built environment microbiome : what makes this...
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Built environment microbiome : What makes this environment unique and
perspective on the field?
Gary L. [email protected]
Lawrence Berkeley LaboratoryUniversity of California, Berkeley
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Outline
• Setting the stage: microbes in the atmosphere– Factors influencing dispersal
• What are the sources of microbes in the built environment and how do they differ from the outdoor air?
• Case studies: Sources of microbes in homes and hospitals.
• Are indoor microbes active/viable?
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Microbial community in atmospherePopulation is sum of:
Immigration – emigration
Growth – death
Source of microbes – Soil, plants, water, animal, biofilms, various surfaces
Dispersal into atmosphere – passive or active
Removal from atmosphere – precipitation, thermal, gravity
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Factors Influencing Local and Long Range Microbial Composition
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Microbial species composition in urbanand rural aerosols in California
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BioWatch
APDS
Autonomous Pathogen Detection System
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Assess diversity by time (week) and location (city).
Microbial Diversity in Aerosols: What are the major environmental drivers?
•Leverage samples from BioWatch filters, a >$100M/Y program to monitor urban locations for pathogens
•A number of documented “false-positive”detections each year
•Determine background levels of microbes, including pathogens.
•Sequential 17 weekly samples for 2 cities to determine scope of variability
Gulf of Mexico
AustinSan Antonio
PNAS (2007) 104:299-304
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Actinomycetes FirmicutesBacteroides Cyanobacteria Alpha-proteobacteriaBeta-proteobacteriaGamma-proteobacteria
Multivariate regression tree analysis:Interaction of environmental factors with aerosol bacterial dynamics
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Austin City WeekSan Antonio City Week
Environmental factors1.) Week2.) Temp3.) PM 2.54.) Mean SLP
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Amount of DNA detected on chip
degrees F
R = 0.64, p = 0.026Adjusted for multiple testing
M. tuberculosissubgroup
Does Mycobacterium detection increase with air temperature?
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What is unique about the microbial ecology of the built environment?
Origin of indoor microbes in “healthy buildings”:•Outdoor environment•Shedding from human and pet microbiome•Selection from building-specific factors
Are there microbes that are unique to indoor environments?• Selection• Genetic Drift
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People as source of microbes in the air
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Thermal Emission of Bacteria
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(2010) PNAS 107: 13748–13753
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Conclusions from worldwide survey of 72 buildings from 6 continents
• Fungal diversity was higher in temperate locations than in the tropics
• Building function had no influence on indoor fungal composition
• Outdoor environment had greater influence on indoor microbial community than human sources
• Distribution of individual taxa is significantly range- and latitude limited
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100m
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Petri dish sampling of dust for 1 month
Two seasons,Four rooms/building12 buildings2 seasonsPyrosequence fungal ITS
0 10 20 30 40
020
040
060
080
010
00
Number of samples
Cha
o1 e
stim
ator
of r
ichn
ess
Winter
Summer
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Isolation by distance in < 0.5 km
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Photo: Jason Stenson (Energy Studies in Buildings Lab)
Jessica Green, University of OregonISME J. (2012) 6:1469-1479
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0 10 20 30 40
Diversity
1
0.75
0.5
0.25
0
Pot
entia
l Pat
hoge
ns
MechanicalOpen WindowOutdoor
Sources of Air
Kembel et al. ISME 2014
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Kembel et al. ISME 2014
Com
mun
ity C
ompo
sitio
n 2
Community Composition 1
MechanicalOpen WindowOutdoor
Sources of Air
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Architecture influences indoor microbial ecology
Earlier observations suggested that open windows in hospital rooms resulted in healthier patients
Phylogenetic diversity of airborne microbial communities was lowest in mechanically ventilated hospital rooms with window-ventilated rooms and outdoor air having higher bacterial diversity
Indoor mechanically ventilated rooms had high levels of potential pathogens that were rare in outdoor air
Humans as potential vectors of pathogens and other bacteria indoors?
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Jack Gilbert – University of Chicago
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Home is where your microbiome is!
Each family left its own microbial fingerprint on their
home, within 24 hours of moving in!
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Microbial forensics
A young couple shared more microbes than they did with a lodger they were
living with, suggesting physical interaction
Lax et al., 2014 Science
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Microbial ecology of NICU with potential outbreak of necrotizing enterocolitis
Jill Banfield – UC Berkeley
NEC is a gastrointestinal disease (mostly) of premature infants. It is one of the most common causes of disability and death in these infants. It is widely believed to have a microbial origin:
APPROACH: Genome-resolved time-series analyses of gut colonization in premature newborns that become sick to identify the organism responsible for a NEC “outbreak”.
Hypothesis: one organism, likely fairly abundant, shared by sick infants and not present (or rare) in healthy infants
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Finding: strains in almost all co-hospitalized infants are distinct!?!
No strain in the infants that developed NEC was shared! (typical gene surveys could not reveal this)
NEC “Outbreak”: May, June of 2014
Predict an abundant organism common to infants that developed NEC and absent or rare in those that did not develop NEC
However, as expected, strains in the same infant are mostly the same
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gyrA (nt) multi-sequence alignmentSadka et al. eLife, 2015
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DOL 16
DOL 17
DOL 19
DOL 21
DOL 22
DOL 39
1. Veillonella parvula2. Enterococcus faecalis3. Citrobacter KTE324. Klebsiella oxytoca5. Clostridium ultunense-related6. Streptococcus anginosus-related7. Staphylococcus epidermidis-related8. Bifidobacterium MSTE12-related9. Clostridium butyricum10.Enterobacter aerogenes11.Klebsiella pneumoniae-related12.Haemophilus parainfluenza13.Paenibacillus dendritiformis-related14.Clostridium sporogenes-related15.Atopobium minutum-related16.Pseudomonas aeruginosa17. Streptococcus mitiis-related
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Nor
mal
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erag
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 Rank
Example: Infant 3
Premature infant gut communities are assemblages
of hospital-acquired
pathogens
NEC
Ab.
Bacteria with predicted high
antibiotic resistance potential persist
through antibiotic treatments
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What they found:
During initial colonization of the infant gut, communities have high dominance and a few organisms – early communities are simple microbial communities
Microbial community composition varies with with infant health and nutrition Antibiotic administration causes radical, but somewhat predictable changes
Strain variants matter: differ in pathogenicity
Contrary to expectation, infants that developed NEC did not have common gut colonists (although that would not be apparent from standard surveys).
The infants were colonized by a wide variety of (potential) pathogens - likely other factors determine which infants develop NEC
(Statistical analysis of case stats should precede identification of “outbreaks”)
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Propidium Monoazide for live-dead discrimination
Intercalates into DNA
Cross-linked DNA after photolysis
PMA enters dead cells
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Vaishampayan (2013) ISME J 7:312-324
16S
rRN
Age
ne c
opy
num
ber
Detection of viable spores in presence ofinactivated spores using PMA method
108
107
106
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102
101
1 2 3 4 5 6 7 8 9 10 11 12 13 15 16 17 18 19 20 21 Live spores (107
to 103 mixed with 10 7 inactivated spores
Live spores (107
to 103 mixed with 10 7 inactivated spores +PMA
Live spores (107
to 103
Live
Dead
Dead+PM
A
Live +PMA
NTC
• Viable spores (107 to 103) mixed with inactivated spores (107) were selectively detected by PMA treatment.