Downloaded 224 times
Uploaded byJonathan Eisen
BIS2C: Lecture 13: The Human Microbiome
The document summarizes a lecture on the human microbiome. It discusses how humans are colonized by vast numbers of microbes, forming complex microbial ecosystems. There is enormous variation in microbiome composition both within and between individuals, and this variation is associated with health states and phenotypes. Research has identified some possible causes of microbiome variation and suggests it may be possible to alter or restore microbiome composition.
More Related Content
Similar to BIS2C: Lecture 13: The Human Microbiome
BIS2C: Lecture 13: The Human Microbiome
- 1. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Lecture 13: The Human Microbiome BIS 002C Biodiversity & the Tree of Life Spring 2016 Prof. Jonathan Eisen 1
- 2. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Where we are going and where we have been • Previous Lecture: !12: Novelty • Current Lecture: !13: The Human Microbiome • Next Lecture: !14: Big Organisms 2
- 3. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Key Concepts and Outline • Humans are swarming with microbes • Microbiomes are Complex Ecosystems • Enormous Variation within & between People • Variation is Associated with Various Health States and Phenotypes • Possible Causes of the Variation Have Been Identified • It May Be Possible to Alter / Restore the Microbiome 4
- 4. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 5
- 5. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 6
- 6. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 The Human Microbiome 7
- 7. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Summer 2012 Workshop in Biology and Multimedia for High School Teachers Microbes are all over us 8 http://commons.wikimedia.org/wiki/ File:Man_shadow_-_upper.png Thousands of different species on the skin alone Some thrive on dry patches of the elbow, others thrive in moist environment of armpit There are millions of microbes per square inch on your body It is estimated that there are more microbes in your intestine than there are human cells in your body!
- 8. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Who Are We? 9
- 9. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Who Are We? 10 50
- 10. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 microBIOME or microbiOME • microbi-OME !collection of genomes of microbes from a community (emphasis on OME) • micro-BIOME !a community of microbes (emphasis on BIOME) • see http://tinyurl.com/definemicrobiome 11
- 11. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Clicker 12
- 12. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Clicker Which of the following lineages contain microbes? A: Bacteria B: Archaea C: Eukaryotes D: All of the above E: None of the above 13
- 13. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Clicker Which of the following lineages contain microbes? A: Bacteria B: Archaea C: Eukaryotes D: All of the above E: None of the above 14
- 14. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 The Rise of the Microbiome 15 0 350 700 1050 1400 00 01 02 03 04 05 06 07 08 09 10 11 12 Pubmed “Microbiome” Hits
- 15. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 16 Why All The Attention for Commensalism?
- 16. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 17 Is this Mutualism?
- 17. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 18 Is this Parasitism?
- 18. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 19 Some of Each
- 19. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Why Now? Studies Like This … 20 Turnbaugh et al Nature. 2006 444(7122):1027-31.
- 20. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Microbiome Involved in Many Functions • Digestion • Vitamin Production • Protection from parasites / pathogens • Metabolic rate • Immune regulation • Odor • Behavior 21
- 21. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 22 Why Now II: DNA Sequencing Advances
- 22. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Great Plate Count Anomaly 23 <<<< Culturing Observation CountCount http://www.google.com/url? sa=i&rct=j&q=&esrc=s&source=images&c d=&docid=rLu5sL207WlE1M&tbnid=CRLQ YP7d9d_TcM:&ved=0CAUQjRw&url=http %3A%2F%2Fwww.biol.unt.edu %2F~jajohnson %2FDNA_sequencing_process&ei=hFu7U_ TyCtOqsQSu9YGwBg&psig=AFQjCNG-8EB dEljE7- yHFG2KPuBZt8kIPw&ust=14048739512114 24 DNA or RNA
- 23. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Archaea Woese Classification of Cultured Taxa by rRNA 24 rRNA rRNArRNA ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG EukaryotesBacteria Carl Woese
- 24. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 25 rRNA Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New ACCCCAGCTCTGCCTCG EukaryotesBacteria Archaea Culture Independent Studies ACTGC ACCTAT CGTTCG ACTGC ACCTAT CGTTCG ACTGC ACCTAT CGTTCG Many sequences from one sample all point to the same branch on the tree Norm Pace
