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EXPLORING THE GREAT INDOORS The Built Environment & Human Health
Roxana Hickey, Ph.D.University of Oregon
September 7, 2016
@roxana_hickey
THE HUMAN MICROBIOME
9/7/16 © University of Oregon BioBE Center 2
THE HUMAN BODY IS
TEEMING WITH BACTERIA,
FUNGI, VIRUSES AND OTHER MICROBES
~39 TRILLION MICROBIAL
CELLS: ~1-3% OF TOTAL
BODY MASS
MOST FUNCTIONS OF HUMAN-ASSOCIATED MICROBES
STILL UNKNOWN
9/7/16 © University of Oregon BioBE Center 3Illustration: Charis Tsevis (flickr)
The microbiome & health
• Nutrition
• Protection against pathogens
• Allergies and immunity
• Disease and cancer
• Cognitive and mental health
Image: Charis Tsevis (flickr)9/7/16 © University of Oregon BioBE Center 4
MICROBES ALL AROUND US
9/7/16 5© University of Oregon BioBE Center
9/7/16 © University of Oregon BioBE Center 6
HUMANS SPEND UP TO 90% OF THEIR LIVES INDOORS
Photo: www.pexels.com
MICROBIOLOGY
EVOLUTIONARY ECOLOGY
ARCHITECTURE BUILDING SCIENCE
MECHANICAL ENGINEERING BIOLOGY
& THE BUILT ENVIRONMENT
CENTER
9/7/16 7© University of Oregon BioBE Center
MICROBIOLOGY
EVOLUTIONARY ECOLOGY
ARCHITECTURE BUILDING SCIENCE
MECHANICAL ENGINEERING BIOLOGY
& THE BUILT ENVIRONMENT
CENTER
9/7/16 8© University of Oregon BioBE Center
Dr. Jessica Green University of Oregon
Dr. Kevin Van Den Wymelenberg
University of Oregon
GZ Charlie Brown University of Oregon
MICROBIOLOGY
EVOLUTIONARY ECOLOGY
ARCHITECTURE BUILDING SCIENCE
MECHANICAL ENGINEERING BIOLOGY
& THE BUILT ENVIRONMENT
CENTER
9/7/16 9© University of Oregon BioBE Center
GOAL: OPTIMIZE THE DESIGN & OPERATION OF BUILDINGS TO PROMOTE HUMAN HEALTH &
ENVIRONMENTAL SUSTAINABILITY
9/7/16 10© University of Oregon BioBE Center
Illustration: Cameron Slayden (Cosmocyte) & BioBE
9/7/16 11© University of Oregon BioBE Center
Illustration: Cameron Slayden (Cosmocyte) & BioBE
HUMAN HEALTH
BUILDING DESIGN & ENERGY
MICROBIAL ECOLOGY
9/7/16 12© University of Oregon BioBE Center
Illustration: Cameron Slayden (Cosmocyte) & BioBE
HOW DOES THE DESIGN, USE, AND OCCUPANCY OF BUILDINGS INFLUENCE THE
INDOOR MICROBIOME?
9/7/16 13© University of Oregon BioBE Center
HOW DOES THE DESIGN, USE, AND OCCUPANCY OF BUILDINGS INFLUENCE THE
INDOOR MICROBIOME?
