Täubel ia2011 333_microbiome

Diversity, seasonal dynamics and sources of bacteria in house dust

M. Täubel*, H. Rintala, M. Pitkäranta, M. Toivola, L. Paulin, S.

Laitinen, J. Pekkanen, A. Hyvärinen & A. Nevalainen

108.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel

Motivation/Background Motivation/Background ––Asthma and allergy and indoor microbial exposuresAsthma and allergy and indoor microbial exposures


The "hygiene hypothesis"

→ levels of bacterial markers in house dust are used to assess indoor exposure to bacteria

Associations of microbial exposures and development of allergic diseases have been shown

Motivation/Background Motivation/Background ––Building moisture/dampness/microbial contamination Building moisture/dampness/microbial contamination

and associations with adverse health outcomesand associations with adverse health outcomes


Dampness /

microbial contamination Health effects

causative agents

mechanisms

Knowledge on the exposure is is crucial for Knowledge on the exposure is is crucial for understanding the impact on human healthunderstanding the impact on human health


� bacterial flora in indoor environments (and house dust) only fragmentarily explored (composition?)

� markers represent subpopulations of microbes

� understanding of not only quantity (levels), but also quality/nature and sources is needed

Materials & Methods 1/2Materials & Methods 1/2


Rintala H., et al 2008. BMC Microbiology, 8, 56.

Täubel M., et al 2009. J Allergy Clin Immunol, 124, 834-40.

• two nursing home buildings

(B1, B2), with and without

moisture damage

• Vacuumed settled dust from

hard surfaces, combined over 2

months; four samples per

building (one per season)

Sampling locations Sampling locations

Sample materialSample material

• three flats, one dwelling house

(A, B, C, D)

• Skin surface swabs

• Vacuumed mattress dust

• Vacuumed floor dust

Diversity, Diversity,

seasonal dynamicsseasonal dynamicsSourcesSources

Materials & Methods 1/2Materials & Methods 1/2


Lab workLab work

o duplicate DNA extractions (bead beating)

o universal 16S rRNA gene PCR amplification (10 reactions)

o purification and construction of clone libraries in E. coli

o Sequencing in ABI3700 DNA sequence

Sequence processing and analysisSequence processing and analysis

o full length 16S rRNA gene sequences processed with Staden package

o chimera cleaning using Bellerophone and Chimera_Check

o (SL)OTU definition using DOTUR (97% and 99% cut-offs)

o Phylogeny: alignment against GenBank using BLAST

o sequence analyses: DOTUR, SONS, web-libshuff, UniFrac, …

Bacterial richness in house dustBacterial richness in house dust


Species-level operational taxonomic units (SLOTUs – observed and

Chao estimates) in floor dusts of 2 nursing homes (B1,B2) and from

floor and mattress dust of 4 homes (Hf and Hm; A,B,C,D).

No. of seq., number of sequences; SLOTUs obs., Number of species level OTUs (97%

similarity) observed; SLOTUs Chao, Number of species level OTUs based on CHAO estimator

House dust is a rich reservoir

of different bacteria

Samples:

sub-study 1

No. of seq. SLOTUs obs. SLOTUs Chao

B1f – combined 426 167 440

B1f – 4 seasons 76-144 30-66 99-231

B2f – combined 467 167 464

B2f – 4 seasons 82-159 45-65 131-463

Samples:

sub-study 2

No. of seq. SLOTUs obs. SLOTUs Chao

Hf – combined 1038 248 455

Hf – A,B,C,D 234-308 60-123 83-310

Hm – combined 1067 174 339

Hm – A,B,C,D 242-283 26-90 53-204

Bacterial richness and diversity in floor dust vs. Bacterial richness and diversity in floor dust vs. mattress dustmattress dust


Täubel et al 2009. J Allergy Clin Immunol, 124, 834-40.

Bacterial richness higher in

individual and pooled floor dust

compared to mattress dust samples

mattress floor

home A 2.95 2.99

home B 3.62 3.72

home C 2.31 3.06

home D 1.19 3.49

combined 3.38 4.07

Bacterial diversity higher in

floor dust vs. mattress dust

in homes

Seasonal dynamics of bacteria Seasonal dynamics of bacteria in house dust of nursing homesin house dust of nursing homes


� Bacterial diversity lowest during winter and highest

during spring

spring summer autumn winter combined

building 1 - floor 3.96 3.47 3.88 1.88 4.22

building 2 - floor 3.85 3.28 3.27 3.18 4.10

Bacterial diversity in floor dust according to Shannon Weaver Index

Seasonal dynamics of bacteria Seasonal dynamics of bacteria in house dust of nursing homesin house dust of nursing homes


