Animal Microbiology

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eloci
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200184
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Animal Microbiology
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2013-02-14 00:28:02
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animal science
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  1. What are the three bacterial contributions to the evolution of multicellular animals?
    • 1. a role in the origin of animals
    • 2. a role in the subsequent diversification and the shaping of animal life
    • 3. influenced the evolution of animal development
  2. How many microbial species have been identified?
    4500. (Speculated 3 million)
  3. What has determined the different domains of microbes that have evolved?
    The environment.
  4. What are the three domains?
    Bacteria, Archaea and Eucarya
  5. What are microbial mats?
    Layered groups or communities of microbial populations.
  6. What are four examples of microbial mats?
    • -Hypersaline bodies of water
    • -hot springs
    • -dry temperate deserts
    • -cold dry enviro of Antarctica
  7. List four reasons of why the study of microbial mats is important.
    • 1. Relevance to study of life on Earth
    • 2. Relevance to the study of the co-evolution of life and Earth
    • 3. Relevance to the study of the possibility of life elsewhere
    • 4. Finding life outside our own solar system
  8. What are stromatolites?
    Laminated organo-sedimentary structures formed by the trapping and binding, and/or precipitation of minerals by microorganims by a cyanobacterial microbial mat community. 

    (can be 1300 million years old!!)
  9. Where are cyanobacterial mat communities abundant?
    The ocean
  10. What has been the surviving feature of bacteria since their origin and evolution?
    Microbial symbiosis
  11. What contributes to the origin of the Eukaryotic cell?
    Symbiotic incorporation of bacterial chloroplasts and mitochondria
  12. Age of Bacteria?
    3.5 billion years
  13. Age of animals?
    ~500 million years
  14. What is a microbial consortium?
    A group of different species of microorganisms inhabiting a specific environment and performs some functions
  15. What is bioremediation?
    The use of microorganisms metabolism to remove pollutants
  16. Give an example of a natural microbial consortia.
    Petroleum degradation
  17. Give two examples of artificial microbial consortia.
    • -multiple pollutant biodegradation
    • -waste water treatment
  18. Define symbiosis.
    a condition where two dissimilar organisms live together in an intimate associate that sees both organisms benefit.
  19. Define microbial symbiosis.
    co-existence of two or more microorganisms- supply nutrients to host in return for a place to live. 
  20. List and describe the three bacterial-host interactions.
    • symbiotic- rely on each other
    • commensal- share, but don`t rely on each other 
    • pathogenic- cause disease
  21. Define autochthonous.
    • True residents: long term association with host.
    • Ex. Stable population in a particular region of the gut
  22. Define Allochthonous.
    Passing through: Do not persist in ecosystem, only detectable for a limited time. (can find niche and become autochthonous)
  23. What are three general types of marine microbes?
    • Planktonic
    • Adherent 
    • Colonized
  24. What are some potential applications for marine microbes?
    • drug discovery
    • nanoparticles
    • bioremediation
  25. What percentage of marine bacteria are not identified?
    More than 99.9%
  26. What are four microbial distributions in the ocean?
    • Free bacteria
    • Hot spots
    • marine snow
    • phytoplankton
  27. Describe the distribution of bacteria on seaweed.
    • Distal tips- lowest amount of bacteria (usually require oxygen to survive)
    • Middle Thallus- moderate amount of bacteria
    • Base- greatest amount of bacteria (usually convert nitrogen to nitrates to survive)
  28. What is the oldest, simplest multicellular animal (invertebrate) on earth? When did it originate?
    The MARINE SPONGE- originated over a billion years ago. 
  29. Why is it difficult to grow marine sponges elsewhere from their natural enviro?
    They rely on the associate bacteria to survive. 
