microbial interactions between humans and the built environment (lake arrowhead microbial genomics...
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MICROBIAL INTERACTIONS BETWEEN HUMANS & THE BUILT ENVIRONMENTROXANA HICKEY GREEN LAB & BioBE CENTER // UNIVERSITY OF OREGON LAKE ARROWHEAD MICROBIAL GENOMICS // 09.21.16
@roxana_hickey
Credit: Gwenda Kacsor of Oregon Quarterly
© University of Oregon BioBE Center (2016) Credit: Tomasz Sienicki via Wikimedia Commons
Credit: Aptem via Wikimedia CommonsCredit: BrendelSignature via Wikimedia Commons
Credit: Malate269 via Wikimedia Commons
© University of Oregon BioBE Center (2016)
BIOLOGY & THE BUILT ENVIRONMENT CENTER
© University of Oregon BioBE Center (2016)
BIOLOGY & THE BUILT ENVIRONMENT CENTER @ UNIVERSITY OF OREGON
http://biobe.uoregon.edu/
© University of Oregon BioBE Center (2016)
BIOLOGY & THE BUILT ENVIRONMENT CENTER @ UNIVERSITY OF OREGON
http://biobe.uoregon.edu/
ASHLEY BATEMAN PHD CANDIDATE
CLARISSE BETANCOURT ROMÁN
RESEARCH ASSISTANT
GZ CHARLIE BROWN BIOBE CO-FOUNDER & ESBL DIRECTOR
ASHKAAN FAHIMIPOUR
POSTDOC
JESSICA GREEN BIOBE CO-FOUNDER
& CO-DIRECTOR
ROXANA HICKEY POSTDOC
JEFF KLINE RESEARCH ASSOCIATE
GWYNNE MHUIREACH PHD CANDIDATE
DALE NORTHCUTT SR RESEARCH
ASSISTANT
JASON STENSON RESEARCH ASSISTANT
KEVIN VAN DEN WYMELENBERG ESBL DIRECTOR &
BIOBE CO-DIRECTOR
KYLA SIEMENS RESEARCH ASSISTANT
HANNAH WILSON RESEARCH ASSISTANT
© University of Oregon BioBE Center (2016)
BIOLOGY & THE BUILT ENVIRONMENT CENTER @ UNIVERSITY OF OREGON
http://biobe.uoregon.edu/
© University of Oregon BioBE Center (2016)
BIOLOGY & THE BUILT ENVIRONMENT CENTER @ UNIVERSITY OF OREGON
http://biobe.uoregon.edu/
© University of Oregon BioBE Center (2016)
HOW DOES THE DESIGN, OPERATION & OCCUPANCY OF BUILDINGS INFLUENCE
THE INDOOR MICROBIOME?
© University of Oregon BioBE Center (2016)
A BRIEF HISTORY OF BioBE RESEARCH
Founded c/o Alfred P. Sloan Foundation grant
2010
Ventilation source & hospital room air Kembel et al. ISME 2012
Architecture, ventilation strategy, occupancy influence university building air & dust
Meadow et al. Indoor Air 2013 Kembel et al. PLOS One 2014
Microbiome of classroom surfaces related to human contact
Meadow et al. Microbiome 2014
Human bioaerosols: the microbial cloud
Meadow et al. PeerJ 2015
Urban green space & outdoor air microbiome
Mhuireach et al. Env Sci & Tech 2016
Antimicrobials & antibiotic resistance genes in dust
Hartmann et al. ES&T 2016
© University of Oregon BioBE Center (2016)
© University of Oregon BioBE Center (2016)
Kembel et al. ISME 2012
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
North side:Window supply
South side:Mechanical supply
Kembel et al. PLOS One 2014; Meadow et al. Indoor Air 2013
Meadow et al. PeerJ 2015
© University of Oregon BioBE Center (2016)
Kembel et al. ISME 2012
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
North side:Window supply
South side:Mechanical supply
Kembel et al. PLOS One 2014; Meadow et al. Indoor Air 2013
Meadow et al. PeerJ 2015
ARCHITECTURAL DESIGN, VENTILATION & OCCUPANCY INFLUENCE THE MICROBIOME OF THE BUILT ENVIRONMENT
© University of Oregon BioBE Center (2016)
CURRENT RESEARCH @ BioBE
Effects of light source (UV, visible) on dust microbiome viability
Home weatherization & microbiome diversity +
homeowner health, behavior
Multiple-occupancy & ventilation effects on
microbial cloud
Microbial transmission from plants & dogs to human skin
via the built environment
Child gut microbiome, home dust & psychological stress
Antimicrobials & antibiotic resistance in athletic facilities
Theoretical models of building occupancy & microbiome diversity
© University of Oregon BioBE Center (2016)
HUMAN INTERACTIONS WITH THE BUILT ENVIRONMENT
ANTIMICROBIAL CHEMICALS & THE
BUILT ENVIRONMENT MICROBIOME
COLONIZATION OF THE HUMAN SKIN
MICROBIOME VIA THE BUILT ENVIRONMENT
CLOUDS IN A CROWD: DISPERSAL OF HUMAN
BIOAEROSOLS
© University of Oregon BioBE Center (2016)
HUMAN INTERACTIONS WITH THE BUILT ENVIRONMENT
ANTIMICROBIAL CHEMICALS & THE
BUILT ENVIRONMENT MICROBIOME
COLONIZATION OF THE HUMAN SKIN
MICROBIOME VIA THE BUILT ENVIRONMENT
CLOUDS IN A CROWD: DISPERSAL OF HUMAN
BIOAEROSOLS
© University of Oregon BioBE Center (2016)
ANTIMICROBIAL CHEMICALS & RESISTANCE IN THE BUILT
ENVIRONMENT
ERICA HARTMANN @ericamhartmann
© University of Oregon BioBE Center (2016)
ANTIMICROBIAL CHEMICALS IN THE BUILT ENVIRONMENT
STERILIZING THE BUILT ENVIRONMENT
© University of Oregon BioBE Center (2016) Source: Collegiate Images via Getty Images
GERLINGER HALL, UNIVERSITY OF OREGON Est. 1921
HOW DOES THE CONCENTRATION OF ANTIMICROBIAL CHEMICALS CORRELATE WITH THE MICROBIOME & ANTIBIOTIC RESISTANCE GENES IN INDOOR DUST?