� Seasonal variation in the bacterial community structure

using statistical tools (Libshuff, Unifrac): differences

observed between seasons in the buildings, but not all

significant and not very consistent

� Seasonal differences (percentual proportions) in the

higher taxonomic levels (phylum, class): overall small

(alpha- and betabacteria higher in spring and summer)

� Seasonal differences (percentual proportions) on the

species level: high, i.e. 75% of SLOTUs in one building

were found in only one season

� Bacterial diversity lowest during winter and highest

during spring

Bacterial composition of house dust in homesBacterial composition of house dust in homes


% SLOTUs / % sequences

Proteobacteria

Firmicutes

Actinobacteria

30/1718/523/3

33/5752/7031/61

25/2120/2144/36

Bacterial composition of house dust in homesBacterial composition of house dust in homes


Most common SLOTUs in floor and mattress dust:

Staphylococcus, Corynebacterium, Lactobacillus,

Propionibacterium, Streptococcus, Lactococcus

Bacterial composition of house dust in nursing Bacterial composition of house dust in nursing home buildingshome buildings

Distribution of clones

25 %

50 %

6 %

6 %

10 %

2 %

1 %

ActinobacteriaFirmicutesAlphaproteobacteriaBetaproteobacteriaDeltaproteobacteriaEpsilonproteobacteriaGammaproteobacteriaAcidobacteriaBacteroidetesChloroflexiDeinococcus-ThermusFusobacteriaPlanctomycetesUnknown


% SLOTUs / % sequences

Homes –floor dust

Nursing homes –hard surface settled dust

Proteobacteria

Firmicutes

Actinobacteria

30/1730/22

33/5742/50

25/2119/25


Bacterial composition of house dust in nursing Bacterial composition of house dust in nursing home buildingshome buildings


25 %

50 %

6 %

6 %

10 %

2 %

1 %

ActinobacteriaFirmicutesAlphaproteobacteriaBetaproteobacteriaDeltaproteobacteriaEpsilonproteobacteriaGammaproteobacteriaAcidobacteriaBacteroidetesChloroflexiDeinococcus-ThermusFusobacteriaPlanctomycetesUnknown



Most common SLOTUs of settled dust from floors and other

hard surfaces: Corynebacterium, Propionibacterium,

Streptococcus, Staphylococcus, Lactococcus,

Peptostreptococcus, Lactobacillus

Sources of bacteria in mattress and floor dust in homesSources of bacteria in mattress and floor dust in homes


� 69-88% of bacterial sequences in mattress dust of human origin (skin, oral,

intestinal ..) (34-59% of OTUs)

� 45-55% of bacterial sequences in floor dust of human origin (16-41% of OTUs)

� Sequences of environmental sources better represented in floor dust

(24-30% of sequences)

adapted from Täubel et al,

2009. J Allergy Clin Immunol,

124, 834-40.

Summary, conclusions 1/2Summary, conclusions 1/2


o House dust is a very rich, complex and highly diverse reservoir of

bacteria

o House dusts in our studies were dominated by Gram-positive

bacterial groups of the phyla Firmicutes and Actinobacteria

� accounting for approx. 75% of sequences in floor dust

samples, >90% in mattress dust

→ deserve more attention in bacterial exposure assessments

� Gram-negative Proteobacteria contribute considerably to

the diversity, but were less frequently detected

Summary, conclusions 2/2Summary, conclusions 2/2


o Seasonal differences in the bacterial content of house dust:

� diversity is affected by season

� not very clear on the levels of community structure and on the

higher taxonomic groups

� large difference in the bacterial content on the species level

→ important to consider when measuring/interpreting markers!

o Sources of bacteria in house dust

� bacterial content strongly determined by human-derived bacteria

� other environmental sources better represented in floor dust

� bacterial markers are typically used to assess exposure to

environmental microbes … but do not distinguish whether microbes

are from human or other sources

AcknowledgementsAcknowledgements


Department Environmental Health, National Institute for Health and

Welfare, Kuopio, Finland

Aino Nevalainen

Helena Rintala

Anne Hyvärinen

Katja Saarnio

Juha Pekkanen

Institute of Biotechnology,

University of Helsinki

Miia Pitkäranta

Tanja Horko

Lars Paulin

The Finnish Institute of Occupational

Health, Kuopio, Finland Funding

Sirpa Laitinen Finnish Technology Agency

Virpi Turunen Academy of Finland

Täubel ia2011 333_microbiome

Health & Medicine

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