  30. List the diverse microbial communities that often exist on marine sponges.
    • Bacteria
    • Archaea
    • Microalgae
    • Fungi
  31. How much of the sponge volume do microbial associates compromise?
    40%
  32. What are two ways the the microbial communities may contribute to marine sponge metabolism?
    • Photosynthesis
    • Nitrogen Fixation
  33. Marine sponges are microbial __________.
    Fermenters
  34. Which type of bacteria is on the outer surface of a marine sponge?
    cyanobacteria- serve as barrier and are involved in colouration
  35. Which type of microbes are in the inner core of a marine sponge and what are their functions?
    • Proteobacteria- Nitrification, dehalogenation
    • Actinobacteria- prolific secondary metabolite producers (metabolites prevent viral infections)
    • Archaea 
    • Cyanobacteria
  36. How long has sponge-bacterium symbioses existed?
    600 Million years
  37. How are sponges useful in medical research?
    Used as a model system to unravel workings of the human immune system
  38. List three sponge associated biotechnologies involving microbes.
    • Prolific marine producers- more than 200 new metabolites reported each year
    • Sponge/ microbe derived compounds- terpenoids, alkaloids, peptides and polyketides
    • sponge derived compounds are in medical trials such as anticancer,antibacterial, antiviral, anti-inflammatory, & antifouling
  39. Describe coral/bacterial symbiosis. 
    • Bacteria obtain nutrient supply from coral, protected from protozoan or bacteriophage
    • Coral- protective barrier from pathogens
  40. Define holoboint.
    any organism (animal or plant) and all of its associated symbiotic microbes
  41. Define Hologenome
    the sum of the genetic info of the host and its microbiota
  42. What is the hologenome theory?
    • the holoboint is a unit of selection in evolution
    • - natural selection happens on all levels
    • - microbiota are selected: host enviro and microenviro
    • - the genome being selected by hologenome
    • - diverse microbiota associated with host as part of the evolving holobiont
  43. List the four points of the hologenome theory development.
    • 1. all animals and plants establish symbiotic relationships with microorganims
    • 2. symbiotic microorganims are transmitted between generations
    • 3. The association between host and symbionts affects the fitness of the holobiont within its environment
    • 4. Variation in the hologenome can be brought about by change in host or microbiota genomes; under enviro stress; the symbiotic microbial community can change rapidly. 
  44. Main point of hologenome theory?
    Microbial symbionts can aid host adaptation and evolution
  45. What are the four ways for evolution of the hologenome?
    • -genetic variation passed to offspring
    • - genetic variation gained through amplification of existing strains and gaining new strains from enviro
    • - inheritance of acquired characteristics- (use and disuse)
    • - cooperation and competition effect evolution (natural selection)
  46. What type of gene sequence would be used to identify the genetics of a bacterial species?
    16SrRNA
  47. What type of gene sequence would be used to identify the genetics of a fungi or protozoa species?
    18SrRNA
  48. What are the two goals of evolution and ecology research?
    • - understand different ecological processes particularly the interactions among individuals and populations
    • - understand how above changes influence the evolution of the diversity (richness and abundance of species or genotypes) and function of ecosystem
  49. define richness
    the number of species (diversity)
  50. define abundance
    the number of individuals of a particular species
  51. What are the three main conceptual frameworks relevant to bacterial function and evolution within communities?
    • Adaptive radiation
    • ecological parameters
    • connections
  52. Describe adaptive radiation.
    the members of a community recognizing a niche causing adaptation and evolution
  53. Describe ecological parameters
    the regular structure of a microbial community
  54. describe connections
    how the individual members interact within and between communities
  55. What are the three factors that impact the evolution of host-microbial symbiosis?
    • Physical- temp, pressure, oxygen
    • Chemical- pH, nutrients, peptides, carbs, ion strength
    • Biological- host, species, genetics of host
  56. What drives constant change in communities for genetic diversification?
    Competition or interaction involving: predation, parasitism, disturbance and productivity
  57. What helps determine the diversification of microbes in aquatic environments?
    the diversification of nutrients
  58. Define chemotaxis.
    the ability to sense chemical gradients and direct motility accordingly (causes bacterial accumulation in ocean enviros)
  59. Chemotaxis is one of the mechanisms of _______   _________ for bacteria to adapt to enviro changes. 
    • Microbial evolution. 
