2012 03-07 home microbiome - gsc13 china

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initial findings of the Home Microbiome Study.

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2012 03-07 home microbiome - gsc13 china

  1. 1. DANIEL SMITHARGONNE NATIONAL LABORATORY
  2. 2. YOUR MICROBIOTA 10bacterial cells for every human cell. Human health is dependent on microbiota
  3. 3. YOUR MICROBIOTA Science, 2009
  4. 4. YOUR MICROBIOTA Nature Reviews Microbiology, 2011
  5. 5. YOUR HOME’S MICROBIOME
  6. 6. YOUR HOME’S MICROBIOME Building-specific seasonal patterns in bacteria found on dust. In-progress research is exploring the microbial communities of several locations in houses: kitchen surfaces (including inside the refrigerator), tv screens, pillows, the water inside of water heaters, etc, etc.
  7. 7. INTERACTION OF MICROBIOMES Human shed about 1.5 millions cells per hour, along with their associated 15 million bacteria cells. Direct contact can transfer millions of cells in each event.
  8. 8. INTERACTION OF MICROBIOMES There is a lack of evidence regarding how rapidly the human skin microbiota is transferred to the surfaces of the homes in which we live. Hypotheses:  Microbes from the occupant are transferred rapidly to the home and replace existing communities.  The occupant’s microbiome is reflected by the home’s microbiome.  Bacteria on surfaces will be most similar to the bacteria on the body parts that come into contact with it.
  9. 9. WHEN BIOMES COLLIDE ? + =
  10. 10. FIELD STUDY Monitoring the home and human microbiota of relocating “citizen scientists”.
  11. 11. SAMPLING  Human:  House:  Palm of hand  Kitchen countertop  Heel of foot  Kitchen floor  Inside of nose  Kitchen light switch  Bedroom floor  Front door knob  Bathroom door knob
  12. 12. HOME METADATA Type of paint on walls Countertop material Type of flooring Light intensity HVAC system Pets in household Square footage
  13. 13. DAILY METADATA Placedfive-minute interval data loggers in the bathroom, kitchen, and bedroom to track:  Relative Humidity  Temperature  Dew Point Participants also fill out the form at right each time they collect samples.
  14. 14. DATA LOGGER DATA Temperature Rel. Humidity Dew Point 36 °C 76 RH Bathroom 28 °C 65 RH 20 °C 54 RH 12 °C 43 RH 4 °C 32 RH Bedroom20 °C 47 RH12 °C 38 RH 4 °C 28 RH Kitchen 20 °C 40 RH 12 °C 32 RH 4 °C 24 RH
  15. 15. ANALYSIS PCR-Amplify 16S rDNA V4-V5 Region ↓ Sequence 150bp x2 (paired end) ↓ QIIME Phylogenetic Assignment ↓ Principle Coordinate Analysis
  16. 16. ALPHA DIVERSITY
  17. 17. ALPHA DIVERSITY Most Diverse: Nose, hand, and hand- contact surfaces in house #1. Most Diverse House: House 1, followed by 2, then 3. Front_Door_Knob Bathroom_Floor Kitchen_Floor Kitchen_Light_Switch Bathroom_Door_Knob Hand Bedroom_Floor Nose Kitchen_Counter Foot 0 20 40 60 80 100 120 140 160 Observed Species (average)
  18. 18. HOUSE 1 RESULTS Staphylococcaceae Hand Nose Foot 50% Mycoplasmataceae 50%% Total Population Moraxellaceae (A) 40% 40% 30% Corynebacteriaceae 30% Streptophyta 20% 20% 10% Moraxellaceae (B) 10% 0% Streptococcaceae Actinomycetales 1 5 9 13 0% Pseudomonadaceae Bedroom Kitchen Kitchen Kitchen Bathroom Front Door Floor Floor Counter Light Door Knob Knob % Total Population 80% Switch 60% 40% 20% 0% Tim e
  19. 19. HOUSE 2 RESULTS Person 1 Person 2 Hand Nose Foot Hand Nose Foot100%80%60%40%20% 0% Bedroom Kitchen Kitchen Kitchen Bathroom Front Door Floor Floor Counter Light Door Knob Knob60% Switch50%40%30%20%10% 0% Staphylococcaceae 50% Mycoplasmataceae Moraxellaceae (A) Corynebacteriaceae Streptophyta Moraxellaceae (B) Streptococcaceae 0% Actinomycetales Pseudomonadaceae
  20. 20. HOUSE 3 RESULTS Person 1 Person 2 Person 3 Hand Nose Foot Hand Nose Foot Hand Nose Foot100%80%60%40%20% 0% Bedroom Kitchen Kitchen Kitchen Bathroom Front Door Floor Floor Counter Light Door Knob Knob 80% Switch 60% 40% 20% 0% Staphylococcaceae 50% Mycoplasmataceae Moraxellaceae (A) Corynebacteriaceae Streptophyta Moraxellaceae (B) Streptococcaceae 0% Actinomycetales Pseudomonadaceae
  21. 21. 3D PRINCIPLE COORDINATEPLOTS
  22. 22. HAND MICROBIAL COMMUNITIESIndividuals fromdifferent houses Individuals from the same house
  23. 23. BEDROOM FLOORS
  24. 24. KITCHEN COUNTERS
  25. 25. KITCHEN FLOORS
  26. 26. LIVE UPDATES HomeMicrobiome.com Facebook.com/HomeMicrobiome Twitter.com/HomeMicrobiome Alldata publicly available
  27. 27. ACKNOWLEDGEMENTS Jack Gilbert – P.I. Jarrad Hampton-Marcell – Sample Preps Sarah Owens – Sequencing Manager Alfred P. Sloan Foundation - Funding

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