Bacterial Diversity Chapter 10 PDF

Chapter 10: Bacterial Diversity Evolutionary relatedness is measured by comparing the sequences of genes encoding 16S rRNA. The number of sequence differences in rRNA-encoding genes reflects how long it has been since two kinds of bacteria diverge from a common ancestor. There are 30 phyla of...

Chapter 10: Bacterial Diversity Evolutionary relatedness is measured by comparing the sequences of genes encoding 16S rRNA. The number of sequence differences in rRNA-encoding genes reflects how long it has been since two kinds of bacteria diverge from a common ancestor. There are 30 phyla of bacteria from which species can be cultured in the laboratory. what are Bacteroidetes Microbiologists estimate there may really be over 1,000 more phyla we have yet to see. Seven major phyla (superphyla) are known to impact human health and the ecosystem. Gram-positive: Firmicutes and Actinobacteria Thick cell walls that resist drying. They are heterotrophs = they cannot produce their own Include Firmicutes that produces dormant endospores (clostridium). ◦ These are non-active resistant cells that are hard to kill even in hospital settings. O PertainingtoFirmicutes ◦ Endospores - heat, dessication, high-energy radiation, freezing, and chemical disinfectant resistant. Stronger Endospores compared to the spores of actinomycetes. ‣ If the cell experience lack of nutrients they will sporulate. The cell divides near one of its poles instead of at the middle. The polar compartment becomes the forespore (where we find fluorescence). The large compartment, mother cell, provides DNA and nutrients to the growing forespore. Once the mature endospore is released the mother cell disinegrates. The endospore may endure the lack of nutrient for even decades until they find proper nutrients. ◦ “Though skin” - they have thick cell wall characterized by gram positive bacteria. ◦ Several layers of peptidoglycan (horizontal) supported with teichoic acids (vertical). ◦ Low “G+C” content Also includes Actinobacteria, also called Actinomycetes, which grows as radial filaments. ◦ Example would be streptomyces which are soil bacteria that produces antibiotics. ◦ Peptidoglycan with an additional thick waxy coat/ ◦ High “G+C” content. Gram-negative: Proteobacteria and Bacteroidetes they range from being heterotrophs to lithotripsy and photosynthesizers. Proteobacteria is a very diverse phylum that includes species capable of wide range of metabolism. Many are used for biotechnology. Bacteriodetes are all Gram-negative rods; most are obligate anaerobes. ◦ Bacteroides species, for example, are gut microbiota that help us digest food. After surgery, however, these same species may cause abscesses. Spirochaetes share a distinctive form: tightly regulated coiled cells enclosed by a sheath, with periplasmic flagella that run underneath the sheath along the cell body Some spirochetes live in soil or water as digestive symbionts of termites. Others like Borrelia burgdorferi are pathogenic and causes Lyme disease. Chlamydiae the bacteria of the phylum chlamydiae are obligate intracellular pathogens that grow as inclusion bodies within host cells. Cause pneumonia, eye disease trachoma, and the sexually transmitted infection chlamydia. Evolution: Past and Future f Pathogens today continue to evolve New pathogens brew in three basic evolutionary incubators: zoonotic hosts, shelter species, and the environment. Zoonotic host: some pathogens are only able to infect animals and some humans. These animal disease are called zoonoses (singular, zoonosis) When a bacteria infects an animal, these pathogens can net react with the microbiota of the animal, forming recombinant genes that could help the pathogen evolve into a new species that can infect humans.  