    • Ex. fast swimming bacteria will find food source
  60. Define microcosm.
    A small representative system having analogies to a larger system in constitution, configuration or development. 

    AKA a tiny, often microscopic segment of an ecosystem represented by a specialized community of organisms. 
  61. Diversification of richness and abundance is associated with variation of ________   __________. 
    community functions
  62. Interactions between different genotypes can fuel the process of __________.
    Diversification
  63. List three ways that environment can directly impact generation of inheritable variation.
    • DNA sequences
    • DNA maintenance
    • Copying mechanisms
  64. What are the two mechanisms for microbial evolution?
    • Horizontal gene transfer: adaptation, speciation, evolution
    • Random mutagenesis and selection on genome evolution
  65. What are the two types of microbial evolution?
    • Long-term- millions of years
    • Short-term- a hundred years or shorter
  66. What are the contributions of long-term evolution?
    • Mutations & horizontal gene transfer
    • evolution of cellular proteins
    • conserved protein sequences
  67. What are the mechanisms of short-term evolution?
    • Human association with microbes in health and the environment
    • Bacterial evolution of recalcitrance to xenobiotics and industrial pollutants in the environment
  68. Is microbial antibiotic resistance a long term or short term evolution?
    short term
  69. Give an example of short term microbial evolution.
    E.coli and its diversification under different hosts. 
  70. When was Escherichia coli first discovered?
    In the feces from a child in 1885.
  71. How are the virulent strains of E.coli differentiated?
    • clinically, based on epidemiology
    • signs and symptoms
    • microscopic observations and interactions with host cells
    • biotypes
    • unique gene markers
  72. How might have independent pathogenic strains of E.coli evolved?
    • natural occurrence with the evolution of different mammalian hosts
    • Horizontal gene transfer- far more extensively anticipated
  73. What is one of the most important mechanisms of microbial evolution?
    Horizontal gene transfer
  74. Define genome
    All the hereditary information of an organism encoded in the DNA (or RNA for some viruses)
  75. Define Genomics
    The study of an organisms entire genome. Includes intensive efforts to determine the entire DNA sequence of organisms.
  76. Define microbiome.
    all genomics of microorganisms
  77. Define virome.
    All genomes of viruses in a specific community.
  78. Define epigenomics.
    Modification of the genetic material of a cell.
  79. Approximately how many encoded genes do humans, mice and cattle have?
    ~30,000
  80. Approximately how many encoded genes do pigs have?
    ~24,000 to 25,000
  81. Approximately how many encoded genes do chickens have?
    ~20,000 to 23,000
  82. How can DNA and RNA be differentiated graphically?
    • Absorbance levels at 260nm. 
    • Double strand = 50 ug/ml
    • Single strand = 40 ug/ml
  83. Describe PCR.
    • Method to produce many copies of a specific DNA sequence using a heat resistant enzyme
    • Allows researchers to target a specific gene or sequence within a genome
  84. Who invented PCR?
    Kary Mullis 1983- recieved Nobel prize in Chemistry in 1993
  85. What is the general trend for genome sequencing price and time?
    • Decreasing- in 2003 human genome sequence completed after 13 years and $3 billion
    • now it take approx. 2 weeks for $10 000
  86. List ten species that have their genomes sequenced.
    guinea pig, chinese hamster, lab mouse, rat, dog, cat, horse, pig, cow, sheep, etc.
  87. What is gene mapping?
    The creation of a genetic map assigning DNA fragments to chromosomes. 
