Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt

Abstract

The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department) using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level, Prevotella, Bacillus, Porphyromonas, Streptococcus, and Bacteroides were the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.

Effect of Sample Collection (Manual Expression vs. Pumping) and Skimming on the Microbial Profile of Human Milk Using Culture Techniques and Metataxonomic Analysis

“…In relation to bioinformatics, around the time in which our samples were being collected and analyzed, some articles describing the use of the Illumina application for the bioinformatic analysis of metataxonomic data were published [ 30 , 31 ], and we decided to apply such an approach to our work. The Illumina workflow uses a proprietary algorithm for paired-end reads and has the advantages of being an automated and user-friendly method linked to the highly used Illumina platform, offering a rapid and easy-to-use approach, even for those groups that are not familiarized with bioinformatics, which remains a bottleneck for microbiome studies.…”

Biodiversity of the human oral mycobiome in health and disease

“…Although there are many studies on the bacteriome of endodontic infections (Hong et al., ; Tawfik, Azab, Ahmed, & Fayyad, ), there are scant data on its mycobiome evaluated by newer techniques uncovering the uncultivable flora. In a relatively recent study, Gomes, Fidel, Fidel, and de Moura Sarquis () isolated filamentous fungi from over one‐fourth of the root canals of teeth with pulp necrosis and identified Aspergillus spp.…”

Escherichia coli strain INF32/16/A: Dataset of raw reads and assembled draft genome

“…This data consists of raw reads of the E. coli strain INF32/16/A genome that was sequenced via Illumina MiSeq technology [1] . The paired-end data sets were named as 32-16-A_R1.fastq and 32-16-A_R2.fastq.…”