Exploring the dynamic core microbiome of plaque microbiota during head-and-neck radiotherapy using pyrosequencing

Abstract

Radiotherapy is the primary treatment modality used for patients with head-and-neck cancers, but inevitably causes microorganism-related oral complications. This study aims to explore the dynamic core microbiome of oral microbiota in supragingival plaque during the course of head-and-neck radiotherapy. Eight subjects aged 26 to 70 were recruited. Dental plaque samples were collected (over seven sampling time points for each patient) before and during radiotherapy. The V1-V3 hypervariable regions of bacterial 16S rRNA genes were amplified, and the high-throughput pyrosequencing was performed. A total of 140 genera belonging to 13 phyla were found. Four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) and 11 genera (Streptococcus, Actinomyces, Veillonella, Capnocytophaga, Derxia, Neisseria, Rothia, Prevotella, Granulicatella, Luteococcus, and Gemella) were found in all subjects, supporting the concept of a core microbiome. Temporal variation of these major cores in relative abundance were observed, as well as a negative correlation between the number of OTUs and radiation dose. Moreover, an optimized conceptual framework was proposed for defining a dynamic core microbiome in extreme conditions such as radiotherapy. This study presents a theoretical foundation for exploring a core microbiome of communities from time series data, and may help predict community responses to perturbation as caused by exposure to ionizing radiation.

Figure 1. Characterization of all time points rarefaction curves and the correlation analyses between the number of OTUs and radiation dose.

(A) Rarefaction curves were used to estimate richness among the seven time points (0.03 dissimilarity level). (B) For a given number of sequences sampled (e.g., 5,000 sequences, 10,000 sequences, or 15,000 sequences), there was a negative correlation between the number of OTUs and dosage (P<0.01).

Figure 2. Relative abundance of predominant phyla at seven time points.

Members of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were found at all time points in all subjects and comprised the core microbiome. Phyla having the lowest relative abundance cannot be identified in histogram, and they were listed in small font.

Figure 3. Temporal variation in relative abundance of 11 genera found in all subjects (two common taxa and nine “potential common taxa”).

These 11 genera constituted 75.27% of the total sequences. The abscissas and ordinates represent six time points and relative abundance of each genus respectively (different in ordinate scale). The levels of relative abundance of the control group (prior to treatment) are indicated by dotted lines.