PMID- 21325608
OWN - NLM
STAT- MEDLINE
DCOM- 20110526
LR  - 20211020
IS  - 1091-6490 (Electronic)
IS  - 0027-8424 (Print)
IS  - 0027-8424 (Linking)
VI  - 108
IP  - 10
DP  - 2011 Mar 8
TI  - Systems-level analysis of microbial community organization through combinatorial 
      labeling and spectral imaging.
PG  - 4152-7
LID - 10.1073/pnas.1101134108 [doi]
AB  - Microbes in nature frequently function as members of complex multitaxon 
      communities, but the structural organization of these communities at the 
      micrometer level is poorly understood because of limitations in labeling and 
      imaging technology. We report here a combinatorial labeling strategy coupled with 
      spectral image acquisition and analysis that greatly expands the number of 
      fluorescent signatures distinguishable in a single image. As an imaging proof of 
      principle, we first demonstrated visualization of Escherichia coli labeled by 
      fluorescence in situ hybridization (FISH) with 28 different binary combinations 
      of eight fluorophores. As a biological proof of principle, we then applied this 
      Combinatorial Labeling and Spectral Imaging FISH (CLASI-FISH) strategy using 
      genus- and family-specific probes to visualize simultaneously and differentiate 
      15 different phylotypes in an artificial mixture of laboratory-grown microbes. We 
      then illustrated the utility of our method for the structural analysis of a 
      natural microbial community, namely, human dental plaque, a microbial biofilm. We 
      demonstrate that 15 taxa in the plaque community can be imaged simultaneously and 
      analyzed and that this community was dominated by early colonizers, including 
      species of Streptococcus, Prevotella, Actinomyces, and Veillonella. Proximity 
      analysis was used to determine the frequency of inter- and intrataxon 
      cell-to-cell associations which revealed statistically significant intertaxon 
      pairings. Cells of the genera Prevotella and Actinomyces showed the most 
      interspecies associations, suggesting a central role for these genera in 
      establishing and maintaining biofilm complexity. The results provide an initial 
      systems-level structural analysis of biofilm organization.
FAU - Valm, Alex M
AU  - Valm AM
AD  - Marine Biological Laboratory, Woods Hole, MA 02543, USA.
FAU - Mark Welch, Jessica L
AU  - Mark Welch JL
FAU - Rieken, Christopher W
AU  - Rieken CW
FAU - Hasegawa, Yuko
AU  - Hasegawa Y
FAU - Sogin, Mitchell L
AU  - Sogin ML
FAU - Oldenbourg, Rudolf
AU  - Oldenbourg R
FAU - Dewhirst, Floyd E
AU  - Dewhirst FE
FAU - Borisy, Gary G
AU  - Borisy GG
LA  - eng
GR  - 1RC1-DE020630/DE/NIDCR NIH HHS/United States
GR  - 1F31-DE019576/DE/NIDCR NIH HHS/United States
GR  - R01 EB002583/EB/NIBIB NIH HHS/United States
GR  - RC1 DE020630/DE/NIDCR NIH HHS/United States
GR  - U01 DE016937/DE/NIDCR NIH HHS/United States
GR  - F31 DE019576/DE/NIDCR NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20110216
PL  - United States
TA  - Proc Natl Acad Sci U S A
JT  - Proceedings of the National Academy of Sciences of the United States of America
JID - 7505876
SB  - IM
CIN - Nat Rev Microbiol. 2011 Apr;9(4):226. PMID: 21526511
CIN - Nat Methods. 2011 Apr;8(4):288. PMID: 21574278
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - *Microbiology
PMC - PMC3054005
COIS- The authors declare no conflict of interest.
EDAT- 2011/02/18 06:00
MHDA- 2011/05/27 06:00
PMCR- 2011/09/08
CRDT- 2011/02/18 06:00
PHST- 2011/02/18 06:00 [entrez]
PHST- 2011/02/18 06:00 [pubmed]
PHST- 2011/05/27 06:00 [medline]
PHST- 2011/09/08 00:00 [pmc-release]
AID - 1101134108 [pii]
AID - 201101134 [pii]
AID - 10.1073/pnas.1101134108 [doi]
PST - ppublish
SO  - Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4152-7. doi: 
      10.1073/pnas.1101134108. Epub 2011 Feb 16.