Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus

Abstract

Human microbial communities are highly complex ecosystems, but it remains unclear if microbial compositions have any similarity in distinct sites of the oral cavity and esophagus in particular. Clinical samples were collected from three niches (saliva, tongue dorsum and supragingival plaque) of the oral cavity and three segments (upper, middle, and lower) of the esophagus in 27 healthy individuals. Bacterial V3-V4 region of 16S rRNA gene in these samples was amplified and sequenced on Illumina sequencing platform, followed by data analysis using QIIME and LEfSe softwares. Highly diverse bacterial flora with 365 genera belonging to 29 phyla resided in the oral cavity and 594 genera belonging to 29 phyla in the esophagus. The phyla Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and TM7 were most abundant in both the oral cavity and the esophagus, but the phyla Actinobacteria and Bacteroidetes were preferable in the oral cavity and Firmicutes in the esophagus. The genera Streptococcus, Neisseria, Prevotella, Actinobacillus, and Veillonella were most abundant in both oral cavity and esophagus, but Neisseria was preferable in the oral cavity and Streptococcus in the esophagus. Different niche-specific bacterial signatures were found in the oral cavity, e.g., the class Flavobacteria in the supragingival plaque, class Bacteroides in the saliva and the class Clostridia in the tongue dorsum. By contrast, no site specific bacteria for three different segments of esophagus were found. However, high variability of microbial compositions between individuals was observed. In conclusion, this study confirmed microbial diversity at different taxonomic levels in healthy oral cavity and esophagus, and identified the site-preferable bacterial signatures in six niches of the upper digestive tract. These findings provide a critical baseline for future studies interpreting microbiome-related diseases.

Keywords: 16S rRNA gene sequencing; esophagus; microbial preference; microbial similarity; oral cavity.

FIGURE 1

The relative abundance of human microbiome in the oral cavity and esophagus. (A) At the phylum level. (B) At the genus level. Sa, saliva; TD, tongue dorsum; SP, supragingival plaque; UE, upper esophagus; ME, middle esophagus; LE, lower esophagus.

FIGURE 2

The similarity of community structure within and between the oral cavity and esophagus. (A) Three-dimensional ordination of human microbial profiles by principal coordinate analysis (PCoA) of average Bray-Curtis index in different body sites. Red indicating LE, Blue indicating ME, Brown indicating Sa, Green indicating SP, Purple indicating TD, and Yellow indicating UE. (B) The similarity of microbial diversity in three sites of the esophagus estimated by Bray-Curtis index. Values expressed as the median and quartitle of Bray-Curtis index. Sa, saliva; TD, tongue dorsum; SP, supragingival plaque; OC, oral cavity; UE, upper esophagus; ME, middle esophagus; LE, lower esophagus; EE, entire esophagus; OE, oral cavity and esophagus.

FIGURE 3

Circular cladogram for niche specialization of microbial compositions in the oral cavity and esophagus using the linear discriminant analysis effect size (LEfSe) analysis of the abundance patterns of bacterial taxa. The circles used in this diagram represent the taxonomic categories of organisms from the phylum level as the outermost circle to genus (or species) level as the innermost cycle. Within each given taxon, each small cycle represents its lower taxon. The yellow nodes indicate no statistically significant differences of specific taxa between the samples from the oral cavity and the esophagus, the red nodes indicate significantly higher relative abundance in the esophagus than in the oral cavity, and the green nodes indicate significantly higher relative abundance in the oral cavity than the esophagus. The size of the node is in proportion to the linear discriminant analysis (LDA) score (detailed in Supplementary Figure S1). The links (lines) between the nodes mean hypothetically phylogenetic relationships among organisms, which can be traced back to where the lines branch off (hypothetical ancestor).

FIGURE 4

Relative abundance of most predominant discriminative microbiota between the oral cavity and the esophagus in terms of the phylum level (A) and the genus level (B).

FIGURE 5

Circular cladogram for niche specialization of microbial compositions in three sites in the oral cavity using the linear discriminant analysis effect size (LEfSe) analysis of the abundance patterns of bacterial taxa. The circles used in this diagram represent the taxonomic categories of organisms from the phylum level as the outermost circle to genus (or species) level as the innermost cycle. Within each given taxon, each small cycle represents its lower clade. The yellow nodes indicate no statistically significant differences of a given taxon between the samples of three sites, the red nodes indicate significantly higher relative abundance in saliva than other two sites, the green nodes indicate significantly higher relative abundance in the supragingival plagues than other two sites, and the blue nodes indicate significantly higher relative abundance in tongue dorsum than other two sites in oral cavity. The size of the node is in proportion to the LDA score. The links (lines) between the nodes mean hypothetically phylogenetic relationships among organisms, which can be traced back to where the lines branch off (hypothetical ancestor). Sa, saliva; TD, tongue dorsum; SP, supragingival plaque.