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

Kenny Yeo; Fangmeinuo Wu; Runhao Li; Eric Smith; Peter-John Wormald; Rowan Valentine; Alkis James Psaltis; Sarah Vreugde; Kevin Fenix

doi:10.3390/pathogens13100826

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

Pathogens. 2024 Sep 24;13(10):826. doi: 10.3390/pathogens13100826.

Authors

Kenny Yeo^{1

2}, Fangmeinuo Wu^{1

3}, Runhao Li^{1

3}, Eric Smith^{1

3}, Peter-John Wormald⁴, Rowan Valentine², Alkis James Psaltis^{1

2}, Sarah Vreugde^{1

2}, Kevin Fenix²

Affiliations

¹ Discipline of Surgery, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia.
² Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Woodville South, SA 5011, Australia.
³ Department of Haematology and Oncology, Basil Hetzel Institute for Translational Health Research and the Queen Elizabeth Hospital, Central Adelaide Local Health Network, Woodville South, SA 5011, Australia.
⁴ Department of Surgery-Otolaryngology Head and Neck Surgery, The University of Adelaide, Adelaide, SA 5000, Australia.

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.

Keywords: 16S ribosomal RNA; head and neck cancer; oral microbiome; oral rinse; saliva.

Abstract

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