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Lecture 12 - Mutualisms and Microbiomes - BIS2C

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Lecture 12 - Mutualisms and Microbiomes - BIS2C

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Lecture 12 - Mutualisms and Microbiomes - BIS2C

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 12: Mutualisms and Microbiomes Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s Hummingbird
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Anna’s Hummingbird
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Otter at Yolo Bypass
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals • Understand examples of mutualistic symbiosis • Understand the different between commensalism and mutualism • Understand details of the tubeworm - bacteria symbiosis and why it was so surprising • Understand examples of how the human microbiome contributes to human health and how it can be disturbed and restored
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !11: Viruses and Gene Transfer !12: Mutualisms and Microbiomes !13: Endosymbiosis and Organelles Lecture 12 Context
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2: Microbiome Group Presentation • Lab 3: Termite hindgut symbionts • Lab 2: Water fern symbiosis • Lab 2: Legume - Rhizobium symbiosis • Lab 3: Endosymbiosis
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Review of Lecture 11
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 11 Outline • Background and Context • Viruses !Introduction to viruses !Viral origins !Viral diversity • Gene transfer
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 General viral life cycle https://www.youtube.com/watch?v=uIut0oVWCEg
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses Reasons for “No” ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Some Key Features of Viruses Reasons for “Yes” ! Noncellular ! Packaged into virion made up of: ! Genome (RNA or DNA) ! Protective coat (capsid) ! Sometimes additional coatings such as a lipid envelope ! Life history ! Obligately symbiotic and intracellular ! Replicate but only with assistance from host ! Causative agents of 1000s of known diseases including 100s in humans ! Mutate and evolve ! Infectious via virions/virus particles ! No metabolism themselves ! Estimated to be > 10,000,000,000,000,000,000,000,000,000,000 (10^31) virions on earth.
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Four Main Hypothesis Regarding the Origin of Viruses Bacteria Prok Archaea Eukaryotes Four Main Hypothesis Regarding the Origin of Viruses.
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Diversity of viruses
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Transfer of Function Via Plasmids Exchange
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lateral gene transfer (LGT) vs Sexual Recombination • Direction !Sexual recombination is bidirectional with DNA from two parental lineages mixing !LGT is unidirectional with DNA moving from one organism to another. • Amount of genome !LGT involves usually small portions of a genome !Sexual recombination involves whole genomes. • Relatedness !LGT can occur across vast evolutionary distances (but most common among close relatives). !Sexual recombination usually within species but sometimes more distant relatives
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + +
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes Need Help • Eukaryotes as a group are somewhat limited in their metabolic capabilities • However, eukaryotes are remarkably adept at “acquiring” capabilities by engaging in mutualistic symbioses with other organisms • In many of these the symbionts are inside the eukaryotic cells. This may be related to the ability of eukaryotes to undergo phagocytosis
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Mutualistic Symbioses of Bacteria w/ Eukaryotes • Digestive ! Ruminants ! Cellulolytic insects • Defensive • Behavioral ! Squid light organs • Autotrophic ! Photosynthetic (many) ! Chemosynthetic in deep sea • Nutritional ! Aphids ! Nitrogen fixation in legumes
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 I Contain Multitudes Video from Tangled Bank Studios https://youtu.be/8W_ywzhkR90
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Tubeworms and Me …
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question These worms with their symbionts function as chemolithoautotrophs. This is weird because “normal" worms and most other animals are A: Chemolithoheterotrophs B: Chemoorganoautotrophs C: Chemoorganoheterotrophs D: Photolithoautotrophs
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 These worms with their symbionts function as chemolithoautotrophs. This is weird because “normal" worms and most other animals are A: Chemolithoheterotrophs B: Chemoorganoautotrophs C: Chemoorganoheterotrophs D: Photolithoautotrophs Thought Question
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 12 Outline • Background and Context • Mutualisms • The Human Microbiome
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Human Microbiome • We are covered in a cloud of microbes • This “microbiome” (community of microbes) likely is involved in many important human phenotypes • Microbiomes also are involved in health and functioning of other organisms & ecosystems
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Microbes in human microbiome likely benefit. Many interactions with human microbiome likely “commensalism” because we do not know effect on humans
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + +
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Some associations in the human microbiome appear to be mutualistic
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Questions about the Human Microbiome • Who is there? • How do they vary? • What are they doing? • How do they go wrong? • How do we fix this? • Today we focus on three stories
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 1: The Obese Mouse
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 1: The Obese Mouse
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Human Microbiome Involved in Many Functions
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Human Microbiome Involved in Many Functions • Digestion • Vitamin Production • Protection from parasites / pathogens • Metabolic rate • Immune regulation • Odor • Tumor development • Behavior and mood
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 2: Disturbing the Microbiome Antibiotics Diet Changes Hygiene C-sections Story 2: Disturbing the Microbiome (vs expected)
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • ` I Contain Multitudes Video from Tangled Bank Studios
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Story 3: Restoring the Microbiome • C-section story is an example of attempting to restore a disturbed microbiome • Many other examples
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Restoring the Microbiome: Probiotics and Prebiotics
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Restoring the Microbiome: Coprophagia
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Restoring the Microbiome: Transfaunation • http://4.bp.blogspot.com/-ojOdQeA56Fk/ UDUTQsasvRI/AAAAAAAAhtg/ aWotjwTeT4c/s1600/Untitled2.jpg
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Restoring the Microbiome: Last Example … • Clostridium difficile • Can cause persistent GI infections • Antibiotics frequently do not help • People can have this for decades • Kills 30,000+ per year in US • Spore forming member of Firmicutes group
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria: Firmicutes • Gram positive • Some produce endospores • Many of agricultural and industrial use • Some have no cell wall and are extremely small • Includes causes of: • Anthrax • MRSA • Botulism • Tetanus Mycoplasmas • C. diff
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Restoring the Microbiome: Last Example … • Clostridium difficile • Can cause persistent GI infections • Antibiotics frequently do not help • People can have this for decades • Kills 30,000+ per year in US • Spore forming member of Firmicutes group So what can one do?
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Restoring the Microbiome: Fecal “transplants” FECAL TRANSPLANTS
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Openbiome
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 DIY Fecal Transplant
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 DIY Fecal Transplant
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Proceed With Caution …
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Microbiomes • Microbiomes are everywhere • Major impact of health and well being of many species • 100s of faculty at UC Davis work on microbiomes of various kinds
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 !11: Viruses and Gene Transfer !12: Mutualisms and Microbiomes !13: Endosymbiosis and Organelles Lecture 12 Context
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Good Luck on the Test Lecture 12 Context

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