Bacterial biota in the human distal esophagus

Abstract

The esophagus, like other luminal organs of the digestive system, provides a potential environment for bacterial colonization, but little is known about the presence of a bacterial biota or its nature. By using broad-range 16S rDNA PCR, biopsies were examined from the normal esophagus of four human adults. The 900 PCR products cloned represented 833 unique sequences belonging to 41 genera, or 95 species-level operational taxonomic units (SLOTU); 59 SLOTU were homologous with culture-defined bacterial species, 34 with 16S rDNA clones, and two were not homologous with any known bacterial 16S rDNA. Members of six phyla, Firmicutes, Bacteroides, Actinobacteria, Proteobacteria, Fusobacteria, and TM7, were represented. A large majority of clones belong to 13 of the 41 genera (783/900, 87%), or 14 SLOTU (574/900, 64%) that were shared by all four persons. Streptococcus (39%), Prevotella (17%), and Veilonella (14%) were most prevalent. The present study identified approximately 56-79% of SLOTU in this bacterial ecosystem. Most SLOTU of esophageal biota are similar or identical to residents of the upstream oral biota, but the major distinction is that a large majority (82%) of the esophageal bacteria are known and cultivable. These findings provide evidence for a complex but conserved bacterial population in the normal distal esophagus.

Fig. 1.

Microscopic examination of bacterial cells in the esophagus. Esophageal biopsies were fixed in formalin, paraffin-embedded, sectioned, and examined by using Gram-Twort stain. In the biopsy from subject A, monomorphic Gram-negative bacilli were tightly associated with the surface of squamous epithelial cells (×1,000).

Fig. 2.

Correlation of sequence homology with similarity scores. The 900 sequences obtained from this study each were subjected to pairwise comparison with their most closely matched 16S rDNA sequence from the RDP II database. Sequence homology (%) and similarity score using sequence match at RDP II were calculated for each pair. The relationship between the two measurements was analyzed by linear regression. The 97% line represents the boundary of SLOTU defined by sequence homology (28). The 0.8725 line is the corresponding SLOTU boundary defined by similarity scores, as determined by linear regression in this study.

Fig. 3.

Phylogenetic analysis of bacterial 16S rDNA detected in biopsies of the normal distal esophagus from four persons. Sequences were aligned by using sequence aligner at RDP II. Misaligned positions were corrected by using arb. Phylogram was generated by using paup 4.0b10 neighbor-joining analysis, based on HKY85 distance matrices. Bootstrap values (based on 500 replicates) are represented at each node when >50%, and the branch length index is represented below the phylogram. Names of SLOTU are located at the termination of each branch. 16S rDNA clones are potential bacterial species whose phylogenetic positions were designated by PCR-amplified 16S sequences only, represented by the closest genus, followed by the GenBank accession number of the best-matched sequence. Unknowns are represented by the closest taxon followed by the serial number of the clone used in this study, as well as the percent sequence identity (in parentheses). The frequency at which a species was detected and its sources are indicated (on the right). The 95 SLOTU belonging to six phyla, contrasted by alternating red and blue print, are shown (on the right). SLOTU shared by all four persons are highlighted in yellow.