© University of Oregon BioBE Center (2016)
© University of Oregon BioBE Center (2016)
EXPERIMENTAL DESIGN
classrooms gyms
offices circulation
laundry lockers building support pool
ANTIMICROBIALS (LC-MS/MS)
triclosan triclocarban
methylparaben ethylparaben
propylparaben butylparaben
ROLF HALDEN ARIZONA STATE
CURTIS HUTTENHOWER
HARVARD SPH
MICROBIOME & RESISTOME
SHOTGUN METAGENOMICS
ShortBRED & HAllA w/ CARD
database
16S rRNA
UPARSE & QIIME
44 VACUUM DUST SAMPLES
© University of Oregon BioBE Center (2016)
LOWER OVERALL LEVELS OF ANTIBIOTIC RESISTANCE GENE ABUNDANCE
Hartmann, Hickey, Hsu et al. Env Sci Tech 2016
© University of Oregon BioBE Center (2016)
SIX RESISTANCE GENES SIGNIFICANTLY ASSOCIATED WITH [CHEMICALS]
Gene Description Similarity Score q
erm(X) 23S rRNA transferase 0.86 0.036
tet(K) tetracycline resistance efflux pump 0.83 0.036
vga(A) streptogramin res. efflux pump 0.65 0.036
erm(33) 23S rRNA transferase 0.73 0.036
erm(C) 23S rRNA transferase 0.68 0.036
cmr chloramphenicol res. efflux pump 0.58 0.048
Hartmann, Hickey, Hsu et al. Env Sci Tech 2016
TRIC
LOSA
NME
THYL
PARA
BEN
© University of Oregon BioBE Center (2016)
NO MORE TRICLOSAN FOR YOU(R PERSONAL CARE PRODUCTS)
http://www.fda.gov/ForConsumers/ConsumerUpdates/ucm378393.htm
© University of Oregon BioBE Center (2016)
HUMAN INTERACTIONS WITH THE BUILT ENVIRONMENT
ANTIMICROBIAL CHEMICALS & THE
BUILT ENVIRONMENT MICROBIOME
COLONIZATION OF THE HUMAN SKIN
MICROBIOME VIA THE BUILT ENVIRONMENT
CLOUDS IN A CROWD: DISPERSAL OF HUMAN
BIOAEROSOLS
© University of Oregon BioBE Center (2016)
CLOUDS IN A CROWD: DISPERSAL OF HUMAN
BIOAEROSOLSJAMES MEADOW
@JamesMeadowASHKAAN
FAHIMIPOUR @AshkaanF
© University of Oregon BioBE Center (2016)
CLIMATE CHAMBER UO Energy Studies in Buildings
Laboratory, Portland, OR
Control surface & air temperature, humidity, air velocity
© University of Oregon BioBE Center (2016)
SAMPLING THE HUMAN MICROBIAL CLOUD
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
Meadow et al. PeerJ 2015
© University of Oregon BioBE Center (2016)
AN OCCUPIED ROOM IS DISTINCT FROM AN UNOCCUPIED ROOM
Meadow et al. PeerJ 2015
© University of Oregon BioBE Center (2016)
SPACES OCCUPIED BY DIFFERENT PEOPLE HAVE UNIQUE MICROBIAL PATTERNS
Meadow et al. PeerJ 2015
© University of Oregon BioBE Center (2016)
http://www.sciencefriday.com/videos/your-very-special-microbial-cloud/
© University of Oregon BioBE Center (2016)
CAN INDIVIDUALS BE DISTINGUISHED BY THEIR MICROBIAL CLOUD IN A ROOM OF PEOPLE?