Sheltered Species they do not directly interact with humans but do provide shelter for bacteria to evolve. Mixed communities of bacteria and phases within a worm or other shelter species can lead to genetic exchange and evolution of the bacterium. Over time, some of genes could enable a bacterium to infect across a species barrier — to an animal, plant, or human. Natural Environment melting pot where genes are sampled from thousand of species. This is where some genes causing antibiotic resistance originated Plasmids and transopons first evolved, where phases became phases. Phylum Firmicutes: Rods, spheres, and Endospores III Firmicutes derives from Latin meaning “though skin” = thick peptidoglycan, reinforced with techoic acid. Some posses a thick waxy coat that actually excludes the gram stain, despite their genetic affiliation with gram-positive bacteria. Bacillus species grow best by aerobic respiration, they form large, cream coloured colonies on an nutrient agar plate exposed to air. Clostridium are obligate anaerobes. They sporulate at the end of the cell giving it a club shape. Causes C. Tetani and C. Botulinum. The botulism toxin, botulinum or BOTOX. Not survive germinate of ◦ Clostridium spores are found in soil and water, ready topresence andoxygen grow once the environment becomes anaerobic. if you Selected performcatalasetestyouwillseenobubbles Gram-Positive Firmicutes Spore formers with cell wall Bacillus anthracis - rod shaped soil bacterium; causes anthrax Clostridiodes difficile - Rod with bulging spores; causes intestinal disease in patients whose normal clostridium microbiota are diminished by antibiotics. pseudomembranous colitis ◦ Resistant to most antibiotics, so even if there are more normal human gut microbiota in the body when people are being treated wth antibiotics these will diminish, leaving only the C. Dif to be in the system. nocontraction at all Clostridium botulinum - Rod with bulging spores; forbotulism causes botulism; produces Botox ◦ Can grow within the colon of very young infants, and cause infant botulism. neuromuscularsyndrome Clostridium tetanus - Rod with bulging spores; causes tetanus. oppisiteaffectingthesame ngyg.gg.guscular continousmuscular contraction Non-spore formers = they probably lost their ability through reductive evolution. Enterococcus spp. - enteric microbiota (intestinal/gut); cocci Theyareeasiertokill UTI ◦ normal found in the intestinal tract, invasive for immunocompromised hospital patients. Causing urinary tract infection and bacteremia. bacterialinfectionin bloodstream ◦ Commonly treated with Vancomycin Lactobacillus spp. - Rods; Dairy culture catalasetestwould be Lactococcus spp. - Cocci; Dairy culture f ◦ ferment milk to make yogurt and cheese. They are obligate fermenters - they grow in the presence or absence of oxygen, but they don’t use oxygen to respire. They convert sugars to lactic acid, as the lactic acid builds up, ph decreases which halts bacterial growth. Listeria spp. - Rods; intracellular pathogens; grow at refrigerator temperature o ◦ they are facultative anaerobic rods. - they can survive environments with or without oxygen. They can switch between oxygen respiration and fermentation. ‣ Listeria monocytogenes - enteric pathogens, causes listeriosis that can spread to the central nervous system. begins after eating contaminated cheeses, lunch meats, or sauerkraut. They grow at a temperature as low as 4 C. Can grow in soil but can also grow eans and invade mammalian cells, they invade host immune system. secies bacteria is taken up by macrophages, but escape the vesicle to grow in the cytoplasm. They will generate tails of polymerized host actin and propel itself towards neighbouring host cell. Staphylococcus aureus (cluster) - Coccus; infects skin; causes toxic shock syndrome and MRSA - most dangerous strain (methicillin-resistant S. A) ◦ serious skin pathogen - pneumonia, impetigo, toxic shock syndrome, Facultative anaerobic osteomyelitis. salt tolerant ◦ The major cause of hospital acquired infection, esp. infections on surgical wounds. Staphylococcus epidermidis (cluster) - Coccus; skin microbiota Facultative anaerobic ◦ generally salt tolerant, their fermentation generates short fatty acids that inhibits the growth of skin pathogens. 888 our skin has salt Theydonotrequireoxygenbuttolerates itsprescence  Streptococcus (chains) - aerotolerant but metabolize using fermentation. ◦ live on oral or dental surfaces. 