Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing

Abstract

Objectives: Smoking is the commonest cause of oral cavity squamous cell carcinoma (OC-SCC), but the etiology of OC-SCC in nonsmokers is unknown. Our primary goal was to use metagenomic shotgun sequencing (MSS) to define the taxonomic composition and functional potential of oral metagenome in nonsmokers with OC-SCC. Methods: We conducted a case–control study with 42 OC-SCC case and 45 control nonsmokers. MSS was performed on DNA extracted from mouthwash samples. Taxonomic analysis and pathway analysis were done using MetaPhlAn2 and HUMAnN2, respectively. Statistical difference was determined using the Mann–Whitney test controlling false discovery rate. Results: There was no significant difference in age, sex, race, or alcohol consumption between OC-SCC and control patients. There was a significant difference in beta diversity between OC-SCC and controls. At the phylum level, Bacteroidetes and Synergistetes were overly represented in OC-SCC while Actinobacteria and Firmicutes were overly represented in controls. At the genus level, Fusobacterium was overly represented in OC-SCC compared with controls, while Corynebacterium, Streptococcus, Actinomyces, Cryptobacterium, and Selenomonas were overly represented in controls. Bacterial pathway analysis identified overrepresentation in OC-SCC of pathways related to metabolism of flavin, biotin, thiamin, heme, sugars, fatty acids, peptidoglycans, and tRNA and overrepresentation of nucleotides and essential amino acids in controls. Conclusions: The oral microbiome in nonsmoker patients with OC-SCC is significantly different from that of nonsmoker control patients in taxonomic compositions and functional potentials. Our study’s MSS findings matched with previous 16S-based methods in taxonomic differentiation but varied greatly in functional differentiation of microbiomes in OC-SCC and controls.

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma

“…Therefore, future studies should examine the mycobiome as well as the microbiome in any microbiological investigative studies. Although not included in our search criteria it is noteworthy that there are additional considerations other than the microbiome and mycobiome, including the phageome, virome and meta‐transcriptome with the oral environment (56).…”

Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap

“…Functional differences were also analysed in these metagenomic studies. Two studies concordantly reported a decrease in nucleotide metabolism and amino acid metabolism in cancer patients [ 103 , 104 ]. Ganly et al [ 103 ] also noted an increase in OSCC patients of several biosynthesis pathways, including vitamins, heme, sugars, and fatty acids (flavin, biotin, and thiamine).…”

“…Two studies concordantly reported a decrease in nucleotide metabolism and amino acid metabolism in cancer patients [ 103 , 104 ]. Ganly et al [ 103 ] also noted an increase in OSCC patients of several biosynthesis pathways, including vitamins, heme, sugars, and fatty acids (flavin, biotin, and thiamine). In contrast, folate biosynthesis, anaerobic energy metabolism, and pyruvate fermentation pathways were reported to be less active in OSCC patients.…”

“…Metagenomic studies reported a significantly increased abundance of cancer-related pathogen species F. nucleatum and a depletion of the genus Streptococcus and Actinomyces sp. ICM47 in OSCC patients [ 87 , 103 , 104 ]. Functional differences were also analysed in these metagenomic studies.…”

“…The identification of the microbiota composition is certainly important. Based on such information, it seems that the diversity of bacterial communities decreases during cancer development and that the physiology of many cancers benefits from high levels of Fusobacteria spp., especially F. nucleatum , in both the gut microbiome and the microbial environment specific to the tumour [ 28 , 32 , 33 , 34 , 58 , 60 , 61 , 87 , 103 , 106 ]. Moreover, other oral commensal species (e.g., Prevotella and Parvimonas ) have been consistently reported to be overabundant in the gut microbiome or tumour tissues of cancer patients [ 59 , 74 , 75 , 78 , 87 , 89 , 92 ].…”