PMID- 20147218
OWN - NLM
STAT- MEDLINE
DCOM- 20100614
LR  - 20111209
IS  - 1559-6095 (Electronic)
IS  - 1559-6095 (Linking)
VI  - 2009
IP  - 7
DP  - 2009 Jul
TI  - Use of fluorescence in situ hybridization and the daime image analysis program 
      for the cultivation-independent quantification of microorganisms in environmental 
      and medical samples.
PG  - pdb.prot5253
LID - 10.1101/pdb.prot5253 [doi]
AB  - Conventional cultivation-based methods to measure microbial abundance are 
      unsuitable for quantifying uncultured microorganisms that constitute the majority 
      of microbial life in most environmental or medical samples. This problem is 
      solved by the quantification approach described here, which combines fluorescence 
      in situ hybridization (FISH) with rRNA-targeted probes and digital image 
      analysis. By measuring the areas of probe-labeled biomass in randomly recorded 
      image pairs, an unbiased estimate of the relative biovolume of the population of 
      interest can be obtained. This approach expresses abundance as "biovolume 
      fraction" (relative to the total biovolume of the whole microbial community). 
      This value equals the share of biochemical reaction space occupied by the 
      quantified population and thus can be more relevant ecologically than absolute 
      cell numbers (e.g., a few large cells can contain the same biovolume as many 
      small cells). Another advantage lies in the complete independence of this method 
      from the morphology of the quantified organisms. Regardless of whether the target 
      microbes occur as single cells in plankton samples, as filaments, or as dense 
      aggregates in biofilms, this cultivation-independent method allows the 
      composition of complex microbial communities to be determined.
FAU - Daims, Holger
AU  - Daims H
AD  - Department of Microbial Ecology, Vienna Ecology Centre, University of Vienna, 
      A-1090 Vienna, Austria. daims@microbial-ecology.net
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Cold Spring Harb Protoc
JT  - Cold Spring Harbor protocols
JID - 101524530
RN  - 0 (RNA, Ribosomal)
SB  - IM
MH  - Bacteria/genetics
MH  - Biofilms
MH  - Biomass
MH  - Computational Biology/methods
MH  - Ecology
MH  - Image Processing, Computer-Assisted
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - *Microbiological Techniques
MH  - Plankton/metabolism
MH  - RNA, Ribosomal/genetics/metabolism
MH  - Software
EDAT- 2010/02/12 06:00
MHDA- 2010/06/15 06:00
CRDT- 2010/02/12 06:00
PHST- 2010/02/12 06:00 [entrez]
PHST- 2010/02/12 06:00 [pubmed]
PHST- 2010/06/15 06:00 [medline]
AID - 2009/7/pdb.prot5253 [pii]
AID - 10.1101/pdb.prot5253 [doi]
PST - ppublish
SO  - Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.prot5253. doi: 
      10.1101/pdb.prot5253.