Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal RNA gene amplicons was used to study the stool microbiota of hospitalized patients and to examine the effect of antibiotic therapy. For one patient, 16 anaerobic species identified by random cloning and sequencing of PCR-ampli...

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Bibliographic Details
Published in:	Journal of microbiological methods 2003-08, Vol.54 (2), p.249-256
Main Authors:	Donskey, Curtis J., Hujer, Andrea M., Das, Sarbani M., Pultz, Nicole J., Bonomo, Robert A., Rice, Louis B.
Format:	Article
Language:	eng
Subjects:	Actinobacteria - genetics Actinobacteria - isolation & purification Anti-Bacterial Agents - therapeutic use Antibiotics Bacterial Infections - drug therapy Bacterial Infections - microbiology Bacteroides - genetics Bacteroides - isolation & purification Bifidobacterium - genetics Bifidobacterium - isolation & purification Biological and medical sciences Clostridium - genetics Clostridium - isolation & purification Denaturing gradient gel electrophoresis (DGGE) DNA, Bacterial - analysis DNA, Bacterial - chemistry Electrophoresis, Polyacrylamide Gel Feces - microbiology Fundamental and applied biological sciences. Psychology Fusobacterium - genetics Fusobacterium - isolation & purification Hospitalization Humans Intestinal Microbiology Microbiota Nucleic Acid Denaturation Ribosomal RNA RNA, Ribosomal, 16S - analysis Species Specificity Time Factors
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Summary:	Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal RNA gene amplicons was used to study the stool microbiota of hospitalized patients and to examine the effect of antibiotic therapy. For one patient, 16 anaerobic species identified by random cloning and sequencing of PCR-amplified rRNA genes from stool were represented by bands on the DGGE gel. DGGE analysis and similarity index comparisons demonstrated that the anaerobic microbiota of this individual remained stable in the absence of antibiotic therapy, was minimally affected by ciprofloxacin but markedly reduced by clindamycin therapy, and recovery of some organisms was evident within days after discontinuation of clindamycin. DGGE analysis of additional patients demonstrated similar disruptions of the intestinal microbiota associated with antibiotic therapy. The DGGE banding patterns of nine patients showed considerable variability, but several bands were shared among patients. Thus, our findings are consistent with previous studies that utilized culture techniques, and suggest that DGGE is a useful technique for analysis of the stool microbiota of hospitalized patients.
ISSN:	0167-7012 1872-8359