26.5.2015

MOLECULAR TOOLS AND MICROBIAL ECOLOGY OF BUILDINGS - A PRACTITIONER’S VIEW

Miia Pitkäranta, PhD

Vahanen Group

Healthy Buildings Europe 2015

26.5.2015

Goal: to understand the microbiological processes in building structures and indoor environment and their potential health impacts

Microbial ecology of the buildings – a field of academic and practical research

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- condition investigation risk assessment

- choosing effective remedial actions in damaged buildings

- controlling the success of remediation

- new building design principles

- building physical modelling

- architectural design

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Molecular methods – the toolbox

• Target DNA ▪ ”Barcode genes” for species detection / identification

▪ Independent of cell viablity

▪ Microbial community sequencing & other methods

• Since 1980… 1990

• In building studies since 1995 … 2000

• NGS ~2010 ”explosion” … ”sequence everything”

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Franzosa et al. 2015, Nature Rev Microbiol

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• Undamaged buildings, dry surfaces:

▪ Core species, wide overall diversity

▪ Plenty of “rare unknowns”

▪ Fungi: mainly from outdoors (architecture and materials do not make a significant difference)

– Pitkäranta 2008, Amend 2010, Adams 2013, Adams 2014, Yamamoto 2015) ”Sinks are sources, other surfaces are sinks” (Adams in microBEnet 2013)

▪ Bacteria: mainly from inhabitants (human, pet)

– Täubel 2009, Fujimura 2010, Hospodsky 2012, Adams 2014

• Undamaged buildings, wet surfaces:

▪ Enrichment of osmophilic and biofilm-forming fungi and bacteria (Kelley et al. 2004, Adams 2013, Adams 2014)

MOLECULAR STUDIES – KEY FINDINGS

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Image: Kosteus- ja hometalkoot/ ww.hometalkoot.fi

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MOLECULAR STUDIES – KEY FINDINGS

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Adams et al. 2014, PLOS One 9(3)

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MOLECULAR STUDIES – KEY FINDINGS

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Amend et al. 2010, PNAS 107

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MOLECULAR STUDIES – KEY FINDINGS

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Amend et al. 2010, PNAS 107

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MOLECULAR STUDIES – KEY FINDINGS

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Täubel et al. 2009, JACI 124

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MOLECULAR STUDIES – MORE FINDINGS

▪ Dust resuspension significantly contributes to the amount and types of airborne microbes

▪ Human effect strongest in most densely populated spaces (both pathogen-related and beneficial taxa)

▪ Opening windows brings in outdoor air, outdoor-borne bacteria, affects T & RH and dilutes human-borne bacterial assemblages

▪ Close-by rooms contain more similar bacterial assemblies than distantly located ones

▪ Age of home correlates with fungal sp. richness

– Kembel et al. 2012, ISME J. 6

– Hospodsky et al. 2012, PLOS One 7(4)

– Meadow et al. 2014, Indoor Air 24(1)

– Kembell et al. 2014, PLOS One 9(1)

– Yamamoto et al. 2015, Env Sci Technol 49(8)

– Kettleson et al. 2015, Environ Res 138

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MOLECULAR METHODS – THE USE FOR A PRACTITIONER?

1. Direct health-based exposure assessment?

▪ Nope. Holistic approach needed

2. “Building diagnostics”? ▪ Quantitative PCR (in use)

– AIR: Detect abnormal situation a proxy for potential microbial growth

• ERMI, local primer selections

• Local reference data needed!

– MATERIALS: Detect growth verify damages

• Works but information is “flat”

• Problems with old natural materials

– Advantages:

• Speed, speed speed

– Problems:

• Selectivity - we see what we look for - are we missing something?

• Wide species coverage too expensive

▪ Community barcode sequencing

– Today: Too much (useless) information!

– Quantitation = problem (OTU frequencies ≠ Natural taxon frequencies too severe bias?

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MOLECULAR METHODS – THE USE FOR A PRACTITIONER?

