Table 1: Changes in oral bacteria in oropharyngeal cancer patients.

Cancer	Phylum	Genus/species	Main findings	N	Technology used	Case sample	Control Sample	Reference
GSCC	Bacteroidetes	Porphyromonas gingivalis	Relative abundance increased in GSCC samples compared to the healthy epithelium	10 patients, and 5 controls	IHC	Biopsy paraffin-embedded blocks of GSCC	Non-neoplastic gingival tissue	Katz et al., 2011 [68]
HNSCC	Actinobacteria	Rothia mucilaginosa	Relative abundance increased in HNSCC samples compared to samples from healthy controls from JHU and HMP	17 HNSCC patients, and 25 healthy controls (JHU Cohort). Compared to 154 participants of the Human Microbiome Project (HMP)	16S rRNA next-generation sequencing	Saliva from HNSCC patients	Saliva from healthy controls	Guerrero-Preston et al., 2017 [62]
	Firmicutes	Lactobacillus gasseri/johnsonii	Relative abundance increased in samples from HNSCC patients treated with surgery and chemoradiation when compared to patients only treated with surgical removal of the tumour and to controls
		Lactobacillus vaginalis
		Streptococcus salivarius/ vestibularis	Relative abundance increased in HNSCC samples compared to samples from healthy controls from JHU and HMP
	Fusobacteria	Fusobacterium nucleatum
KCOT	Firmicutes	Gemella morbillorum	Relative abundance increased in KCOTs compared to RCs	6 KCOTs samples, and 10 RCs samples	Biochemical tests	Cyst fluid aspiration KCOTs	Cyst fluid aspiration RC	Scalas et al., 2013 [71]
OC	Bacteroidetes	Prevotella melaninogenica	Relative abundance significantly increased in cancer patient samples compared to healthy matching tissue	10 cancer patients, and 8 pre-cancer patients	16S rRNA pyrosequencing	Tumour sample from cancer and pre-cancer patients	Contralateral healthy tissue from the same patient	Schmidt et al., 2014 [58]
	Fusobacteria	Fusobacterium
OMTC	Actinobacteria	Rothia mucilaginosa	Relative abundance significantly increased in the tumour group compared to their matching non-tumour samples	37 patients	16S rRNA sequencing	Tumour sample	Matching healthy tissue from the same patient	Mukherjee et al., 2017 [44]
	Firmicutes	Streptococcus
OPMD	Actinobacteria	Rothia mucilaginosa	Presence found in OPMD lesions but not presented in healthy tissue	7 patients	Metagenomic sequencing	Tumour sample	Healthy tissue from the same patient	Decsi et al., 2018 [61]
	Bacteroidetes	Capnocytophaga gingivalis
		Capnocytophaga ochracea
		Prevotella melaninogenica
	Firmicutes	Gemella morbillorum
		Granulicatella adiacens
		Streptococcus gordonii
		Streptococcus parasanguinis
		Streptococcus salivarius
	Fusobacteria	Fusobacterium nucleatum	Relative abundance increased in OPMD lesions compared to healthy tissue
OSCC	Bacteroidetes	Gemella haemolysins	Relative abundance increased in OSCC lesions compared to healthy tissue	10 patients	16S rRNA sequencing	Tumour sample	Healthy tissue from the same patient	Pushalkar et al., 2012 [65]
		Gemella morbillorum
		Peptostreptococcus stomatis
		Streptococcus gordonii
		Streptococcus parasanguinis
		Streptococcus salivarius
	Bacteroidetes	Prevotella melaninogenica	Presence found in tumour samples but not presented in healthy tissue	20 patients	16S rRNA sequencing	Tumour sample	Healthy tissue from the same patient	Hooper et al., 2006 [64]
	Firmicutes	Gemella haemolysans
		Streptococcus gordonii
	Fusobacteria	Fusobacterium nucleatum	Relative abundance increased in OSCC samples compared to healthy tissue	20 OSCC patients, and 20 matching controls	16S rRNA sequencing	Tumour sample	Anatomical matching sites from healthy controls	Al-Hebshi et al., 2017 [59]
Bacteroidetes	Porphyromonas gingivalis	Relative abundance increased in OSCC samples compared to healthy tissue	6 patients	16S rRNA sequencing	Tumour sample and adjacent paracancerous tissue	Healthy tissue from the same patient (subgingival plaque)	Chang et al., 2019 [60]
OSCC	Fusobacteria							Fusobacterium nucleatum
	Bacteroidetes	Porphyromonas	Presence increased in tumour samples compared to healthy tissue	21 patients	Cell culturing	Tumour sample	Contiguous healthy mucosa from the same patient	Nagy et al., 1998 [56]
		Prevotella
	Firmicutes	Streptococcus
	Fusobacteria	Fusobacterium
	Actinobacteria	Rothia	Relative abundance increased in OSCC samples compared to healthy samples	3 patients, and 2 controls	16S rRNA pyrosequencing	Saliva sample from cases	Saliva sample from healthy control	Pushalkar et al., 2011 [63]
	Bacteroidetes	Porphyromonas
	Firmicutes	Gemella
		Lactobacillus
		Peptostreptococcus
		Streptococcus
	Firmicutes	Peptostreptococcus	Relative abundance increased in the cancer patient group	125 cancer patients, 124 epithelial precursor lesion patients, and 127 healthy patients	16S rRNA sequencing	Saliva from OSCC patients	Saliva from controls	Lee et al., 2017 [69]
	Bacteroidetes	Capnocytophaga gingivalis	Increased counts in OSCC samples compared to healthy samples	45 OSCC patients, and 45 matching healthy controls	Checkerboard DNA-DNA hybridization	Saliva from OSCC patients	Saliva from healthy controls	Mager et al., 2005 [67]
		Prevotella melaninogenica
	Firmicutes	Streptococcus mitis
	Firmicutes	Peptostreptococcus stomatis	Relative abundance markedly increased in OSCC samples compared to healthy matching tissue	40 patients	Metagenomic sequencing	Swabs from oral lesions	Swabs from anatomically matching healthy sites	Zhao et al., 2017 [57]
	Fusobacteria	Fusobacterium