Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis

Abstract

Exploring microbial community compositions in humans with healthy versus diseased states is crucial to understand the microbe-host interplay associated with the disease progression. Although the relationship between oral cancer and microbiome was previously established, it remained controversial, and yet the ecological characteristics and their responses to oral carcinogenesis have not been well studied. Here, using the bacterial 16S rRNA gene amplicon sequencing along with the in silico function analysis by PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2), we systematically characterized the compositions and the ecological drivers of saliva microbiome in the cohorts of orally healthy, non-recurrent oral verrucous hyperplasia (a pre-cancer lesion), and oral verrucous hyperplasia–associated oral cancer at taxonomic and function levels, and compared them with the re-analysis of publicly available datasets. Diversity analyses showed that microbiome dysbiosis in saliva was significantly linked to oral health status. As oral health deteriorated, the number of core species declined, and metabolic pathways predicted by PICRUSt2 were dysregulated. Partitioned beta-diversity revealed an extremely high species turnover but low function turnover. Functional beta-diversity in saliva microbiome shifted from turnover to nestedness during oral carcinogenesis, which was not observed at taxonomic levels. Correspondingly, the quantitative analysis of stochasticity ratios showed that drivers of microbial composition and functional gene content of saliva microbiomes were primarily governed by the stochastic processes, yet the driver of functional gene content shifted toward deterministic processes as oral cancer developed. Re-analysis of publicly accessible datasets supported not only the distinctive family taxa of Veillonellaceae and Actinomycetaceae present in normal cohorts but also that Flavobacteriaceae and Peptostreptococcaceae as well as the dysregulated metabolic pathways of nucleotides, amino acids, fatty acids, and cell structure were related to oral cancer. Using predicted functional profiles to elucidate the correlations to the oral health status shows superior performance than using taxonomic data among different studies. These findings advance our understanding of the oral ecosystem in relation to oral carcinogenesis and provide a new direction to the development of microbiome-based tools to study the interplay of the oral microbiome, metabolites, and host health.

The Composition and Functional Capacities of Saliva Microbiota Differ Between Children With Low and High Sweet Treat Consumption

“…This may in part explain the similar caries status we found in low and high sweet treat consumption groups. Gondoate is a long-chain unsaturated fatty acid, and its biosynthesis pathway was enriched in the saliva microbiota of adult patients with oral squamous cell carcinoma ( 60 ). In the gut microbiome, gondoate biosynthesis decreased during the exacerbation of Crohn’s disease ( 61 ).…”

Salivary Microbiota Composition in Patients with Oral Squamous Cell Carcinoma: A Systematic Review

“…However, a wide heterogeneity was observed which made it impossible to perform an advanced statistical analysis. Eight studies were case–control [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 ], two were cohort studies [ 35 , 36 ], and one was a cross-sectional cohort study [ 37 ]. Of the eleven studies, five were from Taiwan [ 30 , 34 , 35 , 36 , 37 ], three were from China [ 28 , 29 , 32 ], one was from the USA [ 27 ], one was from Sudan [ 31 ], and one was from Japan [ 33 ].…”

“…Only four studies included both genders (179 male and 113 female) [ 28 , 29 , 31 , 33 ], four studies analysed exclusively the salivary microbiota of male patients (n. 534) [ 34 , 35 , 36 , 37 ], and in three studies the gender of the patients is not specified [ 27 , 28 , 30 ].…”

“…One study analysed salivary sample of patients affected by OSCC without a control group [ 35 ]. Three studies compared the oral microbiome of patients affected by OSCC, healthy controls, and oral potentially malignant disorders (OPMD) [ 27 , 30 , 36 ]. One study compared the oral microbiomes of patients affected by OSCC, healthy controls, and patients affected by gingivitis or periodontitis [ 29 ].…”

“…All studies analysed unstimulated saliva, except one study in which the participants were asked to chew gum for 5 min before salivary collection [ 33 ]. After collection, all samples were stored frozen at −80 °C [ 28 , 29 , 30 , 31 , 32 , 33 , 34 , 36 , 38 , 39 ], except in one study where the swab collections were stored at −20 °C [ 37 ].…”