Table 1.

General characteristics of the included studies

Study	Primer region	Sample	Patient number/PPI status	Findings	Quality of the study
Benitez et al. 18	V1V2	Pediatrics oral swab and esophageal biopsy	68 participants (33 EoE cases, 35 non‐EoE controls),66 were on PPIs	Non‐EoE controls: ↑ Streptococcus and Atopobium Active EoE: ↑ Neisseria and Corynebacterium genus In addition to food trigger to diet: ↑ Granulicatella and Campylobacter genus	8*
Hiremath et al. 19	V4	Pediatrics salivary samples	45 participants (15 active EoE, 11 inactive EoE, 19 non‐EoE controls), 33 were on PPIs	Active EoE: ↑ Haemophilus PPI use: ↑ Streptococcus, Corynebacterium, and Rothia Active EoE: ↓ Leptotrichiaceae, Actinomyces, Lactobacillus, and Streptococcus Non‐EoE controls: ↑ Neisseriaceae	9*
Harris et al. 20	V1V2	Pediatrics and adults, EoE and GERD using esophageal string test	70 participants (11 active EoE, 26 inactive EoE, 33 controls), some control subjects and half of the EoE subjects were on PPIs	↑ Bacterial load in active EoE, non‐active EoE, and GERD EoE: ↑ Haemophilus, Pasteurella, Fusobacterium, and Aggregatibacter EoE: ↓ Actinomyces, Veillonella, and Rothia	8*
Arias et al. 21	V4	Adult esophageal biopsy	20 participants (10 controls, 10 EoE before and after remission) PPI non‐responsive EoE patients	Active EoE: ↑ bacterial load Microbial load normalized after food elimination diet	9*
Laserna‐Mendieta et al. 22	V4	Adult middle esophageal biopsy in active EoE and after remission through different treatments	40 participants (30 active EoE, 10 PPI responsive, 10 swallowed topical corticosteroids,10 food‐elimination diet, 10 non‐EoE controls)	Control: ↑ Proteobacteria ↓ Bacteroidetes Active EoE: ↓ Filifactor, ↓ Parvimonas, ↓ Porphyromonas Treated with swallowed topical corticosteroid: ↓ Firmicutes, ↑ Proteobacteria, Bacteroidetes and Fusobacteria Treated with PPIs: ↓ Bacteroidetes and Fusobacteria	9*
Benitez et al. 23	V1V2	Pediatric esophageal biopsy	33 active EoE, 36 inactive EoE, 10 controls (all patient were on PPIs)	Active EoE: ↑ Haemophilus EoE: ↓ Alloprevotella STC in EoE: ↓ Haemophilus ↑ Candida	8*
Johnson et al. 24	V3V4	PPI non‐responsive adults, mid‐esophageal biopsy	24 PPI non‐responsive EoE patients (all on PPI), 25 non‐EoE controls (16 on PPI)	No significant differences found between EoE cases and controlsPPI use: ↑ Burkholderia, Eikenella, and Kingella	8*
Parashette et al. 25	Not specified	Pediatric biopsy	22 healthy, 5 PPI‐responsive EoE, 9 PPI‐non responsive EoE	PPI non‐responsive EoE: ↑ Gemella, Hallela PPI responsive EoE: ↑ Actinomyces, Catonella, Porphyromonas	abstract
Smith et al. 26	V4	Pediatric cytology brush samples	18 controls, 7 reflux esophagitis, 6 active EoE, 7 treated EoE, 5 untreated IBD, 5 treated IBD	Esophagus: EoE: ↑ Bacteroidetes Colon: Non‐active EoE: ↑ Clostridia Controls: ↑ Bacteroidia	abstract
Ghisa et al. 27	Not specified	Not specified	8 active, 8 inactive	Active EoE: ↑ Actinobacillus, Alloprevotella, Spirochaetes Non‐active EoE: ↑ Firmicutes	abstract