The impact of various time intervals on the supragingival plaque dynamic core microbiome

PLoS One. 2015 May 5;10(5):e0124631. doi: 10.1371/journal.pone.0124631. eCollection 2015.

Abstract

Objective: The aim of this study was to examine the influence of various time intervals on the composition of the supragingival plaque microbiome, especially the dynamic core microbiome, and to find a suitable observation interval for further studies on oral microbiota.

Methods and materials: Eight qualified volunteers whose respective age ranges from 25 to 28 years participated in the present study. The supragingival plaque was collected from the buccogingival surface of the maxillary first molar at eight time slots with different intervals (day 0, 1 day, 3 days, 1 week, 2 weeks, 3 weeks, 1 month, and 3 months). Bioinformatic analyses was performed based on 16S rDNA pyrosequencing (454 sequencing platform) targeting at the hypervariable V4-V5 region, in order to assess the diversity and variation of the supragingival plaque microbiome.

Results: A total of 359,565 qualified reads for 64 samples were generated for subsequent analyses, which represents 8,452 operational taxonomic units identified at 3% dissimilarity. The dynamic core microbiome detected in the current study included five phyla, 12 genera and 13 species. At the genus level, the relative abundance of bacterial communities under the "1 day," "1 month," and "3 months" intervals was clustered into sub-category. At the species level, the number of overlapping species remained stable between the "1 month" and "3 months" intervals, whereas the number of dynamic core species became stable within only 1 week.

Conclusions: This study emphasized the impact of different time intervals (days, weeks and months) on the composition, commonality and diversity of the supragingival microbiome. The analyses found that for various types of studies, the time interval of a month is more suitable for observing the general composition of the supragingival microbiome, and that a week is better for observing the dynamic core microbiome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Biodiversity
  • Cluster Analysis
  • Computational Biology
  • Dental Plaque / microbiology*
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Male
  • Metagenome
  • Microbiota*
  • RNA, Ribosomal, 16S / genetics
  • Time Factors

Substances

  • RNA, Ribosomal, 16S

Grant support

This work was supported by the National Science & Technology Pollar Program during the 12th Five-year plan Period (Grant No.2012BAL07B03). This work was also supported by Grant No. 81070826/81371143 from the National Natural Science Foundation of China and was partly supported by Shanghai Rising-Star Program No. 12QH1401400. ZWH received the funding.