0000000 ◦ Causes pneumonia, strep throat, erisipelas, and scarlet fever. ◦ Can be grouped by antibody reactions to cell-surface glycoproteins (launcefield grouping). Typicalpneumonia mixedclassificationof strepandstaph We can differentiate staph and strep by their ability to hemolysis red blood cells. ◦ Alpha - partly hemolyze Rbc via hydrogen peroxide reaction -> generates greenish halo. ◦ Beta - fully hemolyze RBC via hemolysis enzyme -> clear halo. strept staph We can alsoanalyzeusinghockeypucks Mollicutes (lack of cell wall) — formerly belonging to the phylum Firmicutes willbehave as They have only have their cell membrane - cannot stain gram positive. In nature they only grow in tissuenegative gram of a host organism. No cell wall makes it faster to reproduce since it has more energy to consume. All known class of multicellular organism is parasitized by mycoplasmas. In humans they cause pneumonia and meningitis. fried shape egg genitalium - ameboid shape; genital microbiota Mycoplasma Mycoplasma pneumoniae - Ameboid shape; cause pneumonia. atypical no cellwall Typical atypicalpneumonia typicalhascellwall nocellwall Selected Gram-Positive Actinobacteria High GC gram positives, includes major pathogens and antibiotic producers, as well as essential decomposes in natural environment. Most actionbacteria can be identified under the microscope using acid fast stain. Acid fast property is associated with unusual cell wall lipids, such as the mycolic acids of Mycobacterium Tuberculosis. hardtostainthatswhyyouneedto useacidfaststain Actinomycetes group -they are called mycetes because they form mycelia that are branching filaments, they behave like fungi! There are also Nocardia that are part of this group that hairlike, beloved to be the result from inhaling bacteria from the environment. Actinomyces Israelii - forms branched mycelia filaments; causes actionmycosis. Actinobacteria that are not actinomycetes: no hair like. They contain mycolic acid and cells stain acid fast. Corynebacterium diphtheriae - Irregular rod; causes diphtheria Cutibacterium acnes - Rod shape; causes acne Mycobacterium leprae - short rod; acid fast; causes leprosy 1TEur Yhikhthe.is Mycobacterium tuberculosis - short rod, acid fast; extremely thick cell wall with mycolic acids; causes tuberculosis. They stain gram- negative because of the mycolic acid! ◦ Detected via acid fast stain as tiny rods associated with sloughed cells in sputum. ◦ Has exceptionally thick, complex membrane that includes some of the longest chain acids known, up to 90 carbons. ◦ Mycolic acid is linked to arabinogalactan. This complex forms a waxy coat that impedes the entry of nutrients through porins. ◦ As a result this complex slows down the growth rate, but it defends the bacterium from host defenses and antibiotics, which is why tuberculosis takes time to cure. Iwt d Phylum Proteobcteria: A diverse Superphylum pyanhardtocturistownproductiated Includes heterotrophs, litothrophs, and photosynthesizers. They are all gram negative! ◦ The gram negative envelope includes an outer membrane, a cell wall of peptidoglycan permeated by the periplasm, and an inner membrane. The outer membrane is packed with receptor proteins and porins. They contain long sugar polymer extensions (LPS), LPS has toxic effects on the host. risk ofendotoxic ◦ Enterobacteriaceae is a family under proteobacteria shock that mostly appear as rod. They can be distinguish by a variety of biochemical tests. Proteusmirabilis GUT UTI ‣ Ph indicator test - the pH changes during the process of fermentation. Fermentation pathways distinguish between closely related species. ‣ All are facultative anaerobic rods that may grow in human or animal digestive tracts or in lakes and streams. ‣ Many species have flagella that makes the bacterium motile (swimmers or swarmers). Some also form biofilms that increases their resistance to antibiotics. ◦ Pseudomonadaceae - pseudomonas are rod shaped obligate respires - requires a terminal electron acceptor like oxygen to make energy. ‣ P. aeruginosa commonly grows in soil as decomposed, but in humans; surgical wounds or form biofilms in the lungs of cystic fibrosis patients.  