  88. What is a gene marker?
    A gene or DNA sequence with a known location on a chromosome- may have a variation (mutation or alteration)
  89. What is SNP?
    Single Nucleotide Polymorphism- is DNA sequence variation when a single nucleotide differs between members of a species. (ex. mutation of base guanine to thymine)
  90. What is genotyping?
    the process of determining the genotype of an individual using biological assays.
  91. Why do mutations have greater impacts on bacterial functional changes?
    Because bacteria are so small.
  92. What are the 4 steps to microbial whole genome sequencing?
    • 1. Library construction
    • 2. Random sequencing phase
    • 3. Closure phase
    • 4. Complete genome sequence
  93. What is the purpose of whole genome sequencing?
    Insights into all genes; prediction and explanation of phenotypic traits
  94. Define metagenomics.
    Identification of genes from all microorganisms.
  95. Where was PCR discovered?
    In heat resistant bacteria in hotsprings (Yellowstone national park?)
  96. What may be a benefit of the metagenomic approach of sequencing microbial genomes?
    Can help to identify new/ uncultivated microorganisms
  97. How can the metagenomic approach help to identify uncultivated microorganisms?
    • understand the function of total microbial community
    • predict the function of unculturable species
    • identify function of these species
    • discovery of microbial enzymes/proteins/peptides
  98. What is bioinformatics?
    The science of developing and utilizing computer databases and algorithms to accelerate and enhance biological research
  99. What are three characteristics that can impact fecal bacterial community composition?
    • Host phylogeny
    • Gut morphology
    • Diet
  100. What is non-coding RNA?
    Any RNA molecule that is not translated into a protein.- Regulator of gene expresssion
  101. What percentage of the mammalian genome is non-coding?
    98%
  102. Four roles of mammalian non-coding RNA?
    • biological development
    • cell proliferation and differentiation
    • cancer initiation and progression
    • disease and immune response
  103. Two roles of microbial non-coding RNA?
    • Enviro changes
    • Stress growth conditions
  104. Where on the body are commensal microbes found?
    normally on parts of body exposed to or communicate with external environment
  105. Define microflora.
    • A group of microorganisms present in a specific location
    • Ex. bacterial colonies found in human gut
  106. Define microbiota.
    Microorganisms that are normally associated with a particular tissue or organ
  107. Define microbiome.
    All the microbes, their genetic elements (genome) and environmental interactions in a defined environment
  108. List the six features of a host-associated microbial community.
    • host specific
    • differ from surrounding community
    • similar microbial population from the same species (geographically separated)
    • different microbial population from different species at same location
    • different communities often dominate different tissues of the same organism
    • large diversity, certain bacterial groups dominate
  109. Where do termites live?
    Prominent in arid ecosystems
  110. What is significant about termites?
    They have the ability to breakdown lignocellulose at a rate of 85-90%
  111. What percent of global methane emissions are termites responsible for?
    4%
  112. What are the three parts to a termite gut?
    foregut, midgut and hindgut
  113. What is the difference between lower and higher termites?
    • Higher termites don't have protozoa in their guts whereas lower termites do.
    • ANNND higher termites have better social skills
  114. Describe nitrogen fixation and recylcing.
    inorganic nitrogen is converted to ammonia and the ammonia is utilized by the host for protein and amino acid production.
  115. What is acetogenesis/ methanogenesis?
    anaerobic metabolism pathways that utilize H2 and CO2 to synthesize acetate and methane
  116. Which is dominant in a termite gut acetogenesis or methanogenesis?
    methanogenesis
  117. Describe cellulose degradation in a termite gut.
    Cellulose---> malate--(uses ATP)---> CO2, H2, acetate
  118. What is the dominant substance absorbed by the termite after cellulose degradation and used for energy and biosynthesis?
    Acetate
  119. What are the two major microbial interactions of the termite gut?
    • 1. Bacteria closely associated with protists as symbionts.
