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The Effect of Geographic Location on the Composition and Function of Indoor
Microbes
Shelly L. Miller
Outline
• 1200 US homes (Barberán et al. 2015 Proc R Soc B)• Cross sectional study
• 15 Boulder CO homes (Emerson et al. 2016 Indoor Air)
• Longitudinal study
• CU Boulder Dorm Rooms (Luongo et al. 2016 Indoor Air)• 2.5 – 12 month study
• Boulder CO Flood (Emerson et al. 2015 Environ Sci Technol)
• One month study
1200 US homes (Barberán et al. 2015 Proc R Soc B)
If you want to change the types of fungi you are exposed to in your home, then it is best to move to a different home (preferably one far away). If you want to change your bacterial exposures, then you just have to change who you live with in your home.
Outer and inner main door trim as passive dust collector
1,500 samples collected
Barberán et al. 2015. PNAShomes.yourwildlife.org
Indoor communities were distinct from those found outdoors
Barberán et al. 2015. Proc. Royal Soc. B.
BACTERIA FUNGI
inside outsideinsideoutside
Indoor communities had greater diversity
Barberán et al. 2015. Proc. Royal Soc. B.
BACTERIA FUNGI
inside outsideinsideoutside
Indoor and outdoor samples harbored distinct microbial communities
Barberán et al. 2015. Proc. Royal Soc. B.
BACTERIA FUNGI
outside
inside
AspergillusFusariumPenicilliumEurotium
Common household molds
Wood‐degraders
Human skin associated
Fungi more common inside homes:
MalasseziaTrichosporon
StereumTrametesSchizophyllumChaetomium
Skin
Chloroplast
Stool
Soil
Insect
Sea
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100
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0
10
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0
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0.01 0.10 0.25 0.50 1.00Proportion
Num
ber o
f sam
ples
Bacteria found indoors are more likely to come from home occupants
indooroutdoor
FUNGI
BACTERIA
Outdoor environment strongly influences indoor fungi (predicable by soil, climate, geography)
FUNGI
Home occupants structure indoor bacterial communities (not predicable by soil, climate, geography)
BACTERIA
15 Boulder CO homes (Emerson et al. 2016 Indoor Air)
most airborne bacterial communities in homes are just as different a few weeks apart as they are many months apart.
16
Outdoor and indoor airborne particles actively sampled with additional environmental variables
15 homes x 2 days per season x 4 seasons = 120 samples
Home air contains spore formers (e.g., Bacilli) and human skin, mouth, and gut bacteria (e.g., Comamonadaceae, Prevotella, and Veillonella)
What bacteria are we inhaling indoors, and how do they vary over time?
17
B.
Actinobacteria
Alphaproteobacteria
Gammaproteobacteria
Betaproteobacteria
Bacilli
Clostridia
Saprospirae
Cytophagia
Thermoleophilia
Bacteroidia
Most Variable Indoor Air (Home K) Least Variable Indoor Air (Home Q)100
80
60
0
40
20
100
80
60
40
20
0
Rela
tive
Abu
ndan
ce (%
)
Rela
tive
Abu
ndan
ce (%
)
1/15/1
3
Date Date
5/3/1
36/1
0/13
7/12/1
38/2
0/13
9/26/1
311/1
/13
1/18/1
32/1
9/13
4/15/1
35/2
6/13
7/22/1
39/1
/13
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Highest temporal variability
Figure 2
0.7
0.8
0.9
1.0
Bray
-Cur
tis D
issi
mila
rity
K J N P H G E R C A M D F B Q
indoor air
outdoor air
A.
Home
Highest temporal variability
CU Boulder Dorm Rooms (Luongo et al. 2016 Indoor Air)
By examining the abundances of bacterial genera, we can predict the sex of room occupants.
Passively sampled indoor dust over 2.5 months
Actively sampled fan coil unit air over 1 year
Lactobacillus
Corynebacterium
qPCR
Boulder CO Flood (Emerson et al. 2015 Environ SciTechnol)
The impact of flooding is persistent. Bacterial and fungal community composition, and fungal abundances, are different in flooded homes despite remediation.
2013 Colorado Front Range flood
25
Passive Dust Sampler
Study Basements
Study Homes in South Boulder
26HVAC Filter
Emerson et al., 2015
Are microbial communities different in flooded homes? YES
p = 0.004p = 0.001
FUNGIBACTERIA
FloodedNot Flooded
Are microbial abundances different in flooded homes? YES
Flooded homes 76% higher (not statistically significant, p = 0.2)
Flooded homes 210% higher (significant, p = 0.01)
Emerson et al., 2015
Univ. of Colorado Albert BarberánJoanne EmersonNoah FiererJessica HenleyPat Keady Jon LeffJulia LuongoShelly Miller
North Carolina State Univ.Rob DunnHolly Menninger
Funding provided by:National Science FoundationA.P. Sloan FoundationPersonal Genome ProjectJames. S. McDonnell Foundation
References• Barberán, Albert, Robert R. Dunn, Brian J. Reich, Krishna Pacifici, Eric B. Laber, Holly L. Menninger, James M. Morton et al. "The ecology of microscopic life in household dust." In Proc. R. Soc. B, vol. 282, no. 1814, p. 20151139. The Royal Society, 2015.
• Emerson, Joanne B., Patricia B. Keady, Tess E. Brewer, Nicholas Clements, Emily E. Morgan, Jonathan Awerbuch, Shelly L. Miller, and Noah Fierer. "Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood." Environmental science & technology 49, no. 5 (2015): 2675‐2684.
• Emerson, Joanne B., Patricia B. Keady, Nicholas Clements, Emily E. Morgan, Jonathan Awerbuch, Shelly L. Miller, and Noah Fierer. ”High temporal variability in airborne bacterial diversity and abundance inside single‐family residences." Indoor Air (2016).
• Luongo, Julia C., Albert Barberán, Robin Hacker‐Cary, Emily E. Morgan, Shelly L. Miller, and Noah Fierer. "Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants." Indoor air (2016).