1. Basic knowledge Increased understanding of the exposures

vs. disease mechanisms

o new taxa to look out for?

o new genes to look out for?

o new metabolites to look out for?

Improved targeted building diagnostics?

▪ Community barcode sequencing

▪ Community metagenomics

▪ Community metabolomics

One day in building diagnostics?

– Intelligent pipelines to fish for the “health signal” ?

(or at least the “damage signal”?)

▪ Other protocols?

– DNA probing systems (DNA chips)

– FISH

– EIA

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Microbial ecology of the buildings

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Seekin’ for microbial hot spots?

1. Hidden, often in aging buildings

SURFACES?

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Seekin’ for microbial hot spots? SURFACES

STRUCTURES 1. Hidden, often in aging buildings

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Microbial ecology of the buildings - niches

Nunez and Hammer 2014,

Indoor Air 24(5)

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Example: A HOUSE

▪ A = 100 m2, V = 270 m3

▪ Average air leakage rate (determined @ –50 pa) = 4 ac/h (q50=3,51)

▪ Leakage @ -50 pa ~ 1000 m3/h

▪ Leakage in 0 … -5 pa ~ 30 - 50 m3/h

Why should we be interested in the inside of the structures?

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Transmission and routes

Source: Leeds Beckett University, http://www.leedsbeckett.ac.uk

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Age of dwelling stock

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Images: Kerrostalot 1880 -2000. Rakennustieto Oy 2006. Modified.

1952

1958

1963

1975

1996

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Images: Vahanen Oy.

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Pressure difference – the driving force

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Andersen et al. 2011, AEM 77(12)

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BUILDING MICROBIOLOGY - research needs (a pratitioner’s view!)

Deep characterization of the full mechanistics of common problem sources

• Niche-based characterization of building microbiomes, physico-chemical conditions and emissions

▪ “Omics” tools for microbial community & metabolite analysis

▪ In-situ techniques (eg. FISH), microscopy

▪ Small-scale sensors

▪ Material compound (degradation) chemistry

▪ Building physical modelling

• Long term dynamics of mixed microbial communities, eg.

▪ Natural microbial populations thriving on aged, originally mold and microbial resistant materials

▪ Material resistance and bioreceptivity

Proper renovation techniques, new building design principles

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Pietarinen et al. 2008, JEM 10

26.5.2015 Ettenauer et al. 2014. PLoS ONE 9(8)

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Ettenauer et al. 2014. PLoS ONE 9(8)

Cultivation: Bacteria

DNA-based: Archaea

DNA-based: Bacteria

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IAQ – A SUM OF FACTORS

In problem buildings microbiological contamination is commonly accompanied by other factors such as:

• Chemical material emissions

• Particulate and fibrous contaminants

• Physical conditions

May or may not have a common root cause with the microbial contaminants

Eg.

• Old, degrading mineral wool insulation

• alkaline degradation of PVC materials

• HVAC system contamination

• construction moisture (bio)degradation

• old surface dust (accumulation of SVOCs)

Multidisciplinary approach in exposure & health studies!

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To summarize…

Dirty kids and kids with a dog are healthy kids, but kids in moldy buildings are asthmatic

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1. MOLECULAR TOOLS HAVE REVEALED AN UNSEEN

MICROBIOLOGICAL DIVERSITY IN THE INDOOR ENVIRONMENT

2. THE CURRENT FOCUS IS HEAVILY ON INDOOR AIR &

SURFACES 3. MICROBIAL HOT SPOTS

(NICHES) IN BUILDINGS ARE OFTEN HIDDEN

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7. HOW CAN I AVOID IT? HOW DO I FIX IT?

To summarize…

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4. MICROBIAL NICHES ARE IMPORTANT SOURCES OF

INDOOR AIR CONTAMINATS

5. WE DON’T FULLY UNDERSTAND WHAT’S

GOING ON IN THE STRUCTURES

6. IT’S NOT JUST ABOUT THE MOLD…

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Images: J. Säntti, Vahanen Oy