Table 2: Oral bacteria associated with oropharyngeal healthy controls.

Cancer understudy	Phylum	Genus/species	Main findings	N	Technology used	Case sample	Control Sample	Reference
HNSCC	Fusobacterium	Leptotrichia buccalis	Relative abundance decreased in HNSCC samples compared to samples from healthy controls from JHU and HMP	17 HNSCC patients, and 25 healthy controls (JHU Cohort). 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]
OC	Actinobacteria	Rothia	Relative abundance significantly decreased in cancer patients 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 patients	Schmidt et al., 2014 [58]
	Firmicutes	Streptococcus	Relative abundance significantly decreased in cancer and pre-cancer patients compared to healthy matching tissue
OPMD	Bacteroidetes	Porphyromonas gingivalis	Presence not found in OPMD lesions but presented in healthy tissue	7 patients	Metagenomic sequencing	Tumour sample	Healthy tissue from the same patient	Decsi et al., 2018 [61]
		Prevotella bergensis
	Firmicutes	Gemella haemolysans	Relative abundance markedly decreased in tumorous samples compared to healthy tissue
		Streptococcus mitis
	Proteobacteria	Neisseria meningitidis	Presence not found in OPMD lesions but presented in healthy tissue
		Neisseria subflava
OSCC	Firmicutes	Granulicatella adiacens	Relative abundance decreased 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]
		Streptococcus mitis
	Actinobacteria	Rothia mucilaginosa	Presence predominantly associated with controls	20 OSCC patients, and 20 matching controls	16S rRNA sequencing	Tumour sample	Anatomical matching sites from healthy controls	Al-Hebshi et al., 2017 [59]
	Firmicutes	Streptococcus mitis
	Actinobacteria	Rothia mucilaginosa	Relative abundance decreased in tumorous samples compared to healthy tissue	20 patients	16S rRNA sequencing	Tumour sample	Healthy tissue from the same patient	Hooper et al., 2006 [64]
	Bacteroidetes	Prevotella veroralis	Presence not found in OSCC lesions but presented in healthy tissue
	Firmicutes	Streptococcus mitis	Relative abundance decreased in tumorous samples compared to healthy tissue
		Streptococcus salivarius
Bacteroidetes	Porphyromonas gingivalis	Presence not found in OSCC samples but presented in healthy tissue	10 patients	16S rRNA sequencing	Tumour sample	Non-tumorous mucosal tissue specimen from the same patient	Hooper et al., 2007 [66]
OSCC	Firmicutes	Granulicatella adiacens						Relative abundance decreased in tumorous samples compared to healthy tissue
		Streptococcus mitis/oralis
	Bacteroidetes	Capnocytophaga	Relative abundance decreased in OSCC lesions compared to healthy tissue	3 patients, and 2 controls	16S rRNA pyrosequencing	Saliva sample from cases	Saliva sample from healthy control	Pushalkar et al., 2011 [63]
		Prevotella
	Fusobacteria	Leptotrichia
	Proteobacteria	Neisseria
	Actinobacteria	Rothia	Relative abundance markedly decreased in OSCC samples compared to healthy control samples	40 patients	Metagenomic sequencing	Swabs from oral lesions	Swabs from anatomically matching healthy sites	Zhao et al., 2017 [57]
	Firmicutes	Granulicatella
		Streptococcus