Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates

Abstract

Background: Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with disease; however, little is known about the baseline bacterial profiles from various human habitats of healthy Chinese undergraduates.

Results: Using parallel barcoded 454 pyrosequencing targeting on the 16S rRNA gene V3 region, the bacterial diversity of the nasopharynx, saliva, dominant hands, and feces were investigated from 10 healthy Chinese junior boarding undergraduates at Zhejiang University. The participants were 21-24 years of age with a body mass index (BMI) < 24 kg/m(2). A total of 156,717 high-quality pyrosequencing reads were obtained for evaluating bacterial diversity, which represented 29,887 unique phylotypes. The overall taxonomic distribution of the 16S rRNA gene-based amplicons demonstrated that these 4 habitats of the human body harbored distinct microbiota and could be divided into different clusters according to anatomic site, while the established patterns of bacterial diversity followed the human body habitat (feces, hands, saliva, and nasopharynx). Although significant inter-individual variation was observed, the healthy microbiota still shared a large number of phylotypes in each habitat, but not among the four habitats, indicating that a core microbiome existed in each healthy habitat. The vast majority of sequences from these different habitats were classified into different taxonmies that became the predominant bacteria of the healthy microbiota.

Conclusions: We first established the framework of microbial communities from four healthy human habitats of the same participants with similar living environments for the Chinese undergraduates. Our data represent an important step for determining the diversity of Chinese healthy microbiota, and can be used for more large-scale studies that focus on the interactions between healthy and diseases states for young Chinese adults in the same age range.

Figure 1

The Shannon index was used to estimate diversity (i.e., a combined assessment of the number of 3% dissimilar bacterial taxa and their abundance) among nasopharynx, saliva, dominant hand and feces from healthy Chinese undergraduates (Data shown as mean with SEM).

Figure 2

Rarefaction curves were used to estimate richness (in this case the number of taxa at a 3% dissimilarity level) among nasopharynx, saliva, dominant hand and feces from healthy Chinese undergraduates. The vertical axis shows the number of OTUs that would be expected to be found after sampling the number of tags or sequences shown on the horizontal axis.

Figure 3

Differentiation in bacterial communities from all participants (interpersonal variations). Community differentiation was measured by using the unweighted UniFrac algorithm; the scale bar indicated the distance between clusters in UniFrac units. All of the branch nodes shown here were found to be significant, indicating that bacterial community from each habitat was divided into a distinctive cluster.

Figure 4

3D PCoA plots of individual bacterial communities from the four healthy habitats in Chinese undergraduates obtained by mothur program and Sigmaplot. 3D PCoA plots demonstrating that primary clustering was by anatomical site, with the saliva, feces, dominant hand and nasopharynx separate.

Figure 5

Venn diagrams illustrating overlap of OTUs by habitat, for male and female subjects.

Figure 6

A Venn diagram illustrating overlap of OTUs for nasopharynx, saliva, dominant hand and feces from healthy Chinese undergraduates. A total of 7916 OTUs were detected. Only thirty-seven OTUs were detected in all four habitats.

Figure 7

Compositional differences in the microbiome by anatomical site. The relative proportion of sequences determined at the phylum and genus level for all four habitats from healthy Chinese undergraduates.

Figure 8

The relative abundance of predominant genera obtained by pyrosequencing from nasopharynx (A), saliva (B), dominant hand (C) and feces (D) of male and female healthy Chinese undergraduates.