Abstract
This study offers a novel description of the sinonasal microbiome, through an unsupervised machine learning approach combining dimensionality reduction and clustering. We apply our method to the International Sinonasal Microbiome Study (ISMS) dataset of 410 sinus swab samples. We propose three main sinonasal ‘microbiotypes’ or ‘states’: the first is Corynebacterium-dominated, the second is Staphylococcus-dominated, and the third dominated by the other core genera of the sinonasal microbiome (Streptococcus, Haemophilus, Moraxella, and Pseudomonas). The prevalence of the three microbiotypes studied did not differ between healthy and diseased sinuses, but differences in their distribution were evident based on geography. We also describe a potential reciprocal relationship between Corynebacterium species and Staphylococcus aureus, suggesting that a certain microbial equilibrium between various players is reached in the sinuses. We validate our approach by applying it to a separate 16S rRNA gene sequence dataset of 97 sinus swabs from a different patient cohort. Sinonasal microbiotyping may prove useful in reducing the complexity of describing sinonasal microbiota. It may drive future studies aimed at modeling microbial interactions in the sinuses and in doing so may facilitate the development of a tailored patient-specific approach to the treatment of sinus disease in the future.
Footnotes
Funding information, Disclosures and Conflicts of Interest (COI):
Mohammad Javed Ali:
Receives royalties from Springer for his treatise “Principles and Practice of Lacrimal Surgery” and “Atlas of Lacrimal Drainage Disorders”.
No conflict of interest relevant to this study.
Ahmed Bassiouni, Clare Cooksley, Mahnaz Ramezanpour, Sophia Moraitis:
No conflict of interest to declare.
Benjamin Bleier:
Grant Funding: R01 NS108968-01 NIH/NINDS (Bleier PI) – This isn’t relevant to this study. Consultant for: Gyrus ACMI Olympus, Canon, Karl Storz, Medtronic, and Sinopsys.
Equity: Cerebent, Inc, Arrinex. COI: None relevant to this study.
Claudio Callejas:
No conflict of interest to declare.
J Gregory Caporaso, Matthew R Dillon, Arron Shiffer:
No conflicts of interest to declare. This work was funded in part by National Science Foundation Award 1565100 to JGC.
Emily K Cope:
Financial information: This work was partially funded under the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University.
No relevant disclosures or COI.
Marjolein E Cornet:
No financial relationships or sponsors. No conflicts of interests.
Richard G Douglas:
Received consultancy fees from Lyra Therapeutics and is a consultant for Medtronic. These are not relevant to this study.
Daniel Dutra:
No conflict of interest to declare.
Richard J Harvey:
Consultant with Medtronic, Olympus and NeilMed pharmaceuticals. He has also been on the speakers’ bureau for Glaxo-Smith-Kline, Seqiris and Astra-Zeneca.
No direct conflict of interest to declare.
Christos Georgalas:
No conflicts of interest to declare.
Peter H Hwang:
Financial Relationships: Consultancies with Arrinex, Bioinspire, Canon, Lyra Therapeutics, Medtronic, Tivic.
Conflicts of Interest: None.
Amber U Luong:
Serves as a consultant for Aerin Medical (Sunnyvale, CA), Arrinex (Redwood City, CA), Lyra Therapeutics (Watertown, MA), and Stryker (Kalamazoo, MI) and is on the advisory board for
ENTvantage (Austin, TX).
Her department receives funding from Genetech/Roche (San Francisco, CA) and AstraZeneca (Cambridge, England).
No COI to declare related to this study.
Sathish Paramasivan:
Supported by a Garnett Passe and Rodney Williams Memorial Foundation Academic Surgeon Scientist Research Scholarship.
No conflicts of interest to declare.
Alkis J Psaltis:
Consultant for Aerin Devices and ENT technologies and is on the speakers’ bureau for Smith and Nephew. Received consultancy fees from Lyra Therapeutics. These are not relevant to this study.
Rodney J Schlosser:
Grant support from OptiNose, Entellus, and IntersectENT (not relevant to this study). Consultant for Olympus, Meda, and Arrinex (not relevant to this study).
Pongsakorn Tantilipikorn:
No financial disclosures or conflict of interest.
Marc A Tewfik:
Principal Investigator: Sanofi, Roche/Genentech, AstraZeneca. Speaker/Consultant: Stryker, Ondine Biomedical, Novartis, MEDA, Mylan. Royalties for book sales: Thieme.
Sarah Vreugde:
No conflicts of interest relevant to this study.
Peter–John Wormald:
Receives royalties from Medtronic, Integra, and Scopis, and is a consultant for NeilMed. These are not relevant to this study.