mostcommon UTI Escherichia coli - Rod; main vehicle for biotechnology; strains cause intestinal and bladder infections. ◦ Part of the Enterobacteriaceae produces ◦ Most commonly growing in the human intestine. vitamink ◦ Most common reason why children die under 5. ◦ Escherichia coli - commensalism it benefitswhilethehumandoesnot ◦ E.coli O157:H7 - pathogen fromone unicellurarrangement swimmer they turninto multicellular swarmmer UTInotcommon verycharacteristicof UTI colonizegastriclining at extremelylowpH chronicgastritis stomacular Helicobacter pylori - Wide spiral cell; survives in the stomach acid; causes gastritis. cancer Legionella pneumophila - Rod; grows within amebas or macrophages; causes lung infection legionellosis. ◦ Related to pseudomonas, incapable of growth on sugars. requires oxygen t grow on amino acids. ◦ Grows inside ameba and in human macrophages ◦ Transmission to humans occurs through inhalation of aerosolized ameba with Legionella inside. ◦ Humans who unknowingly inhales the aerosol can develop a serious lung disease known as legionellosis. causeofpneumonia Atypicalpneumonia intracellularpathogen a Neisseria gonorrhoeae - Diplococcus (pair of cocci); causes gonorrhea ◦ Family of Neisseriaceae occurs as paired cocci ◦ Causes the sexually transmitted infection gonorrhea. Neisseria meningitidis - Diplococcus; cause meningitis ◦ Causes meningitis, infection of the brain and spinal cord lining. Rickettsia rickettsi - Rod; intracellular pathogen; causes Rocky Mountain spotted fever. ◦ The mitochondria evolved from the lineage of the intracellular pathogen Rickettsia (Family Rickettsiaceae) 4 ◦ Are carried by tick vectors, causing Rocky Mountain spotted fever. Salmonella enterica - Rod; enteric pathogen, may grow intracellularly. ◦ Also part of the genera Enterobacteriaceae. ◦ Cause diseases such as enteritis and typhoid fever. Vibrio cholera - Comma-shaped rod, causes cholera ◦ Comma shaped with a single flagellum. ◦ Causes diarrheal disease cholera, major problem for countries that have poor sanitation. Yersinia pestis - Rod; causes bubonic plague. ◦ Also part of the genera Enterobacteriaceae. lymphaticnodule ◦ Cause of the bubonic plague inflammedlymphdone buboes ◦ Gram negative bacilli ◦ Can be transmitted from animals to humans through an infected flee or when the disease progress to the pneumonic stage and the disease can be spread through respiratory droplets from coughing. ◦ Y. Pestis is a variant of Y. Pseudotuberculosis that only diverged some thousand of years ago. horizontally transferredplasmi ‣ Y.pseudotuberculosis causes gastrointestinal disease that can mimic appendicitis and is transmitted from animals to humans by contaminated food or water. Plasmids - are short circular pieces of DNA that can be acquired from the environment by transformation or from a donor cells by conjugation. Two plasmids acquired by Y. Pestis is important virulence factors: phospholipase - digests the phospholipids ◦ When a flea bites an animal infected with Y. Pestis, the phospholipase inactivates a toxic component of ingested blood and helps the microbe colonize the flea midgut. It will then replicate in large numbers. ◦ The Y. Pestis is trapped in a blood clot , the bacterial protease will be secreted that will activate the host plasmin that will dissolve the clot. This allows the Y. Pestis to dessiminate through the hosts bloodstream ◦ The horizontal acquired peptide capsule will protect it from the hosts immune system. ◦ Unique capsule made from peptide rather than the polysaccharides that compose most bacterial capsules. Protease (plasminogen activator) taht dissolves clots in the human bloodstream.  