Täubel ia2011 333_microbiome

650 views

Published on

Presentation on bacterial content in house dust during Indoor Air 2011, Austin, Texas

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
650
On SlideShare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
7
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Täubel ia2011 333_microbiome

  1. 1. 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. Nevalainen08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 1
  2. 2. Motivation/Background – Asthma and allergy and indoor microbial exposuresAssociations of microbial exposures and development of allergicdiseases have been shown The "hygiene hypothesis" → levels of bacterial markers in house dust are used to assess indoor exposure to bacteria08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 2
  3. 3. Motivation/Background –Building moisture/dampness/microbial contamination and associations with adverse health outcomes Dampness /microbial contamination Health effects causative agents mechanisms08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 3
  4. 4. Knowledge on the exposure is is crucial for understanding 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 needed08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 4
  5. 5. Materials & Methods 1/2Diversity, Sourcesseasonal dynamics Sampling locations• two nursing home buildings • three flats, one dwelling house(B1, B2), with and without (A, B, C, D)moisture damage Sample material• Vacuumed settled dust from • Skin surface swabshard surfaces, combined over 2 • Vacuumed mattress dustmonths; four samples per • Vacuumed floor dustbuilding (one per season)Rintala H., et al 2008. BMC Microbiology, 8, 56.Täubel M., et al 2009. J Allergy Clin Immunol, 124, 834-40.08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 5
  6. 6. Materials & Methods 1/2Lab worko duplicate DNA extractions (bead beating)o universal 16S rRNA gene PCR amplification (10 reactions)o purification and construction of clone libraries in E. colio Sequencing in ABI3700 DNA sequenceSequence processing and analysiso full length 16S rRNA gene sequences processed with Staden packageo chimera cleaning using Bellerophone and Chimera_Checko (SL)OTU definition using DOTUR (97% and 99% cut-offs)o Phylogeny: alignment against GenBank using BLASTo sequence analyses: DOTUR, SONS, web-libshuff, UniFrac, …08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 6
  7. 7. Bacterial richness in house dustSpecies-level operational taxonomic units (SLOTUs – observed andChao estimates) in floor dusts of 2 nursing homes (B1,B2) and fromfloor and mattress dust of 4 homes (Hf and Hm; A,B,C,D).Samples: No. of seq. SLOTUs obs. SLOTUs Chaosub-study 1B1f – combined 426 167 440B1f – 4 seasons 76-144 30-66 99-231 House dust is a rich reservoirB2f – combined 467 167 464 of different bacteriaB2f – 4 seasons 82-159 45-65 131-463Samples: No. of seq. SLOTUs obs. SLOTUs Chaosub-study 2Hf – combined 1038 248 455Hf – A,B,C,D 234-308 60-123 83-310Hm – combined 1067 174 339Hm – A,B,C,D 242-283 26-90 53-204No. 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 estimator08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 7
  8. 8. Bacterial richness and diversity in floor dust vs. mattress dust Bacterial diversity higher in floor dust vs. mattress dust in homes 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 richness higher in individual and pooled floor dust compared to mattress dust samplesTäubel et al 2009. J Allergy Clin Immunol, 124, 834-40. 08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 8
  9. 9. Seasonal dynamics of bacteria in house dust of nursing homes Bacterial diversity lowest during winter and highest during spring Bacterial diversity in floor dust according to Shannon Weaver Index 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 4.1008.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 9
  10. 10. Seasonal dynamics of bacteria in house dust of nursing homes Bacterial diversity lowest during winter and highest during spring 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 season08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 10
  11. 11. Bacterial composition of house dust in homes % SLOTUs / % sequencesActinobacteria 44/36 20/21 25/21Firmicutes 31/61 52/70 33/57Proteobacteria 23/3 18/5 30/1708.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 11
  12. 12. Bacterial composition of house dust in homesMost common SLOTUs in floor and mattress dust:Staphylococcus, Corynebacterium, Lactobacillus,Propionibacterium, Streptococcus, Lactococcus08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 12
  13. 13. Bacterial composition of house dust in nursing home buildings Distribution of clones 1% Distribution of clones 2% 10 % 25 % Actinobacteria Firmicutes 6% Alphaproteobacteria Betaproteobacteria Deltaproteobacteria 6% Epsilonproteobacteria Gammaproteobacteria Acidobacteria Bacteroidetes Chloroflexi Deinococcus-Thermus Fusobacteria Planctomycetes 50 % Unknown % SLOTUs / % sequences Nursing homes – Homes – hard surface settled dust floor dustActinobacteria 19/25 25/21Firmicutes 42/50 33/57Proteobacteria 30/22 30/1708.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 13
  14. 14. Bacterial composition of house dust in nursing home buildings Distribution of clones 1% Distribution of clones 2% 10 % 25 % Actinobacteria Firmicutes 6% Alphaproteobacteria Betaproteobacteria Deltaproteobacteria 6% Epsilonproteobacteria Gammaproteobacteria Acidobacteria Bacteroidetes Chloroflexi Deinococcus-Thermus Fusobacteria Planctomycetes 50 % UnknownMost common SLOTUs of settled dust from floors and otherhard surfaces: Corynebacterium, Propionibacterium,Streptococcus, Staphylococcus, Lactococcus,Peptostreptococcus, Lactobacillus08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 14
  15. 15. Sources of bacteria in mattress and floor dust in homes adapted from Täubel et al, 2009. J Allergy Clin Immunol, 124, 834-40. 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) 08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 15
  16. 16. Summary, conclusions 1/2o House dust is a very rich, complex and highly diverse reservoir ofbacteriao House dusts in our studies were dominated by Gram-positivebacterial 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 detected08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 16
  17. 17. Summary, conclusions 2/2o 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 08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 17
  18. 18. AcknowledgementsDepartment Environmental Health, National Institute for Health andWelfare, Kuopio, FinlandAino NevalainenHelena RintalaAnne HyvärinenKatja SaarnioJuha PekkanenInstitute of Biotechnology,University of HelsinkiMiia PitkärantaTanja HorkoLars PaulinThe Finnish Institute of OccupationalHealth, Kuopio, Finland FundingSirpa Laitinen Finnish Technology AgencyVirpi Turunen Academy of Finland08.06.2011 Indoor Air 2011; Bacteria in house dust; M Täubel 18

×