DESIGN Ventilation source in hospital rooms Kembel et al. ISME 2012 Architectural design of a university building Kembel et al. PLOS One 2014; Meadow et al. Indoor Air 2013
USE Human interaction with classroom surfaces Meadow et al. Microbiome 2014 Antimicrobials and resistance Hartmann et al. Environmental Science & Technology, in press
OCCUPANCY Human microbial cloud Meadow et al. PeerJ 2015
MEASURING MICROBES
9/7/16 14© University of Oregon BioBE Center
9/7/16 © University of Oregon BioBE Center 15
MICROBES CAN’T BE EASILY DIFFERENTIATED BY EYE
Photo: Scimat via GeVy Images
LESS THAN 1% OF MICROBIAL LIFE CAN BE CULTIVATED IN A PETRI DISH
9/7/16 16© University of Oregon BioBE Center
Photo: Tasha Sturm, Cabrillo College
Hug et al. Nature Microbiology (2016)
9/7/16 17© University of Oregon BioBE Center
Cultivation-independent workflow
9/7/16 © University of Oregon BioBE Center 18
Environmental sample
Extract and purify DNA
Amplify marker gene (16S rRNA)
Generate DNA sequences
Perform bioinformatic analyses
ARCHITECTURAL DESIGN INFLUENCES THE
MICROBIOME OF THE BUILT ENVIRONMENT
9/7/16 © University of Oregon BioBE Center 19
9/7/16 20© University of Oregon BioBE Center
HOW DOES VENTILATION SOURCE INFLUENCE THE AIR MICROBIOME IN HOSPITAL ROOMS?
Dr. Steven Kembel University of Quebec
9/7/16 © University of Oregon BioBE Center 21
PROVIDENCE MILWAUKIE HOSPITAL PORTLAND, OR
9/7/16 © University of Oregon BioBE Center 22!
WINDOW VENTILATION
MECHANICAL VENTILATION
OUTDOOR AIR
9/7/16 © University of Oregon BioBE Center 23
WINDOW VENTILATION
MECHANICAL VENTILATION
9/7/16 © University of Oregon BioBE Center 24
OUTDOOR AIR
Diversity varies with air source
9/7/16 © University of Oregon BioBE Center 25
Kembel et al. ISME (2012)
Less diverse communities had a higher proportion of taxa closely
related to human pathogens
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WINDOW
MECHANICAL
OUTDOOR
Kembel et al. ISME (2012)
9/7/16 27© University of Oregon BioBE Center
9/7/16 © University of Oregon BioBE Center 28
Dr. Steven Kembel University of Quebec
Dr. James Meadow Phylagen
WHAT FACTORS DRIVE MICROBIOME COMPOSITION AT THE BUILDING SCALE?
Restrooms!Offices!Classrooms!9/7/16 © University of Oregon BioBE Center 29
LILLIS BUSINESS COMPLEX UNIVERSITY OF OREGON, EUGENE, OR
Room (short-term scale) sampling: air, surfaces
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Building (long-term scale) sampling: vacuum dust
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High human traffic
Low human traffic
Data from Kembel et al., PLOS One (2014)
Dust microbiome varies with space and environment
Mechanical vs. window ventilation
9/7/16 © University of Oregon BioBE Center 33
North side:Window supply
South side:Mechanical supply
Kembel et al., PLOS One (2014)
CAP 1
NM
DS
1
DeinococcusAchromonobacterSpiroplasmaRoseomonasRhabdochlamydiaLysobacterLysinibaccillusPigmentiphagaAcidisphaeraBrenneria
MethylobacteriumSphingomonasStreptococcus
RhizobiumMycoplana
AgrobacteriumBrevundimonas
mechanical window
p=0.005 constrained inertia=2.5%
a
0.05
0.10
0.15
0.20
0.25
0.30
Dei
noco
ccus
rela
tive
abun
danc
e
air supplymechanical window
p<0.001b
0.02
0.04
0.06
0.08
0.10
0.12
0.14
Met
hylo
bact
eriu
m re
lativ
e ab
unda
nce
air supplymechanical window
p<0.001c
9/7/16 © University of Oregon BioBE Center 34
9/7/16 © University of Oregon BioBE Center 35
Spatially connected rooms are more similar to each other
2 4 6 8 10 12
0.05
0.10
0.15
0.20
Bio
logi
cal S
imila
rity
(1 -
Can
berr
a di
stan
ce)
How many doors between offices?Kembel et al., PLOS One (2014)
9/7/16 © University of Oregon BioBE Center 36
HUMAN INTERACTIONS WITH THE BUILT
ENVIRONMENT ALTER THE INDOOR MICROBIOME
9/7/16 © University of Oregon BioBE Center 37
9/7/16 © University of Oregon BioBE Center 38
HOW DO HUMAN INTERACTIONS WITH VARIOUS SURFACES SHAPE THE COMPOSITION
OF THE INDOOR MICROBIOME?
