Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples

Abstract

Little is known about bacterial communities that colonize mucosal surfaces in the human gastrointestinal tract, but they are believed to play an important role in host physiology. The objectives of this study were to investigate the compositions of these populations in the distal small bowel and colon. Healthy mucosal tissue from either the terminal ileum (n = 6) or ascending (n = 8), transverse (n = 8), or descending colon (n = 4) of 26 patients (age, 68.5 +/- 1.2 years [mean +/- standard deviation]) undergoing emergency resection of the large bowel was used to study these communities. Mucosa-associated eubacteria were characterized by using PCR-denaturing gradient gel electrophoresis (DGGE), while real-time PCR was employed for quantitative analysis. Mucosal communities were also visualized in situ using confocal laser scanning microscopy. DGGE banding profiles from all the gut regions exhibited at least 45% homology, with five descending colon profiles clustering at ca. 75% concordance. Real-time PCR showed that mucosal bacterial population densities were highest in the terminal ileum and that there were no significant differences in overall bacterial numbers in different parts of the colon. Bifidobacterial numbers were significantly higher in the large bowel than in the terminal ileum (P = 0.006), whereas lactobacilli were more prominent in the distal large intestine (P = 0.019). Eubacterium rectale (P = 0.0004) and Faecalibacterium prausnitzii (P = 0.001) were dominant in the ascending and descending colon. Site-specific colonization in the gastrointestinal tract may be contributory in the etiology of some diseases of the large intestine.

FIG. 1.

Dendrogram produced with the unweighted pair group method with arithmetic mean showing the percent matching of DGGE fingerprints derived from terminal ileum, ascending colon, transverse colon and descending colon tissue samples. The dendrogram was produced using the BioNumerics Fingerprint software package.

FIG. 2.

CLSM micrographs (magnification, ×60) of transverse sections of healthy gut mucosa, stained with DAPI, showing the occurrence of helical bacteria in the mucus layer lining a crypt and individual bacterial cells in the mucus layer of an ileum sample (A) and a heterogeneous assembly of microorganisms in the mucus layer of a tissue sample from the ascending colon (B).

FIG. 3.

CLSM fluorescent light micrographs (magnification, ×60). (A) Healthy rectal mucosa from the ascending colon stained with a Bacteroides genus-specific 16S rRNA probe labeled with Cy3 and with a Bifidobacterium genus-specific 16S rRNA oligonucleotide probe labeled with FITC. (B and C) Transverse sections of biopsy samples from the transverse colon (B) and descending colon (C), stained with the E. rectale/C. coccoides group probe (Cy3) and an atopobium cluster probe labeled with FITC. The bacteria can be seen to be present throughout the mucosae in the samples, growing in discrete colonies and in assemblages.