Neufeld erin 2012 for posting


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Extended Learning Opportunities talk, Feb 23, 2012. Josh Neufeld.

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Neufeld erin 2012 for posting

  1. 1. Our bodies, our microbes, ourselves jneufeld@uwaterloo.caExtended Learning Opportunities Erin, Ontario Feb 23, 2012 Twitter @JoshDNeufeld
  2. 2. Linking function and phylogenyStable-isotope probing and metagenomics Carbon cycling and biofuel bugs Discovery of novel N-cycle players Denitrification Nitrification Anammox Diversity of microbial communitiesFactors (pH, latitude), human microbiome Rare members, undetected organisms Method development
  3. 3. Today’s lecture – an overview Microbial ecology Why is this so hard to study? Microbiology of youWhat’s in you and why does it matter?
  4. 4. Thanks Handelsman  J.  2007.  Encyclopedia  of  Life  Sciences  
  5. 5. 1021 Number of stars in the Universe1031 Number of microbial cells on Earth1011 Stars in the Milky Way1015 Microbial cells with each human1014 Human cells with each human1010 Microbial cells per gram of soil106 Microbial cells per mL of seawater107 Viral particles per mL of seawater Microbial World
  6. 6. I then most always saw,with great wonder, that inthe said matter there were h9p://  many very little livinganimalcules, very prettilya-moving.
  7. 7. Carl Woese, Professor of Microbiology atthe University of Illinois at Urbana-ChampaignOne of the first to use the sequences of ribosome genes for taxonomy Bacterial taxonomybecame “a field freshwith the excitement of the experimental harvest”
  8. 8. 16S  rRNA  genes   Why  so  ubiquitous  for  microbial  ecology  studies?  “The  small  subunit  ribosomal  RNA  genes  were  ideal  because  of  their   universal  distribu.on,  structural  conserva.on,  the  presence  of   conserved  and  variable  regions,  and  resistance  to  lateral  gene   transfer”  Neufeld  and  Mohn  (2005)  
  9. 9. CharacterizaWon  of  microbial  isolates   universal  phylogeneWc  tree   PROKARYOTES   EUKARYOTES   You   Bacteria   Archaea   Eukarya   are   here.   Animals   Entamoebae   Slime Green nonsulfur molds   bacteria   Euryarchaeota   Fungi   Mitochondrion   Methanosarcina   Methano- Extreme Plants   Gram- Crenarchaeota   bacterium   halophiles   Proteobacteria   positive Thermoproteus   bacteria   Methano- Ciliates   Chloroplast   Pyrodictium   coccus   Thermoplasma   Cyanobacteria   Thermococcus  Flavobacteria   Flagellates   Marine Pyrolobus   Crenarchaeota   Methanopyrus   Trichomonads   Thermotoga Thermodesulfobacterium Microsporidia   Aquifex Diplomonads Universal (Giardia)   ancestor  
  10. 10. Sampling  microbial  communiWes   Sampling  microbial   irds   Costa  Rica  b communiWes  is  akin  to   sampling  diverse   communiWes  from   other  areas  of  biology.     Sampling  is  usually  done   by  capturing   sequences  rather  than   capturing  organisms.  Hughes  et  al.  2001   Problem?  
  11. 11. Today’s lecture – an overview Microbial ecology Why is this so hard to study? Microbiology of youWhat’s in you and why does it matter?
  12. 12. Who are we? What we’ve learned from ribosomal RNA surveys of our bodies and the environment.Image  by  Feel  MysWc  
  13. 13. DISCLAIMERNo medical advice in this talk.
  14. 14. There are more bacteria in your gut than there are people on the planet.
  15. 15. 10  ba cteria l  cells  :  1  hu man  c ell  
  16. 16. 1 g of feces = 1 million bacteria Every surface of our body is a niche for microbes 90% microbe, 10% human 100X more microbial genes than human genes Humans are like “spaceships” for our bugsOur microbial fingerprint is unique
  17. 17. LocaWon,  locaWon,  locaWon   Mouth:  saliva,  tongue,  mucosal  surfaces,   teeth  and  gums  (700  species;  10  phyla)   Esophagus:  microbes  from  oral  cavity  and   upper  respiratory  tract  (95  species;  6  phyla)   Stomach:  low  numbers;  lactobacilli,   streptococci,  H.  pylori  (128  species;  8  phyla)   Small   -­‐   duodenum:  not  opWmal  to  colonize   -­‐   jejunum:  increase  in  streptococci,   lactobacilli,  Haemophilus,  Bacteroides,  and   Bifidobacteria   -­‐   ileum:  increased  numbers,  resembles  colon       Large  (colon):   -­‐   Lumen:  anaerobes:aerobes  100-­‐1000:1   -­‐   Bacteroides,  Bifido,  Clostridium,  Bacillus,   Fusobacterium  (800  species;  10  phyla)  
