Table 1.
Characteristics and main findings of studies reporting on gut microbiota profile in patients with CD, NCGS, and IBS.
| Diagnosis | First author, year of publication | Study design | Participants (n) | Specimen | Method of detection | Main findings |
|---|---|---|---|---|---|---|
| CD | Golfetto (23) 2014 | Case-control | tCD (14) Control (42) |
Fecal sample | Microscopic analysis | ↓ Bifidobacteria (Actinobacteria) in CD |
| Wacklin (24) 2014 | Cohort | tCD w/symptoms (18) tCD asymptomatic (18) |
Duodenal biopsy | 16s rRNA sequencing PCR |
In symptomatic patients: ↓ Bacteroidetes, Firmicutes, and microbial richness ↑ Proteobacteria |
|
| Nistal (25) 2016 | Case-control | uCD (9) Control (9) |
Duodenal biopsy | 16s rRNA sequencing PCR | Firmicutes and Proteobacteria are the dominant phyla in both CD and HC. No significant differences in bacterial profile ↓ microbial richness in CD |
|
| Quagliarello (26) 2016 | RCT | CD (40) Control (16) |
Fecal sample | 16s rRNA sequencing qPCR | ↑ Bacteroidetes/Firmicutes ratio and ↓ Firmicutes, Actinobacteria, and microbial richness in CD Lower taxonomic levels: ↓ Lactobacillus (Firmicutes) ↑ B. fragilis (Bacteroidetes) |
|
| Herrán (27) 2017 | Case-control | tCD (14) uCD (5) Control (23) |
Duodenal biopsy | 16s rDNA sequencing PCR-DGGE | No significant differences in composition or abundance of bacteria with gluten-hydrolyzing capacity | |
| NCGS | Garcia-Mazcorro (28) 2018 | RCT | NCGS (12) CD (6) Control (12) |
Fecal sample Duodenal biopsy | 16s rDNA sequencing PCR |
Fecal samples Firmicutes (85%) Bacteroidetes (1%) in all ↑ Ruminococcaceae (Firmicutes) in NCGS Duodenal biopsies ↓ Bacteroidetes and Fusobacteria in CD ↑ Saccharibacteria in NCGS |
| Dieterich (29) 2018 | RCT | NCGS (19) Control (10) |
Fecal sample | 16s rRNA sequencing Fluorometric quantitation |
Lower taxonomic levels: ↑ Actinobacillus (Proteobacteria) and Finegoldia (Firmicutes) in NCGS ↑ Sphingobacteria (Bacteroidetes) in HC ↑ Ruminococcaceae, Peptostreptococcaceae (Firmicutes), and ↓ Porphyromonadaceae (Bacteroidetes) in NCGS |
|
| IBS | Halmos (30) 2014 | RCT | IBS (27) Control (6) |
Fecal sample | qPCR | No significant differences in total bacteria count or abundance of bacterial groups |
| Chung (31) 2015 | Case-control | IBS (28) Control (19) |
Fecal sample Jejunal biopsy | 16s rRNA sequencing PCR |
Fecal samples ↑ Firmicutes/Bacteroidetes ratio in IBS-D ↑ Veillonellaceae (Firmicutes) in IBS-D Jejunal biopsies ↑ Firmicutes/Actinobacteria ratio in IBS-M ↑ Prevotellaceae (Bacteroidetes) in IBS ↓ Mycobacteriaceae (Actinobacteria) and Neisseriaceae (Proteobacteria) in IBS |
|
| Pozuelo (32) 2015 | Case-control | IBS (113) Control (66) |
Fecal sample | 16s rRNA sequencing PCR | ↑ Bacteroidetes and Tenericutes in IBS ↓ Firmicutes and microbial richness in IBS Lower taxonomic levels: ↓ Lachnobacterium (Firmicutes) in IBS ↓ Strains within Firmicutes in IBS-D and IBS-M |
|
| Rangel (33) 2015 | Case-control | IBS (35) Control (16) |
Fecal sample Colonic biopsy | 16s rRNA sequencing |
Fecal samples ↑ Actinobacteria and Proteobacteria and ↓ Bacteroidetes in IBS Lower taxonomic levels: ↑ Bacilli and altered composition of species within Clostridia (Firmicutes) Colonic biopsies ↓ Clostridiales (Firmicutes) in IBS |
|
| Shukla (34) 2015 | Case-control | IBS (47) Control (30) |
Fecal sample | 16s rRNA sequencingq PCR | ↑ Gram-negative bacteria in IBS Lower taxonomic levels: ↓ Bifidobacteria (Actinobacteria) ↑ species within Firmicutes and Proteobacteria ↓ Lactobacillus (Firmicutes) and ↑ Bacteroides species (Bacteroidetes) in IBS-D than IBS-C |
|
| Tap (35) 2016 | Case-control | IBS (110) Control (39) |
Fecal sample Colonic biopsy | 16s rRNA sequencing qPCR | No significant differences between fecal and mucosal microbiota in IBS or HC ↑ Bacteroides (Bacteroidetes) in IBS-D and IBS-M ↓ Prevotella (Bacteroidetes) and microbial richness in IBS |
CD: celiac disease; IBS: irritable bowel syndrome; IBS-C: constipation-predominant IBS; IBS-D: diarrhea-predominant IBS; IBS-M: mixed type IBS; NCGS: non-celiac gluten sensitivity; PCR: polymerase chain reaction; PCR-DGGE: PCR denaturing gradient gel electrophoresis; RCT: randomized controlled trial; tCD: treated celiac disease; uCD: untreated celiac disease; qPCR: quantitative PCRNotes: The arrow marks represent increase and decrease.