Work Description

Title: Plaque microbiome in caries-active and caries-free teeth by dentition: ASV Data Table Open Access Deposited

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Attribute Value
Methodology
  • *DNA extraction and Sequencing* DNA was extracted from thawed samples. If no liquid was present in the stored plaque sample following thawing, 300ul of cell lysis solution (Promega) was added. 100ul of plaque-containing liquid was added to an enzyme mastermix containing lysozyme (15mg/ml), mutanolysin (375U/ml), RNase A (150ug/ml), and lysostaphin (240ug/ml) (all from Sigma Aldrich). DNA was extracted using a Qiagen Qicube enzymatic lysis and DNA extraction protocol. DNA was quality control checked using a NanoDrop2000 (Thermo Scientific™). The V4 region of the 16s rRNA gene was sequenced using the Illumina MiSeq platform, with a dual indexing sequencing strategy (JJ et al. 2013). The library preparation kit was MiSeq Reagent Kit V2 500 cycles (Illumina cat# MS102-2003). Each plate of samples was submitted with a positive mock community control, a DNA extraction kit control, and a negative water control. Both positive and negative controls were sequenced simultaneously. Sequences have been submitted to the NCBI Sequence Read Archive.

  • *Bioinformatics* We filtered sequences using the DADA2 package in R and assigned taxonomy using the Human Oral Microbiome Database (HOMD) reference database (Escapa et al. 2020). Briefly, DADA2 uses a naïve Bayesian classifier method to assign taxonomy to the sequence variants (Callahan et al. 2016). We removed amplicon sequence variants (ASVs) which were not bacterial and collapsed ASVs assigned to the same species together. ASVs of unknown species were given their assigned ASV number from the DADA2 package. After quality filtering, there were 13,932,494 reads (1,125 to 60,402 per sample), with an average read count of 18,284, and our sequencing was sufficiently deep to detect most of the taxonomic diversity. We identified 188 bacterial ASVs.

  • Files Contained Here: -This file contains the raw ASV counts for our 188 bacterial ASVs, which were assigned to the species level with the HOMD database. Each row represents a de-identified sample and each column represents a different bacterial species.
Description
  • This cross-sectional analysis included 584 participants in the Center for Oral Health Research in Appalachia cohort 1 (COHRA1). We sequenced the V4 region of the 16S rRNA of supragingival plaque from 185 caries-active and 565 caries-free teeth using the Illumina MiSeq platform. Sequences were filtered using the R DADA2 package and assigned taxonomy using the Human Oral Microbiome Database ( http://www.homd.org/).
Creator
Depositor
  • deesha@umich.edu
Contact information
Discipline
Funding agency
  • National Institutes of Health (NIH)
Keyword
Citations to related material
  • In press
Resource type
Last modified
  • 11/23/2022
Published
  • 12/23/2021
DOI
  • https://doi.org/10.7302/1mfw-df60
License
To Cite this Work:
Bhaumik, D. (2021). Plaque microbiome in caries-active and caries-free teeth by dentition: ASV Data Table [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/1mfw-df60

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Files (Count: 3; Size: 2.13 MB)

Thumbnailthumbnail-column Title Original Upload Last Modified File Size Access Actions
Deepblue_Explanation_of_variables.docx 2021-12-09 2021-12-09 12 KB Open Access
Study_Doc_All_Consents_Pitt.pdf 2021-12-09 2021-12-09 1.96 MB Open Access
SUPPLEMENTAL_FILE_1_Raw_ASV_Table.csv 2021-10-29 2021-10-29 165 KB Open Access

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