PMID- 14678165
OWN - NLM
STAT- MEDLINE
DCOM- 20040513
LR  - 20190917
IS  - 1364-5072 (Print)
IS  - 1364-5072 (Linking)
VI  - 96
IP  - 1
DP  - 2004
TI  - Phylogenetic analysis and in situ identification of the intestinal microbial 
      community of rainbow trout (Oncorhynchus mykiss, Walbaum).
PG  - 117-32
AB  - AIMS: To identify the dominant culturable and nonculturable microbiota of rainbow 
      trout intestine. METHODS AND RESULTS: Microbial density of rainbow trout 
      intestine was estimated by direct microscopic counts 
      (4',6-diamidino-2-phenylindole, DAPI) and by culturing on tryptone soya agar 
      (TSA). Differential gradient gel electrophoresis analysis of bacterial DNA from 
      intestinal samples, re-amplification of bands and sequence analysis was used to 
      identify the bacteria that dominated samples where aerobic counts were < or =2% 
      of the DAPI counts. 16S rDNA gene sequences of 146 bacterial isolates and three 
      sequences of uncultured bacteria were identified. A set of oligonucleotide probes 
      was constructed and used to detect and enumerate the bacterial community 
      structure of the gastrointestinal tract of rainbow trout by fluorescence in situ 
      hybridization (FISH). Members of the gamma subclass of Proteobacteria (mainly 
      Aeromonas and Enterobacteriaceae) dominated the bacterial population structure. 
      Acinetobacter, Pseudomonas, Shewanella, Plesiomonas and Proteus were also 
      identified together with isolates belonging to the beta subclass of 
      Proteobacteria and Gram-positive bacteria with high and low DNA G + C content. In 
      most samples, the aerobic count (on TSA) was 50-90% of the direct (DAPI) count. A 
      bacterium representing a previously unknown phylogenetic lineage with only 89% 
      16S rRNA gene sequence similarity to Anaerofilum pentosovorans was detected in 
      intestinal samples where aerobic counts were < or =2% of direct (DAPI) counts. 
      Ten to 75% of the microbial population in samples with low aerobic counts 
      hybridized (FISH) with a probe constructed against this not-yet cultured 
      bacterium. CONCLUSIONS: Proteobacteria belonging to the gamma subclass dominated 
      the intestinal microbiota of rainbow trout. However, in some samples the 
      microflora was dominated by uncultivated, presumed anaerobic, micro-organisms. 
      The bacterial population structure of rainbow trout intestine, as well as total 
      bacterial counts, varied from fish to fish. SIGNIFICANCE AND IMPACT OF THE STUDY: 
      Good correlation was seen between cultivation results and in situ analysis, 
      however, a molecular approach was crucial for the identification of organisms 
      uncultivated on TSA.
FAU - Huber, I
AU  - Huber I
AD  - Biotechnological Institute, Kogle Alle 2, Horsholm, Denmark.
FAU - Spanggaard, B
AU  - Spanggaard B
FAU - Appel, K F
AU  - Appel KF
FAU - Rossen, L
AU  - Rossen L
FAU - Nielsen, T
AU  - Nielsen T
FAU - Gram, L
AU  - Gram L
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - J Appl Microbiol
JT  - Journal of applied microbiology
JID - 9706280
RN  - 0 (DNA, Bacterial)
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - Animals
MH  - Bacteria/classification/*isolation & purification
MH  - Bacterial Typing Techniques/methods
MH  - DNA Fingerprinting
MH  - DNA, Bacterial/genetics
MH  - Electrophoresis, Agar Gel/methods
MH  - In Situ Hybridization, Fluorescence
MH  - Intestines/*microbiology
MH  - Oligonucleotide Probes
MH  - Oncorhynchus mykiss/*microbiology
MH  - Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
EDAT- 2003/12/18 05:00
MHDA- 2004/05/14 05:00
CRDT- 2003/12/18 05:00
PHST- 2003/12/18 05:00 [pubmed]
PHST- 2004/05/14 05:00 [medline]
PHST- 2003/12/18 05:00 [entrez]
AID - 2109 [pii]
AID - 10.1046/j.1365-2672.2003.02109.x [doi]
PST - ppublish
SO  - J Appl Microbiol. 2004;96(1):117-32. doi: 10.1046/j.1365-2672.2003.02109.x.