PMID- 15767007
OWN - NLM
STAT- MEDLINE
DCOM- 20050503
LR  - 20050315
IS  - 0167-7012 (Print)
IS  - 0167-7012 (Linking)
VI  - 61
IP  - 3
DP  - 2005 Jun
TI  - Novel phylogenetic assignment database for terminal-restriction fragment length 
      polymorphism analysis of human colonic microbiota.
PG  - 305-19
AB  - Various molecular-biological approaches using the 16S rRNA gene sequence have 
      been used for the analysis of human colonic microbiota. Terminal- restriction 
      fragment length polymorphism (T-RFLP) analysis is suitable for a rapid comparison 
      of complex bacterial communities. Terminal-restriction fragment (T-RF) length can 
      be calculated from a known sequence, thus one can predict bacterial species on 
      the basis of their T-RF length by this analysis. The aim of this study was to 
      build a phylogenetic assignment database for T-RFLP analysis of human colonic 
      microbiota (PAD-HCM), and to demonstrate the effectiveness of PAD-HCM compared 
      with the results of 16S rRNA gene clone library analysis. PAD-HCM was completed 
      to include 342 sequence data obtained using four restriction enzymes. 
      Approximately 80% of the total clones detected by 16S rRNA gene clone library 
      analysis were the same bacterial species or phylotypes as those assigned from 
      T-RF using PAD-HCM. Moreover, large T-RFs consisted of common species or 
      phylotypes detected by both analytical methods. All pseudo-T-RFs identified by 
      mung bean nuclease digestion could not be assigned to a bacterial species or 
      phylotype, and this finding shows that pseudo-T-RFs can also be predicted using 
      PAD-HCM. We conclude that PAD-HCM built in this study enables the prediction of 
      T-RFs at the species level including difficult-to-culture bacteria, and that it 
      is very useful for the T-RFLP analysis of human colonic microbiota.
FAU - Matsumoto, Mitsuharu
AU  - Matsumoto M
AD  - Fundamental Research Laboratory, Kyodo Milk Industry Co. Ltd., Hinode, Tokyo 
      190-0182, Japan. m-matumoto@meito.co.jp
FAU - Sakamoto, Mitsuo
AU  - Sakamoto M
FAU - Hayashi, Hidenori
AU  - Hayashi H
FAU - Benno, Yoshimi
AU  - Benno Y
LA  - eng
PT  - Journal Article
DEP - 20050111
PL  - Netherlands
TA  - J Microbiol Methods
JT  - Journal of microbiological methods
JID - 8306883
RN  - 0 (DNA, Bacterial)
RN  - 0 (RNA, Bacterial)
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - Adult
MH  - Bacteria/classification/*genetics/*isolation & purification
MH  - Base Sequence
MH  - Colon/*microbiology
MH  - DNA, Bacterial/genetics
MH  - *Databases, Genetic
MH  - Gene Library
MH  - Genes, Bacterial
MH  - Humans
MH  - Male
MH  - *Phylogeny
MH  - *Polymorphism, Restriction Fragment Length
MH  - RNA, Bacterial/genetics
MH  - RNA, Ribosomal, 16S/genetics
EDAT- 2005/03/16 09:00
MHDA- 2005/05/04 09:00
CRDT- 2005/03/16 09:00
PHST- 2004/09/28 00:00 [received]
PHST- 2004/12/08 00:00 [revised]
PHST- 2004/12/14 00:00 [accepted]
PHST- 2005/03/16 09:00 [pubmed]
PHST- 2005/05/04 09:00 [medline]
PHST- 2005/03/16 09:00 [entrez]
AID - S0167-7012(04)00365-3 [pii]
AID - 10.1016/j.mimet.2004.12.009 [doi]
PST - ppublish
SO  - J Microbiol Methods. 2005 Jun;61(3):305-19. doi: 10.1016/j.mimet.2004.12.009. 
      Epub 2005 Jan 11.