Pseudomonaceae obligate aerobic basili related to the Enterobacteriaceae P. aeruginosa commonly grows in soil as a decomposer, but in humans: surgical wounds or form biofilms in the lungs of cystic fibrosis patients. Intrahospital infections, they are hard to treat and there are resistant species. greenishcharacteristic inagarplate Haemophilus influenza intracellular symbionts and predators Most common cause of influenza - no because influenza disease is a cause by a virus. This is a bacteria. - causes pneumonia. M. Catarrhalis Moraxella what characteristic they have in agar plate - When we move the colony they move together (behaves like a hockey puck) Phylum Spirochaetes: Twisted-Cell Pathogens and Symbionts Ien Are a disntictive Claude of bacteria with a cell structure consisting of a long tight spiral that is flexible, like a coiled telephone cord. It is similar to proteibacterial outer membrane but the very thin peptidoglycan cell wall completely separates the sheath from the plasma membrane. most spirochets are slow growing heterotrophs and difficult to culture. Many are free living organisms in soil and water. Many of nonpathogenic spirochetes are digestive symbionts of hosts as diverse as termites and cattle. Cell is surrounded by a thick outer sheath of lipopolysaccharides and proteins. At the end of each cell, one or more flagella extend and double back around the cell body within the periplasmic space. The periplasmic flagella rotate on proton-driven motors, as do extracellular flagella. Because the spirochetes flagella is twine back around the cell body, their rotation forces the entire cell to twist around, corkscrewing through the medium. This is an advantage in highly viscous environments. nonpathogenic spirochetes aredigestive symbiontsinthe termites Treponema pallidum gutof causes the sexually transmitted infection syphilis. Syphilis arises only from strains of the subspecies pallidium (T. Pallidum pallidium) ◦ Three stages of syphilis: bothmaypresent Primary secondary Tertiary ◦ Can cross the placenta an infect the fetus. with alesionthatheals Different subspecies such as pertenue (T. Pallidium pertenue) produces a different disease called yaw. ◦ Is a multistage disease, transmitted through direct skin contact predominantly in developing countries. spontaneously and is ◦ Cannot cross the placenta and infect a developing fetus. laterfollow a rash by stagepainless sore ulcer on hervagina Rash 30nwpleorgmoyid Phylum Chlamydiae: Intracellular Pathogens VN Chlamydiae is a large group of bacteria with cell walls that have very little peptidoglycan. pathogenic species of chlamydiae lack the classic cage like form of paptidoglycan, but they do have a narrow ring of peptidoglycan at mid cell to guide cell division. spendentirelyonthehostfortheir survival I.mg Are obligate parasites or pathogens Though they lack cell wall they possess an outer membrane whose proteins are cross-linked by disulfied bonds, making a tough coat that provides osmotic stability. Persistent infection with C. Trachomatis can lead to pelvic inflammatory disease. ◦ Is the causative agent of a major sexually transmitted infection in the US. ◦ Also a cause of trachoma - eye disease. ◦ Chlamydophila pneumoniae - causes pneumonia and has been implicated in cardiovascular disease. ◦ Can infect a wide range of host cells. Alternate between two developmental stages with different functions: elementary bodies and reticulate bodies. ◦ Elementary body - transmitted outside of the host cells, they resemble endospores in that they are metabolically inert.  To reproduce: The elementary body must adhere to a host cell surface -> endocytosed into the host cell -> (once in the endosome) transform itself into a larger reticulate body. ◦ The reticulate body has active metabolism and divides rapidly, but is incapable of infection and is vulnerable to osmotic shock. Therefor in order to infect they need to divide and transform to a new elementary body before exiting the host. When the host cell lyse, the elementary bodies can infect new cells. Without treatment this can go on indefinitely, this can cause inflammation to the Fallopian tubes and ovaries known as Pelvic inflammatory disease (PID). PID can leave permanent adhesions (fibrous tissue across the organs), common cause of infertility.