  18. 18. What role do microorganismsplay in your body?
  19. 19. Sterile at birthColonization beginsimmediately
  20. 20. “Adult”community by 1 year
  21. 21. Peas  and  formula   ?   AnWbioWcs   Koeniga  et  al.  2011  
  22. 22. Mouth 2 3 1 Supragingival plaque L1 4 2 Subgingival plaque L 3 Supragingival plaque L 4 Supragingival plaque L 5 Tongue biofilm 5 Stomach 6 6 Gastric antrum 7 Gastric body 7 8 Duodenum 8 9 10 Colon 9 Transverse colon 11 10 Sigmoid colon 11 Rectum 12 Stool 12
  23. 23. a Tongue plaque Transverse Colon Sample site Tooth plaque Sigmoid Colon Phylum PC1 (7.9%) Gastric antrum Rectum Gastric body Stool Genus Duodenum Faecalibacterium Bacteroides Coprococcus Verrucomicrobia Campylobacter Blautia Fusobacterium Bacteriodetes Fusobacteria Prevotella Acidobacteria Cyanobacteria Firmicutes Proteobacteria TM7 Neisseria Capnocytophaga Haemophilus Spirochaetes Actinobacteria Streptococcus Veillonella SR1 Parvimonas PC1 (17.0%)b Sample location c Subject d Gender Mouth Stomach Subject 1 Duodenum Subject 2 Female Colon Subject 3 Male Stool Subject 4
  24. 24. Stomach/ Colon DuodenumMouth Stool 173 527 1523 33 578 6567 251 70 18 171 64 69 58 3 112 Subject 1
  25. 25. Women Men
  26. 26. Gut  Microbiome   Ley  et  al.  2006   Germ-­‐free  mouse   colonized  with  microbial   community  of  obese   mouse  or  lean  mouse.  Obese  mice   •  50%  lower  Bacteroidetes,  higher  Firmicutes   •  Weight  loss  =  increased  Bacteroidetes,   decreased  Firmicutes  Same  result  found  in  humans  (Turnbaugh  et  al.  2006)  
  27. 27. Depression
  28. 28. BehaviourPremysl  Bercik,  McMaster  University  (personal  communicaWon)  
  29. 29. “Intestinal dysbiosis might contribute to psychiatric disorders in patients with bowel disorders.”
  30. 30. Implications?
  31. 31. Probiotics "Live microorganisms which whenadministered in adequate amounts confer a health benefit on the host".
  32. 32. Fecal  transplants  have  >90%  success  rate  in  C.  difficile  associated  disease.      How  else  could  they  be  used?    "The  potenWal  is  very  high,  but  the  actual  amount  of  research  is  relaWvely  low”  -­‐Rob  Knight  Fecal transplants
  33. 33. What will wediscover next?
  34. 34. ?
  35. 35. ?
  36. 36. ?
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  42. 42. Gut  Microbiome  summary  Over  800  different  species,  7000  strains  Experimental  evidence  shows  implicaWons  in:  •  metabolism  of  carbohydrates  (obesity)  •  ulcers  and  Helicobacter  pylori  predominance  •  immune  system  (allergies,  asthma,  pathogen  defense)  •  synthesis  of  amino  acids  and  vitamins  •  deacWvaWng  xenobioWcs  (carcinogens)  •  response  to  epithelial  cell  injury  (by  pathogens)  •  colorectal  cancer  (2nd  leading  cause  of  cancer-­‐related  death)    •  inflammatory  bowel  diseases  (Crohn’s  and  coliWs)  •  possible  role  in  mulWple  sclerosis,  Parkinson’s  •  link  to  depression  and  behaviour  
  43. 43. Research  in   my  lab  seeks   to  answer  some  of  these   quesWons     IBS,   depression,   periodonWWs  Turnbaugh  et  al.  2007  
  44. 44. Hygiene  hypothesis  
  45. 45. "The human microbiome has been selected,and passed from mother to child, because thebacterial genes are helpful, but as a result ofmodern practices including widespreadantibiotics use, caesarean sections, amalgamdental fillings, constant cleansing, clean water,smaller families and transmission of thesenormal ancestral microbes has changed, andthere are consequences. Some consequencesmight be good, while others could be bad." Dr. Martin J. Blaser Professor of Microbiology NYU Langone Medical Center  
  46. 46. Implications Health and disease linked to microbesNovel treatments can come from microbesWith understanding, we can be in control What’s next? (invite your help)
  47. 47. Thank you jneufeld@uwaterloo.caExtended Learning Opportunities Erin, Ontario Feb 23, 2012 Twitter @JoshDNeufeld