TABLE 5.

Comparison of quantitative PCR, FISH, and the culture method for detection and quantification of predominant bacteria in fecal samplesa

BacteriaLog10 cells/g (wet wt) fora:
Subject ASubject BSubject CSubject DSubject ESubject F
qPCRbFISHCultureqPCRFISHCultureqPCRFISHCultureqPCRFISHCultureqPCRFISHCultureqPCRFISHCulture
C. coccoides group10.410.410.410.710.410.310.410.29.910.510.510.310.310.310.29.59.4NDc
C. leptum subgroup10.110.310.110.710.29.910.710.010.410.810.410.210.59.810.16.5NDND
B. fragilis group10.510.310.710.110.410.310.110.310.39.49.79.410.010.010.29.78.59.7
Bifidobacterium9.99.79.210.310.39.910.39.910.09.79.39.49.89.49.46.57.8ND
Atopobium cluster9.69.79.99.69.99.910.39.610.29.99.710.19.99.19.86.8NDND
PrevotellaNDNTdNDNDNTND10.2NT9.810.7NT10.4NDNTNDNDNTND
Sum of six groups10.910.911.011.111.010.811.210.810.911.210.810.910.910.610.79.99.59.7
Total bacteriaNT11.0e11.1fNT11.110.9NT10.911.0NT10.911.0NT10.810.7NT9.79.9
Total cells (DAPI)11.211.311.211.111.110.3
  • a Fecal samples collected in the eighth month were used for comparison.

  • b qPCR, quantitative PCR.

  • c ND, not detected.

  • d NT, not tested.

  • e Total number of bacteria determined by hybridization with probe Bact338. In the present study, 66, 63, 46, 60, 53, and 28% (average±standard deviation, 53% ± 14%) of the total cells were detected with the Bact338 probe in samples from subjects A, B, C, D, E, and F, respectively.

  • f Total cultivated bacteria with medium 10.