© University of Oregon BioBE Center (2016)
EXPERIMENTAL DESIGN: SOLO RUN
4’ 2’2’
4’2’
4’2’
10’
1’
20”
1’
10”
Filter Cup
T, RH Sensor
MRT Sensor
4’ 2’2’
9’-6
”1’
30”
1’
40”
Filter Cup
T, RH Sensor
MRT Sensor
Diagram by Jason Stenson, Energy Studies in Buildings Laboratory
© University of Oregon BioBE Center (2016)
EXPERIMENTAL DESIGN: SOLO RUN
4’ 2’2’
4’2’
4’2’
10’
1’
20”
1’
10”
Filter Cup
T, RH Sensor
MRT Sensor
4’ 2’2’
9’-6
”1’
30”
1’
40”
Filter Cup
T, RH Sensor
MRT Sensor
Diagram by Jason Stenson, Energy Studies in Buildings Laboratory
CAN WE DETECT SPECIFIC MEMBERS OF THE SKIN MICROBIOME IN BIOAEROSOLS & MEASURE THEIR
DISPERSAL ACROSS THE ROOM?
© University of Oregon BioBE Center (2016)
EXPERIMENTAL DESIGN: GROUP RUN
4’ 2’2’
4’2’
4’2’
10’
1’
20”
1’
10”
Filter Cup
T, RH Sensor
MRT Sensor
4’ 2’2’
9’-6
”1’
30”
1’
40”
Filter Cup
T, RH Sensor
MRT Sensor
Diagram by Jason Stenson, Energy Studies in Buildings Laboratory
© University of Oregon BioBE Center (2016)
EXPERIMENTAL DESIGN: GROUP RUN
4’ 2’2’
4’2’
4’2’
10’
1’
20”
1’
10”
Filter Cup
T, RH Sensor
MRT Sensor
4’ 2’2’
9’-6
”1’
30”
1’
40”
Filter Cup
T, RH Sensor
MRT Sensor
Diagram by Jason Stenson, Energy Studies in Buildings Laboratory
CAN WE PREDICT WHO WAS PRESENT IN THE ROOM BASED ON THEIR SKIN MICROBIOME & THE
COMPOSITION OF BIOAEROSOLS?
© University of Oregon BioBE Center (2016)
HUMAN INTERACTIONS WITH THE BUILT ENVIRONMENT
ANTIMICROBIAL CHEMICALS & THE
BUILT ENVIRONMENT MICROBIOME
COLONIZATION OF THE HUMAN SKIN
MICROBIOME VIA THE BUILT ENVIRONMENT
CLOUDS IN A CROWD: DISPERSAL OF HUMAN
BIOAEROSOLS
© University of Oregon BioBE Center (2016)
MICROBIAL COLONIZATION OF SKIN VIA THE BUILT
ENVIRONMENTASHLEY BATEMAN
@MicrobesRock
© University of Oregon BioBE Center (2016)
SOURCES OF MICROBES IN THE BUILT ENVIRONMENT
Prussin & Marr Microbiome 2015
HUMANS PETS
PLUMBING SYSTEMS
PLANTSVENTILATION
SYSTEMS MOLD
RESUSPENSION OF SETTLED DUST
OUTDOOR AIR
© University of Oregon BioBE Center (2016)
DOES MICROBIAL EXCHANGE OCCUR TO AND FROM THE BUILT ENVIRONMENT?
© University of Oregon BioBE Center (2016)
ROUTES OF MICROBIAL TRANSMISSION TO THE HUMAN SKIN MICROBIOME
SURFACE
DIRECT CONTACT BE SURFACE INTERMEDIATE BIOAEROSOL INTERMEDIATE
© University of Oregon BioBE Center (2016)
HOW ARE MICROBES EXCHANGED AMONG BUILDINGS, AIR & PEOPLE?
ARE THERE ‘GENERAL LAWS’ IN BUILDING ECOLOGY?
WHAT IS THE RELATIONSHIP BETWEEN THE BUILT ENVIRONMENT, HUMAN MICROBIOME & HEALTH?
Source: BioBE Center with Cameron Slayden of Cosmocyte
© University of Oregon BioBE Center (2016)
OUR TEAM
Jessica Green Kevin Van Den Wymelenberg
G.Z. Charlie Brown Curtis Huttenhower (Harvard)
Rolf Halden (Arizona State)Alejandro Manzo
Gwynne Mhuireach Max Moriyama Dale Northcutt Tim O’Connor
Iman Rejaie Maria Sarao
Andy Siemens Kyla Siemens
Jason Stenson Paul Ward
Hannah Wilson
Adam Altrichter Dan Aughenbaugh Ashley Bateman Clarisse Betancourt Brendan Bohannan Ashkaan Fahimipour Mark Fretz Erica Hartmann Roxana Hickey Keith Herkert Evan Jones Ann Klein Jeff Kline
@roxana_hickey
@JessicaLeeGreen
@Wymelenberg
@ericamhartmann
@AshkaanF
@MicrobesRock
@betancourt_cm