of the capsid? - Does it have a nuclear envelope from the host? - What type of genome there is? -- segmented, circular, linear... - Virus classification is based on: - The genome -- RNA or DNA - Number and sense of DNA/RNA strands - Morphology -- size, symmetry, envelope - Genome sequence similarity - Ecology - Lots of ways the architecture of the genome can look Host Range Varies - We could have a very narrow host range -- only causes disease in one species of animals -- swine killer disease, only infects pigs, can't reach humans - We can have a so-so wide range of hosts -- foot and motu disease doesn't just affect cows, all cloven-hoofed animals can have it - Other zoonotic -- wild animal reservoir, where the virus isn't causing any serious significant harm to the animal, but could spread and cause harm to other animals or people - Rabies is an example Lytic vs Lysogenic - Some, not all, but SOME viruses can take 1 or 2 routes to survive, or disseminate - The two cycles are: - Lytic cycle - Standard cycle the virus will take - Inject its genome in the host, hijack all the mechanics that the cell needs to replicate the proteins, then package it up its capsid, and when its full, it will burst and spread to find another host - Quite common in bacteriophages - DNA/RNA stay separate from the host DNA, takes over the host cell, replicates itself, very quick, enables wide spread to lots of different new hosts - Lysogenic cycle - Viral genome is incorporated into the host DNA prophage - This incorporated viral DNA will be replicated just as the other DNA in the host -- enables spread, but restricted to the progeny of the original host cell - Replicated during the host cell division all the progenies that come from the host cell dividing, will have a copy of the prophage - Viruses can stay in that form for quite a long time, they will be dormant until lytic cycle is triggered, until some kind of external influence makes it change back into the lytic cycle, then it will copy itself and disseminate that wat - In bacteriophages, there are some example of bacteria that have a prophage within their chromosomes, responsible for some of the harm they cause - It can be a reason for AMR spread -- AMR genes can be found in some bacteriophage genomes and incorporated as a prophage Control of Virus Diseases - Vaccination is the main approach -- takes two types - Vaccinate at young age against some serious illnesses - Activated - Inactivated - Antimicrobials/antivirals -- depends on how quickly you administrate them - We've managed to eradicate a number of diseases -- rabies, FMD in the UK - Biosecurity -- important to minimize contact between virus and host, lockdown - Washing of hands in soap breaks down virus membranes, hygiene, masks... - Viruses need close contact, they don't survive particularly well on surfaces, that's why social distance and masks matter Edward Henner and Smallpox - Historically, named as the first person to have used vaccination in a deliberate - In 1776, he noticed that milkmaids, tended to have smaller pastures didn't get infected so bad with smallpox, sometimes infected with cowpox instead - He had this idea that being exposed to the cowpox virus, gave them some protection against smallpox - To test that, he infected a small boy (8 yo) with some pus from a cowpox - The boy got cowpox, he was a bit ill, but then recovered - Then, he infected him with smallpox - The boy didn't develop the disease - Jenner tried to present his results, but the scientific news decide he doesn't have enough evidence, but Jenner experimented with more children, even his own 11-month son - His results are published in 1798 officially, determining the term "Vacca" - HOWEVER, 22 years earlier -- Benjamin Jesty, a farmer vaccinated his family for smallpox, he saw the same thing about cowpox and milkmaids - There was an outbreak smallpox in his community, he persuaded his family to infect themselves with cowpox - Smallpox was officially eradicated in 1980 What Makes Controlling Viruses Difficult? - People, who don't trust vaccines - Mutations in the virus genome -- the vaccine is no longer effective, - Different strains of the same virus may be circulating, not the ones the vaccine is developed against -- people try to predict which influenza virus is going to circulate - We can make assumptions, try to predict the next big pandemic to try and protect ourselves in advance - Example -- Big outbreak of FMD (Foot and Mouth Disease) in 2001, it was thought that this had been as a result of a security breach in a lab, it could be just a simple thing as biosecurity breach in a place, where the virus is being worked on, this can cause an outbreak of a virus - War -- there is a drive internationally to try to eliminate polio, we were doing really well, it has been eradicated in a lot of countries, but in places, where there is war, it is difficult for people to go and get the vaccination, children aren't getting the vaccinations, there are volunteers to go in these countries to try to eradicate polio by vaccinating, but there have been instances, where people have killed the vaccinators -- people think they are spies, they don't trust them - Vaccination could be very expensive