- 25. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 26 DNA Taxa Characters B1 ACTGCACCTATCGTTCG B2 ACTCCACCTATCGTTCG E1 ACTCCAGCTATCGATCG E2 ACTCCAGGTATCGATCG A1 ACCCCAGCTCTCGCTCG A2 ACCCCAGCTCTGGCTCG New1 ACCCCAGCTCTGCCTCG New2 AGGGGAGCTCTGCCTCG New3 ACTCCAGCTATCGATCG New4 ACTGCACCTATCGTTCG EukaryotesBacteria Archaea ACTGC ACCTAT CGTTCG ACTCC AGCTAT CGATCG ACCCC AGCTCT CGCTCG AGGGG AGCTCT CGCTCG AGGGG AGCTCT CGCTCG ACTGC ACCTAT CGTTCG Even with more taxa it still works Culture Independent Studies
- 26. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Metagenomics Has Many Other Purposes 27 metagenomics ACUGC ACCUAU CGUUCG ACUCC AGCUAU CGAUCG ACCCC AGCUCU CGCUCG Taxa Characters S ACUGCACCUAUCGUUCG R ACUCCACCUAUCGUUCG E ACUCCAGCUAUCGAUCG F ACUCCAGGUAUCGAUCG C ACCCCAGCUCUCGCUCG W ACCCCAGCUCUGGCUCG inputs of fixed carbon or nitrogen from external sources. As with Leptospirillum group I, both Leptospirillum group II and III have the genes needed to fix carbon by means of the Calvin–Benson– Bassham cycle (using type II ribulose 1,5-bisphosphate carboxy- lase–oxygenase). All genomes recovered from the AMD system contain formate hydrogenlyase complexes. These, in combination with carbon monoxide dehydrogenase, may be used for carbon fixation via the reductive acetyl coenzyme A (acetyl-CoA) pathway by some, or all, organisms. Given the large number of ABC-type sugar and amino acid transporters encoded in the Ferroplasma type Figure 4 Cell metabolic cartoons constructed from the annotation of 2,180 ORFs identified in the Leptospirillum group II genome (63% with putative assigned function) and 1,931 ORFs in the Ferroplasma type II genome (58% with assigned function). The cell cartoons are shown within a biofilm that is attached to the surface of an acid mine drainage stream (viewed in cross-section). Tight coupling between ferrous iron oxidation, pyrite dissolution and acid generation is indicated. Rubisco, ribulose 1,5-bisphosphate carboxylase–oxygenase. THF, tetrahydrofolate. articles NATURE | doi:10.1038/nature02340 | www.nature.com/nature 5©2004 NaturePublishing Group
- 27. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Clicker 28
- 28. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Clicker How could you tell if one of the rRNA genes you sequence came from a chloroplast? A: It should group in rRNA trees with plant nuclear rRNA genes. B: It should group in rRNA trees with proteobacteria. C: It should group in rRNA trees with cyanobacteria. D. It should group in rRNA trees with TACK E: You can’t tell. 29
- 29. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Clicker How could you tell if one of the rRNA genes you sequence came from a chloroplast? A: It should group in rRNA trees with plant nuclear rRNA genes. B: It should group in rRNA trees with proteobacteria. C: It should group in rRNA trees with cyanobacteria. D. It should group in rRNA trees with TACK E: You can’t tell. 30
- 30. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 How could you tell if one of the rRNA genes you sequence came from a mitochondrion? 31
- 31. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 How could you tell if one of the rRNA genes you sequence came from a fungus? 32
- 32. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Key Concepts and Outline • Humans are swarming with microbes • Microbiomes are Complex Ecosystems • Enormous Variation within & between People • Variation is Associated with Various Health States and Phenotypes • Possible Causes of the Variation Have Been Identified • It May Be Possible to Alter / Restore the Microbiome 33
- 33. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 The Human Microbiome 34
- 34.
- 35. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Key Concepts and Outline • Humans are swarming with microbes • Microbiomes are Complex Ecosystems • Enormous Variation within & between People • Variation is Associated with Various Health States and Phenotypes • Possible Causes of the Variation Have Been Identified • It May Be Possible to Alter / Restore the Microbiome 36
- 36. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 37
- 37. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 38
- 38. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 39
- 39. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Variation Between Countries: Gut 40 The ISME Journal (2013) 7, 85–95; doi:10.1038/ismej.2012.81 MJ Blaser et al. ISMEJ 2012 US Amerindian Actinobacteria (Propionibacteria) Firmicutes (Staphylococcus) Relativeabundance Actinobacteria dominates in the US Boulder NY Platanillal A Platanillal B Proteobacteria
- 40. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Variation Between Countries: Gut 41 The ISME Journal (2013) 7, 85–95; doi:10.1038/ismej.2012.81 MJ Blaser et al. ISMEJ 2012 US Amerindian Actinobacteria (Propionibacteria) Firmicutes (Staphylococcus) Relativeabundance Actinobacteria dominates in the US Boulder NY Platanillal A Platanillal B Proteobacteria
- 41. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Variability Across People 42Huttenhower et al. 2012.