Dr. James Meadow Phylagen
Sampling classroom surfaces
9/7/16 © University of Oregon BioBE Center 39
FLOOR CHAIR WALL DESK
Meadow et al., Microbiome (2014)
Microbiome varies by surfaces with differential human contact
9/7/16 © University of Oregon BioBE Center 40
FLOOR CHAIR WALL DESK
Meadow et al., Microbiome (2014)
-1.0 -0.5 0.0 0.5 1.0 1.5
-1.0
-0.5
0.0
0.5
1.0
1.5
CAP1
CAP2
Chairs
Desks
Walls
Floors
a
-40 -20 0 20 40 60
-40
-20
0
20
40
60
CAP1
CAP2
Lactobacillus
Lactobacillus
Corynebacterium
Lactobacillus
Staphylococcus
Staphylococcus
CorynebacteriumCorynebacterium
Phytoplasma
StreptococcusStreptococcus
Streptococcus
BrevundimonasSphingomonas
Alicyclobacillus
Alicyclobacillus
Rhodopseudomonas
Salmonella
Chroococcidiopsis
Salmonella
Roseomonas
b
9/7/16 © University of Oregon BioBE Center 41
WHAT IS THE RELATIONSHIP BETWEEN ANTIMICROBIAL CHEMICALS & ANTIBIOTIC RESISTANCE IN THE INDOOR MICROBIOME?
Dr. Erica Hartmann Northwestern University
Sanitizing the built environment
9/7/16 © University of Oregon BioBE Center 42
Triclosan is ubiquitous in dust
Location n Detection (%)
Median Conc. (ng/g) Reference
China 47 96 570 Lu, X. et al. Analytical Methods 5, 5339 (2013)
Canada 63 100 571 Fan, X. et al. J. Environ. Monit. 12, 1891-1897 (2010)
Belgium 18 100 220 Geens, T. et al. Chemosphere 76, 755-760 (2009)
Spain 10 100 702 Canosa, P. et al. Anal. Chem. 79, 1675-1681 (2007)
9/7/16 © University of Oregon BioBE Center 43
Sampling dust in a mixed-use university campus building
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Description R p
23S ribosomal RNA methyltransferase 0.80 0.001
23S ribosomal RNA methyltransferase 0.77 0.006
class A beta-lactamase0.73 0.005
Hartmann et al., in review
Antimicrobial resistance in dust
Hartmann et al., Env Sci & Tech (in press)9/7/16 © University of Oregon BioBE Center 45
Antibiotic resistance varies across environments
9/7/16 © University of Oregon BioBE Center 46Hartmann et al., Env Sci & Tech (in press)
9/7/16 © University of Oregon BioBE Center 47
hVp://www.fda.gov/ForConsumers/ConsumerUpdates/ucm378393.htm
HUMANS SHED A PERSONALIZED
‘MICROBIAL CLOUD’ INDOORS
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HOW DO INDIVIDUALS’ MICROBIOMES COLONIZE THE BUILT ENVIRONMENT?
