title: Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients.
abstract: 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.
authors.affiliation: Infectious Diseases Section (111 W), Louis Stokes Cleveland Veterans Affairs Medical Center, 10701 East Blvd., Cleveland, OH 44106, USA. curtisd123@yahoo.com
authors.forename: Curtis J
authors.initials: CJ
authors.lastname: Donskey
authors.forename: Andrea M
authors.initials: AM
authors.lastname: Hujer
authors.forename: Sarbani M
authors.initials: SM
authors.lastname: Das
authors.forename: Nicole J
authors.initials: NJ
authors.lastname: Pultz
authors.forename: Robert A
authors.initials: RA
authors.lastname: Bonomo
authors.forename: Louis B
authors.initials: LB
authors.lastname: Rice
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000302:isolation & purification; D000900:Anti-Bacterial Agents / Q000627:therapeutic use*; D001424:Bacterial Infections / Q000188:drug therapy / Q000382:microbiology*; D001439:Bacteroides / Q000235:genetics / Q000302:isolation & purification; D001644:Bifidobacterium / Q000235:genetics / Q000302:isolation & purification; D003013:Clostridium / Q000235:genetics / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis* / Q000737:chemistry; D004591:Electrophoresis, Polyacrylamide Gel; D005243:Feces / Q000382:microbiology*; D005673:Fusobacterium / Q000235:genetics / Q000302:isolation & purification; D006760:Hospitalization; D006801:Humans; D009691:Nucleic Acid Denaturation; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D013045:Species Specificity; D013997:Time Factors
chemical_list: D000900:Anti-Bacterial Agents; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S