PMID- 20870788
OWN - NLM
STAT- MEDLINE
DCOM- 20110222
LR  - 20211020
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Print)
IS  - 0099-2240 (Linking)
VI  - 76
IP  - 22
DP  - 2010 Nov
TI  - Impacts of inter- and intralaboratory variations on the reproducibility of 
      microbial community analyses.
PG  - 7451-8
LID - 10.1128/AEM.01595-10 [doi]
AB  - With the advent of molecular biological techniques, especially next-generation 
      sequencing and metagenomics, the number of microbial biogeography studies is 
      rapidly increasing. However, these studies involve the synthesis of data 
      generated by different laboratories using different protocols, chemicals, etc., 
      all with inherent biases. The aim of this study was to assess inter- as well as 
      intralaboratory variations in microbial community composition when standardized 
      protocols are applied to a single soil sample. Aliquots from a homogenized soil 
      sample from a rice field in Italy were sent to five participating laboratories. 
      DNA was extracted by two investigators per laboratory using an identical 
      protocol. All DNA samples were sent to one laboratory to perform DNA 
      quantification, quantitative PCR (QPCR), and microarray and denaturing gradient 
      gel electrophoresis (DGGE) analyses of methanotrophic communities. Yields, as 
      well as purity of DNA, were significantly different between laboratories but in 
      some cases also between investigators within the same laboratory. The differences 
      in yield and quality of the extracted DNA were reflected in QPCR, microarray, and 
      DGGE analysis results. Diversity indices (Shannon-Wiener, evenness, and richness) 
      differed significantly between laboratories. The observed differences have 
      implications for every project in which microbial communities are compared in 
      different habitats, even if assessed within the same laboratory. To be able to 
      make sensible comparisons leading to valid conclusions, intralaboratory variation 
      should be assessed. Standardization of DNA extraction protocols and possible use 
      of internal standards in interlaboratory comparisons may help in rendering a 
      "quantifiable" bias.
FAU - Pan, Yao
AU  - Pan Y
AD  - Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 
      Rijksstraatweg 6, NL-3631 AC Nieuwersluis, The Netherlands.
FAU - Bodrossy, Levente
AU  - Bodrossy L
FAU - Frenzel, Peter
AU  - Frenzel P
FAU - Hestnes, Anne-Grethe
AU  - Hestnes AG
FAU - Krause, Sascha
AU  - Krause S
FAU - Luke, Claudia
AU  - Luke C
FAU - Meima-Franke, Marion
AU  - Meima-Franke M
FAU - Siljanen, Henri
AU  - Siljanen H
FAU - Svenning, Mette M
AU  - Svenning MM
FAU - Bodelier, Paul L E
AU  - Bodelier PL
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20100924
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
SB  - IM
MH  - *Biodiversity
MH  - Electrophoresis, Polyacrylamide Gel
MH  - Italy
MH  - Metagenomics/*methods/*standards
MH  - Microarray Analysis
MH  - Nucleic Acid Denaturation
MH  - Oryza
MH  - Polymerase Chain Reaction
MH  - Reproducibility of Results
MH  - *Soil Microbiology
PMC - PMC2976186
EDAT- 2010/09/28 06:00
MHDA- 2011/02/23 06:00
PMCR- 2011/05/01
CRDT- 2010/09/28 06:00
PHST- 2010/09/28 06:00 [entrez]
PHST- 2010/09/28 06:00 [pubmed]
PHST- 2011/02/23 06:00 [medline]
PHST- 2011/05/01 00:00 [pmc-release]
AID - AEM.01595-10 [pii]
AID - 1595-10 [pii]
AID - 10.1128/AEM.01595-10 [doi]
PST - ppublish
SO  - Appl Environ Microbiol. 2010 Nov;76(22):7451-8. doi: 10.1128/AEM.01595-10. Epub 
      2010 Sep 24.