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

International Journal of Microbiology
Sally Ali TawfikDalia Mukhtar Fayyad

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 o...Continue Reading

References

Nov 1, 1994·International Endodontic Journal·B P GomesJ D Lilley
Mar 1, 1993·Journal of Oral and Maxillofacial Surgery : Official Journal of the American Association of Oral and Maxillofacial Surgeons·L J Peterson
Jan 1, 1996·Journal of Dentistry·B P GomesD B Drucker
Sep 12, 2001·Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontics·I Y JungC Y Lee
Mar 27, 2003·International Endodontic Journal·E T PinheiroF J Souza-Filho
Aug 26, 2004·Oral Microbiology and Immunology·J F Siqueira, I N Rôças
Dec 8, 2004·Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontics·Isabela N RôçasAlexandre S Rosado
Jul 8, 2005·Journal of Clinical Microbiology·J F Siqueira, I N Rôças
Dec 8, 2005·Applied and Environmental Microbiology·Catherine Lozupone, Rob Knight
Jun 3, 2006·Science·Steven R GillKaren E Nelson
Aug 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Mitchell L SoginGerhard J Herndl
Jan 20, 2007·Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontics·Luiz Fernando Tomazinho, Mario J Avila-Campos
Jun 6, 2007·Australian Dental Journal·D Figdor, G Sundqvist
Jun 26, 2007·Applied and Environmental Microbiology·Qiong WangJames R Cole
Oct 19, 2007·Nature·Peter J TurnbaughJeffrey I Gordon
Nov 27, 2007·Journal of Endodontics·Geoffrey YoungDavid Figdor
Apr 26, 2008·Journal of Endodontics·Luciana M SassoneMagda Feres
Jun 28, 2008·Oral Microbiology and Immunology·M SakamotoY Benno
Apr 3, 2009·Drug Discovery Today·William W L Hsiao, Claire M Fraser-Liggett
May 26, 2009·Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontics·José F Siqueira, Isabela N Rôças
Aug 12, 2009·Nature Methods·Christopher QuinceWilliam T Sloan
Sep 1, 2009·Nature Methods·Jens Reeder, Rob Knight
Oct 13, 2009·Genome Research·UNKNOWN NIH HMP Working GroupMark Guyer
Oct 16, 2009·Journal of Dental Research·J F Siqueira, I N Rôças
Mar 5, 2010·Journal of Clinical Microbiology·Mangala A NadkarniNeil Hunter
Jun 4, 2010·Journal of Dental Research·L LiA F Fouad
Jan 1, 2009·Journal of Oral Microbiology·José F Siqueira, Isabela N Rôças
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Oct 18, 2011·Journal of Endodontics·José F SiqueiraIsabela N Rôças
Dec 20, 2011·Nature Reviews. Genetics·Justin KuczynskiRob Knight
Jan 27, 2012·Journal of Oral Microbiology·José F SiqueiraIsabela N Rôças
Oct 16, 2012·Journal of Endodontics·Mohamed H SaberJørgen Slots
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Apr 5, 2013·Clinical Microbiology Reviews·José F Siqueira, Isabela N Rôças
Aug 21, 2013·Journal of Endodontics·Bo-Young HongKee Yeon Kum
Sep 14, 2013·Journal of Microbiological Methods·Julia M Di BellaGregor Reid

❮ Previous
Next ❯

Citations

May 23, 2018·Oral Diseases·Herath Mudiyansalage Herath Nihal BandaraLakshman Perera Samaranayake
Mar 19, 2021·Molecular Biology Reports·Chidanandamurthy Thippeswamy Swamy, Devaraja Gayathri

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
electrophoresis
Illumina sequencing

Software Mentioned

MOTHUR
UniFrac
R
gplots
Alpha lnnotech
PAST
FigTree
OTUS
graphing calculator
Illumina

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.