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Cited by 5Oral microbiology and periodontitis researchHead and Neck Cancer StudiesGut microbiota and health

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Is Short-Read 16S rRNA Sequencing of Oral Microbiome Sampling a Suitable Diagnostic Tool for Head and Neck Cancer?

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Yeo, Kenny, Wu, Fangmeinuo, Li, Runhao, Smith, Eric, Wormald, Peter-John, Valentine, Rowan, Psaltis, Alkis James, Vreugde, Sarah, Fenix, Kevin·2024·Pathogens
DOI 10.3390/pathogens13100826PMC PMC11510575

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Abstract

The oral microbiome, studied by sampling the saliva or by oral rinse, has been long thought to have diagnostic capacity for head and neck cancers (HNC). However, previous reports on the HNC oral microbiome provide inconsistent results. The aim of this study is to consolidate these datasets and determine the oral microbial composition between HNC patients to healthy and premalignant individuals. We analyzed 16 published head and neck cancer (HNC) short-read 16S rRNA sequencing datasets, specifically targeting the V3V4, V4 and V4V5 regions. These datasets included saliva and oral rinse samples from donors with HNC, as well as from healthy and premalignant donors. Differences in diversities and microbial abundance were determined. HNC saliva displayed lower alpha diversity than healthy donors. In contrast, the opposite trend was observed for oral rinse samples. Beta diversity scores were largely similar across different patient types. Similar oral phyla were detected for all samples, but proportions were largely dependent on sample type (i.e., saliva or oral rinse) and primer set utilized for 16S rRNA sequencing. Neisseria, Leptotrichia and Megasphaera were elevated in healthy saliva, while Mycoplasma was elevated in HNC saliva. Oral rinse and saliva displayed similar enrichment for Fusobacterium, while Veillonella, Alloprevotella, and Campylobacter showed conflicting results. The sparse partial least squares discriminant analysis model performed effectively in discriminating HNC from healthy or premalignant patients using V3V4 saliva (AUC = 0.888) and V3V4 oral rinse (AUC = 0.928), while poor discriminative capacity was observed for V4 saliva (AUC = 0.688). In conclusion, our meta-analysis highlighted the limitations of 16S rRNA sequencing, particularly due to variations across study batches, primer sets (i.e., V3V4, V4), and sample types. Hence, caution should be exercised when interpreting 16S rRNA sequencing results across studies, especially when different primer sets and sample types are used.

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Metadata

Authors
Yeo, K., Wu, F., Li, R., Smith, E., Wormald, P.-J., Valentine, R., Psaltis, A. J., Vreugde, S., & Fenix, K.
Affiliations
  • Basil Hetzel Institute (AU)
  • The University of Adelaide (AU)
Corresponding author
  • Yeo, Kenny
  • Fenix, Kevin
ORCID
Venue
Pathogens
Publisher
MDPI AG
Published
2024-09-24
Volume
13
Issue
10
Pages
826
ISSN
2076-0817 (ISSN-L)
DOI
10.3390/pathogens13100826
PMC
PMC11510575
OpenAlex
W4402824978
Cited by
5
References
97
Citations by year
2026: 2 · 2025: 3
FWCI
2.29
Type
journal article
Language
en
Open access
Licence
Locations
  • Pathogens (publishedVersion, cc-by)
  • Preprints.org (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • NHMRC (APP1196832)
  • The Garnett Passe and Rodney Williams Senior Fellowship (APP1196832)
  • Ray and Shirl Norman Cancer Research Trust Project (APP1196832)
  • The University of Adelaide Postgraduate Research Scholarship (APP1196832)
Topics
  • Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
  • Health Sciences › Medicine › Otorhinolaryngology › Head and Neck Cancer Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
head and neck cancer, oral microbiota, saliva, mouthwash, 16S rRNA gene sequencing, alpha diversity, beta diversity, precancerous lesions, diagnostic biomarkers, PLS-DA, Fusobacterium, Neisseria, Mycoplasma, Veillonella, Campylobacter
MeSH terms
Bacteria, DNA, Bacterial, Head and Neck Neoplasms, Humans, Mouth, RNA, Ribosomal, 16S, Saliva, Sequence Analysis, DNA, Microbiota

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