Dr. James Meadow Phylagen
Occupied
Unoccupied
Air Filter (12 per treatment)
1 m
0.15 m
Settling Dish (6 per treatment)
Particle Counter (1 per treatment)
2.4 m
3.7
m
2.4 m
2.9
m
9/7/16 50© University of Oregon BioBE CenterMeadow et al., PeerJ (2015)
CLIMATE CHAMBER @ ENERGY STUDIES IN BUILDINGS LAB, PORTLAND, OR
Meadow et al., Peer J 2015
An occupied space has a
distinct microbiome from
an adjacent unoccupied space
9/7/16 © University of Oregon BioBE Center 51
Meadow et al., PeerJ (2015)
9/7/16 © University of Oregon BioBE Center 52
Spaces occupied by
different people display unique
microbial patterns
Meadow et al., PeerJ (2015)
h(p://www.sciencefriday.com/videos/your-very-special-microbial-cloud/
9/7/16 53© University of Oregon BioBE Center
9/7/16 54© University of Oregon BioBE Center
Illustration: Cameron Slayden (Cosmocyte) & BioBE
HOW DOES THE DESIGN, USE, AND OCCUPANCY OF BUILDINGS INFLUENCE THE
INDOOR MICROBIOME AND HUMAN HEALTH?
9/7/16 © University of Oregon BioBE Center 55
Interactions between humans & the built environment
56
CLOUDS IN A CROWD: DISPERSAL
OF THE HUMAN MICROBIAL CLOUD
COLONIZATION OF THE SKIN
MICROBIOME VIA THE BUILT
ENVIRONMENT
EFFECTS OF WEATHERIZATION
ON THE HOME MICROBIOME
9/7/16 © University of Oregon BioBE Center
579/7/16 © University of Oregon BioBE Center
Interactions between humans & the built environment
9/7/16 © University of Oregon BioBE Center 58
CLOUDS IN A CROWD: DISPERSAL
OF THE HUMAN MICROBIAL CLOUD
COLONIZATION OF THE HUMAN (SKIN) MICROBIOME VIA
THE BUILT ENVIRONMENT
EFFECTS OF WEATHERIZATION
ON THE HOME MICROBIOME
599/7/16 © University of Oregon BioBE Center
Interactions between humans & the built environment
9/7/16 © University of Oregon BioBE Center 60
CLOUDS IN A CROWD: DISPERSAL
OF THE HUMAN MICROBIAL CLOUD
COLONIZATION OF THE HUMAN (SKIN) MICROBIOME VIA
THE BUILT ENVIRONMENT
EFFECTS OF WEATHERIZATION
ON THE HOME MICROBIOME
SURFACE
DIRECT CONTACT SURFACE INTERMEDIATE
BIOAEROSOL INTERMEDIATE
9/7/16 © University of Oregon BioBE Center 61
629/7/16 © University of Oregon BioBE Center
9/7/16 63© University of Oregon BioBE Center
HUMAN HEALTH
BUILDING DESIGN & ENERGY
MICROBIAL ECOLOGY
9/7/16 64© University of Oregon BioBE Center
ARE THERE ‘GENERAL LAWS’ IN BUILDING ECOLOGY?
HOW ARE THE BUILT ENVIRONMENT AND HUMAN HEALTH RELATED?
HOW ARE MICROBES EXCHANGED AMONG BUILDINGS, AIR & PEOPLE?
Acknowledgements
9/7/16 © University of Oregon BioBE Center 65
Jessica GreenKevin Van Den Wymelenberg
G.Z. BrownCurtis HuVenhower (Harvard)
Rolf Halden (Arizona State)Jeff Kline
Alejandro ManzoJames Meadow
Gwynne MhuireachDale NorthcuV
Maria SaraoAndy SiemensKyla SiemensJason Stenson
Hannah Wilson
Adam AltrichterAshley BatemanClarisse BetancourtBrendan BohannanAshkaan FahimipourMark FrejErica HartmannDeb Johnson-SheltonSteven KembelAnn Klein
For more information
• Biology and the Built Environment Center– hVp://biobe.uoregon.edu
• Roxana Hickey, Postdoctoral Fellow– rhickey@uoregon.edu, @roxana_hickey
• Jessica Green, BioBE Co-Director– jlgreen@uoregon.edu, @JessicaLeeGreen
• Kevin Van Den Wymelenberg, Co-Director– kevinvdw@uoregon.edu, @Wymelenberg
9/7/16 © University of Oregon BioBE Center 66
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