Table 1.

Summary of the few significant studies on the oral microbiota comprising the bacterial, viral and fungal biota.

Type of microbiota	Samples	Type of Analysis	Reads/contigs/Sequences	Reference
Bacteria	4154	SGB (kSGBs and uSGBs analysis)	Assembled: 56,213, average 14,094 contigs/sample, taxonomically assigned: Saccharimonadaceae (17.99%), Campylobacteraceae (9.51%) Streptococcus (12.88%) and Campylobacter (7.65%),	[98]
	25	RDP, LCA, MySQL, ITS, LCA and phymmBL	Assembly reads 1103 contigs	[99]
	41	QIIME, OUT	17,129 reads per sample; 702,304 sequences	[100]
	747	HOMD, TORQUE	35,000 clone sequences	[101]
	44	PCoA, SOAPaligner 2.1, SOAPdenovo	27.8% ± 16.7% sequences/reads; 49.8% ± 3.8% of the reads/sample	[102]
	88 (31 confirmed patients with COVID-19, 29 flu patients with influenza B, and 28 healthy controls)	Kraken2 v2.0.9, QIIME 2, MEGAHIT	Assembled contigs 3356–842,961 bp/sample Veillonella sp. (22.7%), Streptococcus sp. (20.3%), Prevotella sp. (7.1%), Acinetobacter sp. (5%), Megasphaera sp. (4.21%), Actinomyces sp. (4.19%), Atopobium sp. (3.65%), Klebsiella sp. (3.25%), and Solobacterium sp. (2.07%)	[103]
Viral	88	FGenesV/ BLASTX homology/Qiime	Contig (16% ± 4.2% - 60 days) - 69.9% ± 5.5% versus 30.1% ± 5.5% - 7th day)	[104]
	04	VirSorter/ vConTACT v.2.0	Novel phages (0–7(0–44%) – 3–26 (12–46%) Novel prophages (25–54 (42–59%)− 73–323 (56–77%)	[105]
	05	FGenesV	27 429 nucleotides, 1421 reads,	[21]
	15	vSAGs (Illumina Tech), ProDeGe	MiSeq sequencer (2 × 250, pair-end); Reads ≥ 70% identity, ≥ 70%, viruses with ≥ 40% coverage	[28]
Fungi	20	Internal transcribed spacer (ITS),ITS1 & 2, AFTOL, WASABI, aligned (KALIGN)	39,226 sequence; 1702 sequences per sample/ average length of 248 bases	[32]
	30	Internal transcribed spacer (ITS), ITS1-F/ITS2, QIIME	QIIME/UNITE: 8607,862 reads; OTU- α-diversity (13,000 sequence reads/sample) (Total: 8943 OTUs sequence/read)	[106]
	18	ITS	Merged sequences 712 295 MiSeq: 1 580 028 reads	[107]
	17	ITS (ITS2 & 4)	MiSeq – 250 bp length; R/phyloseq:10,000 sequences per sample; 37,119 sequences	[108]