Table 6 Methodology of included studies

Anirudhan et al. 2008 [29]

Culture and serology for bacteria, herpes simplex and fungi. Urine test for presence of fungal elements

Qualitative analysis

Prevalence

Bardellini et al. 2017 [30]

Culture not specified

Qualitative analysis

Prevalence

De Oliveira 2019 [32]

PCR analysis for detection of DNA of HSV-1, EBV and CMV.

PCR for the β-globin constitutive gene to control false-positive results.

Qualitative analysis

Prevalence

Mendonca 2012 [36]

Primer PCR technique for HSV-1 detection

PCR for the β-globin constitutive gene to control false-positive results.

Blood, chocolate and McConkey agar for bacteria cultures;

Sabouraud agar for fungi cultures.

Qualitative analysis

Prevalence

Olczak-Kowalczyk 2012 [37]

Culture on solid media: blood agar, chocolate agar and the Sabouraud agar.

Bacteria identified upon Gram-staining.

Biochemical identification using commercially available kits: GP and GN cards, the VITEK 2 system, PYR and the optochin sensitivity test.

Density of yeast colonies was assessed according to a 4-tiered scale: 0 – no fungal growth; 1 – < 102 CFU ⁄ ml; 2 – 102 to 103 CFU ⁄ ml; 3 – over 103 CFU ⁄ ml. Yeast type was determined using the ID32 test

Qualitative analysis

Prevalence

Quantitative analysis (density of yeast colonies)

Sixou 1998 [39]

Inoculation on non-selective medium and selective media: TSBV, TBBP, and hypersaline agar.

Bacterial profiles obtained with API ZYM1, Rapid Id32A1 and Rapid Id Strep1 identification systems.

Culture on Columbia blood agar enabled the determination of the total anaerobic viable count (TAVC).

Qualitative analysis

Prevalence

Quantitative analysis (TAVC)

Soares 2011 [40]

Culture on solid media: mannitol salt agar, MacConkey agar, cetrimide agar, and Sabouraud agar.

Characteristics determined by the Gram method modified by Kopeloff-Beerman.

Gram-negative bacteria were identified by Mini-API identification system.

Yeast-like fungi identified as Candida albicans by staining of the colonies on CHROMagar.

Qualitative analysis

Prevalence

Ye 2013 [41]

Bacterial samples analyzed using 454 FLX pyrosequencing with minor modifications.

The PCR products were sequenced using a two-lane PicoTiterPlate on a Genome Sequencer FLX system. Denoised sequences were aligned and

sorted into operational taxonomic units (OTUs).

Qualitative analysis

Prevalence

Quantitative analysis (Unifrac)

Clinical methodology

 Gandhi et al. 2017 [33]

Evaluation of characteristic conditions such as white lesions (candidiasis) or vesicles and/or ulcers (HSV) with different symptoms as pain, burning and others. Systematical examination of buccal and sulcular mucosa, the tongue, the floor of the mouth, the hard and soft palate, the fauces, and free and attached gingiva

 Juarez-Lopez et al. 2018 [34]

Interviewed family and/or caregivers of the participating children to investigate about present symptoms

A dentist examined lips, lanes, palate, oropharynx and tongue

 Levy-Polack et al. 1998 [35]

Diagnosis of oral candidiasis as white, adherent plaque on the oral mucosa or tongue that, if scraped, left a bleeding base

 Pinto et al. 2018 [38]

Intraoral examination to identify abnormalities and oral lesions