- 42. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Key Concepts and Outline • Humans are swarming with microbes • Microbiomes are Complex Ecosystems • Enormous Variation within & between People • Variation is Associated with Various Health States and Phenotypes • Possible Causes of the Variation Have Been Identified • It May Be Possible to Alter / Restore the Microbiome 43
- 43. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Variability is Correlated to Many Health States • Microbial community different in many disease states compared to healthy individuals • Unclear if this is cause or effect in most cases 44
- 44. !45 Morgan et al.Genome Biology 2012 13:R79 doi:10.1186/gb-2012-13-9-r79
- 45. !46 Morgan et al.Genome Biology 2012 13:R79 doi:10.1186/gb-2012-13-9-r79 Age Diet Location Many disease states ExposurePregnant? Breast fed? Obese
- 46. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Microbiome Involved in Many Functions • Digestion • Vitamin Production • Protection from parasites / pathogens • Metabolic rate • Immune regulation • Odor • Behavior 47
- 47. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Key Concepts and Outline • Humans are swarming with microbes • Microbiomes are Complex Ecosystems • Enormous Variation within & between People • Variation is Associated with Various Health States and Phenotypes • Possible Causes of the Variation Have Been Identified • It May Be Possible to Alter / Restore the Microbiome 48
- 48. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Infant Microbiome, Birth, and Milk 49 David Mills
- 49. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Other Sources 50
- 50. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Disturbing the Microbiome 51 Antibiotics Diet Changes Hygiene Hypothesis C-sections
- 51. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 C-Sections Alter “Normal” Colonization 52 Maria Gloria Dominguez-Bello
- 52. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Diet Changes Alter Microbiome 53 Switch to solid foods
- 53. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Response to Antibiotics 54 illustrated by the communities of subjects 14, 15, 16, 18, and 19 that appeared to be comparatively stable over time, whereas others such as subjects 11 and 27 commonly shifted to different community types that were more often associated with higher Nugent scores. The underlying The rapid and sometimes extensive turnover of human vaginal bacte- rial communities was visualized by mapping temporal changes in community composition onto the three-dimensional (3D) community space defined previously in a cross-sectional study by Ravel et al. of A B DC Subject 24 0 20 40 60 80 100 Phylotyperelativeabundance(%) L. crispatus L. iners L. jensenii Staphylococcus L. gasseri Corynebacterium Clostridium Lactobacillales 2 L. vaginalis L. otu5 Subject 29 0 20 40 60 80 100 Phylotyperelativeabundance(%) Subject 6 0 20 40 60 80 100 Phylotyperelativeabundance(%) L. iners Atopobium Sneathia Corynebacterium Gemella Finegoldia Prevotella Peptostreptococcus Peptoniphilus Anaerococcus Streptococcus Parvimonas Staphylococcus Subject 12 0 20 40 60 80 100 Phylotyperelativeabundance(%) Time (weeks) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Time (weeks) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Time (weeks) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Time (weeks) 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 Phylotypes L. crispatus L. iners L. gasseri StaphylococcusL. jensenii Atopobium Prevotella Aerococcus Anaerococcus Streptococcus Clostridium ParvimonasGardnerella Mobiluncus Corynebacterium Gemella Finegoldia Peptostreptococcus Peptoniphilus L. otu5Lactobacillales 2 L. otu3 L. vaginalis L. otu4Sneathia 80 100 Phylotype percent relative abundance 0 20 40 60 L. crispatus Streptococcus L. reuteri Bifidobacterium Anaerococcus Prevotella Finegoldia Peptostreptococcus Escherichia Alloscardovia Atopobium Prevotella Parvimonas Peptoniphilus Sneathia Mobiluncus Lachnospiraceae 10 Ruminococcaceae 3 Gardnerella Lachnospiraceae 11 Aerococcus Moryella Peptococcus Lachnospiraceae 2 Anaerococcus Allisonella Peptostreptococcus Megasphaera Lachnospiraceae 10 Ruminococcaceae 3 Lachnospiraceae 11Moryella PeptococcusLachnospiraceae 2 Allisonella Megasphaera L. reuteri Bifidobacterium Escherichia Alloscardovia onMay2,2012stm.sciencemag.orgDownloadedfrom
- 54. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Hygiene Hypothesis 55 Susan Lynch Dogs, Dust, Microbiomes and Asthma
- 55. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Key Concepts and Outline • Humans are swarming with microbes • Microbiomes are Complex Ecosystems • Enormous Variation within & between People • Variation is Associated with Various Health States and Phenotypes • Possible Causes of the Variation Have Been Identified • It May Be Possible to Alter / Restore the Microbiome 56
- 56. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Microbiome Transplant 57
- 57. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Restoring the Microbiome: Probiotics and Prebiotics 58
- 58. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Intestinal Transplant 59 Hartman et al. PNAS 2009
- 59. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Coprophagia 60
- 60. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Transfaunation 61
- 61. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Fecal “transplants” 62
- 62. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 Openbiome 63
- 63. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 DIY Fecal Transplant 64
- 64. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 65 DIY Fecal Transplant
- 65. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 66
- 66. Slides by JonathanEisen for BIS2C at UC Davis Spring 2014 66
- 67. Slides by JonathanEisen for BIS2C at UC Davis Spring 2016 Get Involved 67 Kitty Microbiome