Built environment microbiome : What makes this environment unique and

perspective on the field?

Gary L. AndersenGLAndersen@lbl.gov

Lawrence Berkeley LaboratoryUniversity of California, Berkeley

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?

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

Factors Influencing Local and Long Range Microbial Composition

Microbial species composition in urbanand rural aerosols in California

BioWatch

APDS

Autonomous Pathogen Detection System

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

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

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?

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

People as source of microbes in the air

Thermal Emission of Bacteria

(2010)  PNAS 107: 13748–13753 

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

100m

Petri dish sampling of dust for 1 month 

Two seasons,Four rooms/building12 buildings2 seasonsPyrosequence fungal ITS

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o1 e

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Isolation by distance in < 0.5 km

Photo: Jason Stenson (Energy Studies in Buildings Lab)

Jessica Green, University of OregonISME J. (2012) 6:1469-1479

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Diversity

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entia

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MechanicalOpen WindowOutdoor

Sources of Air

Kembel et al. ISME 2014

Kembel et al. ISME 2014

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mun

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ompo

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Community Composition 1

MechanicalOpen WindowOutdoor

Sources of Air

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?

Jack Gilbert – University of Chicago

Home is where your microbiome is!

Each family left its own microbial fingerprint on their

home, within 24 hours of moving in!

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

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

DOL 16

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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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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

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”)

Propidium Monoazide for live-dead discrimination

Intercalates into DNA

Cross-linked DNA after photolysis

PMA enters dead cells

Vaishampayan (2013) ISME J 7:312-324

16S

rRN

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Detection of viable spores in presence ofinactivated spores using PMA method

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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.