TABLE 1

Main findings related to microbiota composition in CD subjects a

SubjectsSpecimen type(s)MethodMain finding(s) for comparison between untreated and treated subjects vs controlsReference
26 untreated CD children and 23 controlsFecal samplesCultureBacteroides, Clostridium, and Staphylococcus (untreated vs control) 13
FISH-FCBacteroides-Prevotella and Clostridium histolyticum (untreated vs controls); ↑ Eubacterium rectale-Clostridium coccoides, Atopobium, and sulfate-reducing bacteria (untreated vs control); ↓ Bifidobacterium (untreated vs control)
10 untreated CD children and 10 controlsFecal samplesDGGE↑ bacterial diversity (untreated vs control); ⇆ Lactobacillus diversity (untreated vs control); ↓ Bifidobacterium diversity (untreated vs controls); ↑ prevalence of Lactobacillus curvatus, Leuconostoc mesenteroides, and Leuconostoc carnosum (untreated vs control); ↓ prevalence of Lactobacillus casei group bacteria, including L. casei, L. paracasei, L. rhamnosus, or L. zeae (untreated vs control); Bifidobacterium adolescentis not detected in CD children 25
20 untreated CD children, 10 treated CD children, and 8 controlsDuodenal biopsy specimensFISH-FC↑ total and Gram-negative bacteria (untreated vs treated and control); ↑ Bacteroides-Prevotella group and Escherichia coli (untreated vs control); ↓ Lactobacillus-Bifidobacterium/Bacteroides-Prevotella ratio (untreated and treated vs control); ↓ Gram positive (untreated and treated vs control); ⇆ Atopobium, Eubacterium rectale-Clostridium coccoides, Clostridium histolyticum, Clostridium lituseburense, sulfate-reducing bacteria, and Faecalibacterium prausnitzii groups (untreated vs control) 26
30 untreated CD children, 18 treated CD children, and 30 controlsFecal samplesqPCR↑ prevalence of Bifidobacterium adolescentis and Bifidobacterium breve in untreated CD children; ↑ prevalence of Bifidobacterium dentium (also found in controls); ↓ Bifidobacterium catenulatum (untreated and treated vs control) 27
25 untreated CD children, 8 treated CD children, and 8 controlsDuodenal biopsy specimensqPCR Bifidobacterium longum, Bifidobacterium bifidum, and Bifidobacterium catenulatum detected in all samples; Bifidobacterium dentium detected only in untreated and treated CD children; ↑ Bifidobacterium breve (untreated vs treated and control); ↓ Bifidobacterium lactis (untreated vs treated and control); ↓ Bifidobacterium catenulatum (untreated and treated vs control) 27
25 untreated CD children, 8 treated CD children, and 8 controlsFecal samplesqPCR↑ total bacteria (untreated and treated vs control); ↑ Bifidobacterium dentium (treated vs control); ↑ Bifidobacterium breve (untreated vs treated and control); ⇆ Bacteroides, Clostridium leptum, and Escherichia coli (untreated vs treated); ↑ Staphylococcus (untreated vs treated) 28
Biopsy specimensqPCRClostridium coccoides (untreated and treated vs control); ↑ Lactobacillus group and Akkermansia muciniphila (untreated vs treated and control); ↑ Staphylococcus (untreated and treated vs control); ⇆ Bacteroides, Clostridium leptum, and Escherichia coli (untreated and treated vs control)
7 untreated CD children, 7 treated CD children, and 7 controlsFecal samplesCulture↓ lactic acid bacteria, Bifidobacterium, and Staphylococcus-Micrococcus (untreated and treated vs control); ↑ Bacteroides and Clostridium (untreated and treated vs control); L. plantarum, L. paracasei, L. rhamnosus, and B. longum detected in all groups; L. brevis, L. rossiae, L. pentosus, and Bifidobacterium bifidum not found in untreated children; L. fermentum, L. delbrueckii subsp. bulgaricus, and L. gasseri detected only in controls 29
24 untreated CD children, 18 treated CD children, and 20 controlsFecal samplesIgA coated↓ IgA-coated bacteria (untreated and treated vs control); ↓ total Gram-positive bacterial populations (untreated and treated vs control); ↓ Bifidobacterium proportions, C. histolyticum, C. lituseburense and Faecalibacterium prausnitzii groups (untreated vs control); ↑ Bacteroides-Prevotella group (untreated vs control); ⇆ Escherichia coli, Staphylococcus, Lactobacillus-Enterococcus, and sulfate-reducing bacteria (untreated and treated vs control) 30
19 treated CD children and 15 controlsFecal samples and biopsy specimensDGGEDGGE profiles of fecal samples were richer than those of biopsy specimens; bifidobacteria not found in CD biopsy specimens 31
Fecal samples and biopsy specimensCultureLactobacillus, Enterococcus, and Bifidobacterium (treated vs control) in fecal samples; ↑ Bacteroides-Prevotella, Porphyromonas, and Staphylococcus (treated vs control) in fecal samples; ⇆ Salmonella, Shigella, Klebsiella, and Clostridium (treated vs control) in fecal samples
8 untreated CD children and 5 controls, and 5 untreated CD adults, 5 treated CD adults, and 5 controlsDuodenal biopsy specimens16S rRNA gene sequencing Firmicutes (38% vs 34% for CD adults vs CD children), Proteobacteria (29% vs 38%), Bacteroidetes (17% vs 13%), Actinobacteria (10% vs 4%), Fusobacteria (4% vs 2.9%), Deinicoccus-Thermus (0 vs 2.7%); adults (61 different genera) and children (36 different genera); ↑ Prevotella spp. and Streptococcus spp. (treated vs untreated) in adults; Mycobacterium spp. and Methylobacterium spp. (untreated and treated vs control) in adults; ↓ Streptococcus and Prevotella (untreated vs control) in children; ↑ Neisseria spp. and Haemophilus spp. (untreated vs control) in children 12
10 untreated CD adults, 11 treated CD adults, 11 controls, and 10 controls on GFDFecal samplesDGGE↑ diversity of Lactobacillus and Bifidobacterium groups (untreated and control vs treated); ↑ Lactobacillus sakei (untreated and control vs treated); ↑ Bifidobacterium bifidum and Bifidobacterium catenulatum (untreated vs control) 22
10 untreated CD children, 6 treated CD adults, and 9 controlsDuodenal biopsy specimensMicroarray HITChip⇆ in diversity (untreated vs control) 23
33 untreated CD adults and 18 controlsDuodenal biopsy specimensDGGE↑ microbial diversity and richness (untreated vs control); ↑ composition and structure dominated by Proteobacteria (untreated vs control) 24
  • a The content includes studies developed with distinct populations, samples, and methodology approaches. ↑, higher; ↓, lower; ⇆, no difference. qPCR, quantitative PCR.