Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces

Abstract

The human gastrointestinal (GI) tract harbors a complex community of bacterial cells in the mucosa, lumen, and feces. Since most attention has been focused on bacteria present in feces, knowledge about the mucosa-associated bacterial communities in different parts of the colon is limited. In this study, the bacterial communities in feces and biopsy samples from the ascending, transverse, and descending colons of 10 individuals were analyzed by using a 16S rRNA approach. Flow cytometric analysis indicated that 10(5) to 10(6) bacteria were present in the biopsy samples. To visualize the diversity of the predominant and the Lactobacillus group community, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene amplicons was performed. DGGE analysis and similarity index comparisons demonstrated that the predominant mucosa-associated bacterial community was host specific and uniformly distributed along the colon but significantly different from the fecal community (P < 0.01). The Lactobacillus group-specific profiles were less complex than the profiles reflecting the predominant community. For 6 of the 10 individuals the community of Lactobacillus-like bacteria in the biopsy samples was similar to that in the feces. Amplicons having 99% sequence similarity to the 16S ribosomal DNA of Lactobacillus gasseri were detected in the biopsy samples of nine individuals. No significant differences were observed between healthy and diseased individuals. The observed host-specific DGGE profiles of the mucosa-associated bacterial community in the colon support the hypothesis that host-related factors are involved in the determination of the GI tract microbial community.

FIG. 1.

Flow cytometric dot blots showing the discrimination between the PI-stained cells and the YG beads. The different biopsy locations for one individual with colitis ulcerosa (individual 5) are illustrated. A, T, and D, ascending, transverse, and descending parts of the colon, respectively.

FIG. 2.

Silver-stained DGGE gel showing profiles which represent the predominant community of feces (F) and biopsy samples (A, T, D) of individuals 1, 5, and 10. M represents the marker for DGGE analysis. The physiological conditions of the individuals are indicated.

FIG. 3.

Comparison between fecal and biopsy samples. F, fecal samples; A, T, and D, biopsy samples from the ascending, transverse, and descending parts of the colon, respectively; -, comparison. The means and SD of similarity indices are indicated.

FIG. 4.

Silver-stained DGGE gel showing profiles which represent the Lactobacillus group community of fecal (F) and biopsy (A, T, D) samples of individuals 1, 5, and 10. The physiological conditions of the individuals are indicated.

FIG. 5.

(A) Silver-stained DGGE gel showing profiles which represent the predominant communities of the descending colon biopsy samples from individuals 1 to 10. M represents the marker for DGGE analysis. The physiological conditions of the individuals are indicated. (B) UPGMA dendrogram illustrating the correlation between the different DGGE profiles of panel A. Cluster I and II represent the repetitive clusters obtained using different algorithms. The black bars represent the error bars.

FIG. 6.

Silver-stained DGGE gel showing profiles which represent the Lactobacillus group communities of the descending colon biopsy samples from individuals 1 to 10. The physiological conditions of the individuals are indicated. The arrowheads indicate the amplicons which have been identified by cloning and sequencing.