The Oral Microbiome: Methods and Protocols (Methods in Molecular Biology, 2327)

Preface..
Table of Contents...
Contributing Authors...

1. Increasing Reproducibility in Oral Microbiome Research
Divya Gopinath and Rohit Kunnath Menon

2. Oral Sampling Techniques
Heba Hussein

3. Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome
Supathep Tansirichaiya, Liam J. Reynolds, and Adam P. Roberts

4. Isolation and Functional Characterization of Fusobacterium nucleatum Bacteriophage
Mwila Kabwe, Teagan Brown, Heng Ku, Stuart Dashper, and Joseph Tucci

5. Comparison of Microbiome in Stimulated Saliva in Edentulous and Dentate Subjects
Guy R. Adami, Michael J. Ang, and Elissa M. Kim

6. Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics
Clarisse Marotz, Cristal Zuniga, Livia Zaramela, Rob Knight, and Karsten Zengler

7. A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus
Nicole E. Moore and Laura S. Weyrich

8. Whole-Genome Sequencing of Pathogens in Saliva: A Target-Enrichment Approach for SARS-CoV-2
David J. Speicher, Jalees A. Nasir, Peng Zhou, and Danielle E. Anderson

9. Assessing the Relationship Between Nitrate-Reducing Capacity of the Oral Microbiome and Systemic Outcomes
Charlene E. Goh, Bruno Bohn, and Ryan T. Demmer

10. Identification of Oral Bacterial Biosynthetic Gene Clusters Associated with Caries
Jonathon L. Baker and Anna Edlund

11. Usage of Metatranscriptomics to Understand Oral Disease
Takayasu Watanabe

12. Noninvasive Acquisition of Oral Mucosal Epithelial miRNA and Bacteria DNA/RNA from a Single Site
Guy R. Adami

13. 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, and Uwe Völker

14. Strain Level Profiling of Oral Microbiota with Targeted Sequencing
Chiranjit Mukherjee and Eugene J. Leys

15. Profiling the Human Oral Mycobiome in Tissue and Saliva Using ITS2 DNA Metabarcoding Compared to a Fungal Specific Database
David J. Speicher and Ramy K. Aziz

16. 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, and Craig D. Byron

17. Antibiotic Conditioning and Single Gavage Allows Stable Engraftment of Human Microbiota in Mice
Zhigang Zhu, Thomas Kaiser, and Christopher Staley

Subject Index List...