    • 2. Mutual relationship between Methanogen and protist
  120. How many bacterial cells and how many human cells are there in a human body?
    • bacterial- 1014
    • human cells - 1012
  121. What are three reasons for the variation in commensal flora between individuals?
    • some bacteria are carried only transiently
    • most bacteria are fairly permanent
    • it is very difficult to alter the microflora of a healthy individual
  122. What are the possible resources of commensal microbes?
    • GI tract
    • Urogenital tract
    • skin
    • oronasalpharyngeal cavity
  123. What type of bacteria is predominant on skin?
    Gram-postive
  124. Where is the greatest stability in skin microflora?
    in the nose and ears
  125. Where is the least stability in skin microflora?
    behind the knee ( likely not important)
  126. What are some factors that may influence the difference in the types of microflora that inhabit the skin (not necessarily the microbiome)?
    • moisture
    • body temp
    • pH
    • nutrition
    • skin type
  127. Which type(s) of skin have the most diverse microflora?
    Dry, oily or moist?
    Dry and moist- oily is the most stable
  128. What are some factors that can influence the skin microbiome?
    • weather
    • clothes
    • chemicals
    • hormones
    • water balance
  129. What type of bacteria is known to cause acne?
    propionlbacteria
  130. How many common bugs live in peoples mouth?
    600
  131. Are the majority of oral bacteria beneficial or harmful?
    • mostly good- help maintain teeth and gums
    • few bad- cause tooth decay and gum disease, some linked to heart disease, stroke and premature birth
  132. What is oral bacterial polysaccaride?
    Biofilm= dental plaque
  133. What causes dental cavities?
    lactic acid bacteria
  134. How does a diet high in sucrose promote tooth decay?
    S.mutans produces a polysaccaride adhesive from sucrose and the sugar is used as a substrate to produce organic acids which lower pH.
  135. What prevent S.mutans from causing cavities?
    Xylitol- found in chewing gum!
  136. What types of microflora exist within the lower respiratory tract?
    None. It's usually sterile.
  137. Describe the microflora of the stomach.
    Usually transient and populations are kept low due to acidity. 103 to 106
  138. Describe the microflora of the duodenum.
    sparse 103
  139. Describe the microflora of the ileum.
    Moderately mixed flora. 106 to 108
  140. Describe the microflora of the large bowel.
    Dense! 108 to 1011
  141. What is the GI tract of a fetus like?
    sterile
  142. What is the difference in the gut flora of infants that are breast-fed vs. formula fed?
    • Breast-fed- Bifidobacterium
    • Formula- typical adult gut microbiota
  143. At what age is the gut microflora similar to that of an adult?
    2
  144. What is significant about Bacteroides Plebeius in the gut of Japanese?
    Only Japanese people have this microbe, which may be an evolutionary difference due to the consumption of marine foods such as seaweed.
  145. List 6 factors that influence gut microbes.
    • diet
    • phylogeny
    • age
    • gut morphology
    • host genetics
    • geography
  146. List 5 functions of gut microbiota.
    • digestion of unutilized substrates
    • stimulating cell growth
    • repressing harmful microorganisms
    • protection against epithelial cell injury
    • training the immune system to respond only to pathogens
    • defending against some diseases
    • regulation of host fat storage
  147. Which factors change vaginal flora?
    age, vaginal pH and hormone levels
  148. What types of microorganisms cause vaginitis?
    transient organisms
  149. What type of flora are contained within the urethra?
    sparse mixed flora 104.
