2012 03-07 home microbiome - gsc13 china

DANIEL SMITH ARGONNE NATIONAL LABORATORY

YOUR MICROBIOTA

10 bacterial cells for

every human cell.

Human health is

dependent on

microbiota

YOUR MICROBIOTA

Science, 2009

YOUR MICROBIOTA

Nature Reviews Microbiology, 2011

YOUR HOME’S MICROBIOME

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.

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.

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.

WHEN BIOMES COLLIDE

+ = ?

FIELD STUDY

Monitoring the home and human microbiota

of relocating “citizen scientists”.

SAMPLING

Human:

Palm of hand

Heel of foot

Inside of nose

House:

Kitchen countertop

Kitchen floor

Kitchen light switch

Bedroom floor

Front door knob

Bathroom door knob

HOME METADATA

Type of paint on walls

Countertop material

Type of flooring

Light intensity

HVAC system

Pets in household

Square footage

DAILY METADATA

Placed five-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.

DATA LOGGER DATA Temperature Rel. Humidity Dew Point

Bathroom

Bedroom

Kitchen

76 RH

65 RH

54 RH

43 RH

32 RH

47 RH

38 RH

28 RH

40 RH

32 RH

24 RH

36 °C

28 °C

20 °C

12 °C

4 °C

20 °C

12 °C

4 °C

20 °C

12 °C

4 °C

ANALYSIS

PCR-Amplify 16S rDNA V4-V5 Region

↓

Sequence 150bp x2 (paired end)

↓

QIIME Phylogenetic Assignment

↓

Principle Coordinate Analysis

ALPHA DIVERSITY

ALPHA DIVERSITY

Most Diverse: Nose, hand, and hand-

contact surfaces in house #1.

Most Diverse House: House 1, followed by

2, then 3.

0 20 40 60 80 100 120 140 160

Foot

Kitchen_Counter

Nose

Bedroom_Floor

Hand

Bathroom_Door_Knob

Kitchen_Light_Switch

Kitchen_Floor

Bathroom_Floor

Front_Door_Knob

Observed Species (average)

0%

10%

20%

30%

40%

50%

0%

20%

40%

60%

80%

HOUSE 1 RESULTS

Foot Nose Hand

Bedroom

Floor

Kitchen

Floor

Kitchen

Counter

Kitchen

Light

Switch

Bathroom

Door Knob

Front Door

Knob

% T

ota

l P

op

ula

tion

%

Tota

l P

op

ula

tion

Tim

e

0%

10%

20%

30%

40%

50%

1 5 9 13

Staphylococcaceae

Mycoplasmataceae

Moraxellaceae (A)

Corynebacteriaceae

Streptophyta

Moraxellaceae (B)

Streptococcaceae

Actinomycetales

Pseudomonadaceae

0%

10%

20%

30%

40%

50%

60%

0%

20%

40%

60%

80%

100%

HOUSE 2 RESULTS

Foot Nose Hand Foot Nose Hand

Person 1 Person 2

Bedroom

Floor

Kitchen

Floor

Kitchen

Counter

Kitchen

Light

Switch

Bathroom

Door Knob

Front Door

Knob

0%

50%Staphylococcaceae Mycoplasmataceae Moraxellaceae (A)

Corynebacteriaceae Streptophyta Moraxellaceae (B)

Streptococcaceae Actinomycetales Pseudomonadaceae

0%

20%

40%

60%

80%

100%

HOUSE 3 RESULTS

0%

20%

40%

60%

80%

Bedroom

Floor

Kitchen

Floor

Kitchen

Counter

Kitchen

Light

Switch

Bathroom

Door Knob

Front Door

Knob

Foot Nose

Person 1

Foot Nose Hand

Person 2

Foot Nose Hand

Person 3

Hand

0%

50%Staphylococcaceae Mycoplasmataceae Moraxellaceae (A)

Corynebacteriaceae Streptophyta Moraxellaceae (B)

Streptococcaceae Actinomycetales Pseudomonadaceae

3D PRINCIPLE COORDINATE

PLOTS

HAND MICROBIAL COMMUNITIES

Individuals from

different houses Individuals from the same

house

BEDROOM FLOORS

KITCHEN COUNTERS

KITCHEN FLOORS

LIVE UPDATES

HomeMicrobiome.com

Facebook.com/HomeMicrobiome

Twitter.com/HomeMicrobiome

All data publicly

available

ACKNOWLEDGEMENTS

Jack Gilbert – P.I.

Jarrad Hampton-Marcell – Sample Preps

Sarah Owens – Sequencing Manager

Alfred P. Sloan Foundation - Funding