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The Oral Microbiome

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Guy R. Adami

    1. College of Dentistry, University of Illinois at Chicago, Chicago, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2327)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Increasing Reproducibility in Oral Microbiome Research

    • Divya Gopinath, Rohit Kunnath Menon
    Pages 1-15

  3. Oral Sampling Techniques

    • Heba Hussein
    Pages 17-29

  4. Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome

    • Supathep Tansirichaiya, Liam J. Reynolds, Adam P. Roberts
    Pages 31-50

  5. Isolation and Functional Characterization of Fusobacterium nucleatum Bacteriophage

    • Mwila Kabwe, Teagan Brown, Heng Ku, Stuart Dashper, Joseph Tucci
    Pages 51-68

  6. Comparison of Microbiome in Stimulated Saliva in Edentulous and Dentate Subjects

    • Guy R. Adami, Michael J. Ang, Elissa M. Kim
    Pages 69-86

  7. Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics

    • Clarisse Marotz, Cristal Zuniga, Livia Zaramela, Rob Knight, Karsten Zengler
    Pages 87-92

  8. A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus

    • Nicole E. Moore, Laura S. Weyrich
    Pages 93-118

  9. Whole-Genome Sequencing of Pathogens in Saliva : A Target-Enrichment Approach for SARS-CoV-2

    • David J. Speicher, Jalees A. Nasir, Peng Zhou, Danielle E. Anderson
    Pages 119-137

  10. Assessing the Relationship Between Nitrate-Reducing Capacity of the Oral Microbiome and Systemic Outcomes

    • Charlene E. Goh, Bruno Bohn, Ryan T. Demmer
    Pages 139-160

  11. Identification of Oral Bacterial Biosynthetic Gene Clusters Associated with Caries

    • Jonathon L. Baker, Anna Edlund
    Pages 161-189

  12. Usage of Metatranscriptomics to Understand Oral Disease

    • Takayasu Watanabe
    Pages 191-204

  13. Noninvasive Acquisition of Oral Mucosal Epithelial miRNA and Bacteria DNA/RNA from a Single Site

    • Guy R. Adami
    Pages 205-219

  14. Bottom-Up Community Proteome Analysis of Saliva Samples and Tongue Swabs by Data-Dependent Acquisition Nano LC-MS/MS Mass Spectrometry

    • Alexander Rabe, Manuela Gesell Salazar, Uwe Völker
    Pages 221-238

  15. Strain-Level Profiling of Oral Microbiota with Targeted Sequencing

    • Chiranjit Mukherjee, Eugene J. Leys
    Pages 239-252

  16. Profiling the Human Oral Mycobiome in Tissue and Saliva Using ITS2 DNA Metabarcoding Compared to a Fungal-Specific Database

    • David J. Speicher, Ramy K. Aziz
    Pages 253-269

  17. Measuring Effects of Dietary Fiber on the Murine Oral Microbiome with Enrichment of 16S rDNA Prior to Amplicon Synthesis

    • Lea M. Sedghi, Stefan J. Green, Craig D. Byron
    Pages 271-280

  18. Antibiotic Conditioning and Single Gavage Allows Stable Engraftment of Human Microbiota in Mice

    • Zhigang Zhu, Thomas Kaiser, Christopher Staley
    Pages 281-291

  19. Back Matter

    Pages 293-295
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Keywords

About this book

This volume discusses the oral microbiome, and oral and systemic health. The chapters in this book cover topics such as analytical techniques for identifying and measuring oral bacteria; strategies for controlling common sources of variability in oral microbiome methods for viral bacterial and fungal analysis; ways to study oral DNA and RNA samples to identify molecular pathways to disease; approaches to functional assays for oral bacteriophage, antibiotic purging of systemic bacteria; and metaproteomic analysis of various oral samples. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Cutting-edge and practical, The Oral Microbiome: Methods and Protocols is a valuable resource for any scientist or researcher looking to further study this exciting and developing field.


Editors and Affiliations

  • College of Dentistry, University of Illinois at Chicago, Chicago, USA

    Guy R. Adami

Bibliographic Information

  • Book Title: The Oral Microbiome

  • Book Subtitle: Methods and Protocols

  • Editors: Guy R. Adami

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1518-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1517-1Published: 20 August 2021

  • Softcover ISBN: 978-1-0716-1520-1Published: 21 August 2022

  • eBook ISBN: 978-1-0716-1518-8Published: 19 August 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 295

  • Number of Illustrations: 85 b/w illustrations, 37 illustrations in colour

  • Topics: Microbiology, Medical Microbiology

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