  150. What is the risk of bacterial vaginosis in a pregnant woman?
    spontaneous pregnancy loss in 2nd trimester and spontaneous preterm birth
  151. Give three examples of changes in commensal microflora in humans.
    • changes in physiology and development- female genital tract
    • When antibiotics select for a resistant microflora
    • When new organisms are acquired- ex. pregnancy, diet, environment
  152. _____ microbes are never pathogenic.
    most
  153. ________ microbes are potentially pathogenic.
    many
  154. _______ microbes are always pathogenic.
    very few
  155. What is Quorum sensing?
    a communication mechanism that enables microorganisms/ bacteria to make collective decisions
  156. Give an example of an aquatic animal that takes advantage of quorum sensing.
    The Hawaiian squid- using Vibrio fisheri to for bioluminescence
  157. Explain in 4 steps how quorum sensing works.
    • 1. small chemical signal molecules are synthesized and secreted into the environment
    • 2. using specific detection, systems sense signals and cell density
    • 3. When the concentration of a signal molecule reaches a certain threshold gene expression turns on
    • 4. behaviour of total population changes
  158. What are the 4 mechanisms of quorum sensing?
    • Gram-negative bacteria - uses lactones (AHL)
    • Gram-positive bacteria -autoinducing polypeptides (AIP)
    • Both (-) and (+)- AI-2 
    • beyond bacterial borders- (AI 3) - communication between host and bacteria
  159. Describe Mechanism 1 of quorum sensing.
    Gram postive bacteria- use autoinducing polypeptides (AIP)
  160. Describe Mechanism 2 of quorum sensing.
    Gram negative bacteria uses lactones (AHL) 
  161. Describe Mechanism 3 of quorum sensing.
    uses Gram negative and Gram positive bacteria. Involves autoinducer 2 (AI-2)
  162. List 5 ways in which quorum sensing plays an important role in gene regulation.
    • Biofilm formation
    • Virulence adaptation
    • Production of antimicrobial substances
    • Motility
    • Sporulation
  163. Are there Acyl-Homoserine Lactones in mammalian intestines?
    yes.
  164. What is the quorum sensing mechanism 4?
    -involves autoinducer 3 (AI-3)- pretty much bugs communicating with the host through compounds.
  165. What are the two future perspectives of quorum sensing?
    • 1. Signal molecules as potential biomarkers
    • 2. A theraputic tool to regulate pathogenic bacteria
  166. What is a biofilm?
    A complex aggregation of microorganisms growing on a solid substrate.
  167. Give some examples of places that biofilm can form.
    lakes, oceans, sink drainage, waste treatment plants, gut, surface materials, tissues , medical implant materials
  168. What are biofilms primarily composed of?
    microbial cells and EPS (extracellular polymeric substances) EPS may account for 50-90% of carbon in biofilms
  169. How are biofilms characterized?
    • Structural hetergeneity
    • genetic diversity
    • complex community interactions
    • an extracellular matrix of polymeric substances
  170. What is the predicted biofilm shape?
    • Not a uniform structure:
    • clusters
    • channels
    • matrix
  171. Are bacterial cells on the surface of teh biofilm the same as the cells within the biofilm?
    Probably not
  172. Are the bacteria of biofilms active all the time?
    No, some are dead and some are dormant.
  173. Are the genetics of the bacteria of a biofilm the same?
    They may or may not be. They could all be a single species
  174. List the three important survival mechanisms for bacterial cells of biofilms.
    • A) form a dense and protected environment for free-floating microbes to cooperate and interact with eachother
    • B) facilitates communication among them through chemical and physical signals
    • C) Water channels that help distribute nutrients and signalling molecules
  175. What is a medical concern with biofilms.
    They form on medical products and may cause infection for patients. Ex. biofilms may form on catheters, aritifical hearts, contact lenses, joint replacements, etc. - Expesive to repair/clean/remove
  176. What is the problem with biofilm removal?
    conventional methods of antibiotics and disinfectants are often ineffective. - Cholination doesn't work and using tonns of antibiotics isn't smart for medical or environmental purposes.
  177. What are 2 ways in which biofilm is beneficial?
    • 1. prevent invasion into host epithelial tissue
    • 2. environmental- bioremediation and provides biobarriers to soil and groundwater from contamination and Biofiltering of industrial water
  178. ___% of GI disease in humans can be traced to contaminated egg products
    80%

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