Table 1.
Differences in bacterial abundance between A. paediatric IBD and controls, B. Paediatric IBD disease states, C. CD and UC
| A. Bacterial abundance in paediatric IBD compared with controls | |||
| Ruminococcaceae (Faecalibacterium prausnitzii, Oscillospira, and unclassified Ruminococcaceae) | Increased abundance in CD | Assa et al. [49] | Ileal Biopsies |
| Enterobacteriaceae (Escherichia coli), Fusobacteriaceae (Fusobacterium nucleatum), Gemellaceae (Gemella moribillum), Neisseriaceae (Eikenella corrodens), Pasteurellacaeae (Haemophilus parainfluenzae), Veillonellaceae (Veillonella parvula) | Increased abundance in CD | Gevers et al. [48] | Mucosal tissue biopsies (terminal ileum and rectum) |
| Bacteroidales (Bacteroides vulgatus, Bacteroides caccae), Bifidobacteriaceae (Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium dentum), Clostridiales (Blautia hansenii, Ruminococcus gnavus, Clostridium nexile, Faecalibacterium prausnitzii, Ruminoccus torques, Clostridium bolteae, Eubacterium rectale, Roseburia intestinalis, Coprococcus comes), Erysipelotrichales | Decreased abundance in CD | ||
| Veillonellaceae, Streptococcus | Increased abundance in CD |
Faecal samples (small subset of cohort with stool samples) Faecal samples (small subset of cohort with stool samples) |
|
| Clostridiales (Dorea, Blautia, Ruminococcus) | Decreased abundance in CD | ||
| Enterococcus | Increased abundance in CD | Kowalska-Duplaga et al. [43] | Faecal samples |
| Bifidobacterium (Bifidobacterium adolescentis), Adlercreutzia, Clostridium (Clostridium celatum), Coprococcus, Roseburia (Roseburia faecis), Faecalibacterium (Faecalibacterium prausnitzii), Gemmiger (Gemmiger formicilis), Ruminococcus (Ruminococcus bromii), Veillonellaceae (Dialister) | Decreased abundance in CD | ||
| Lachnospiraceae, Coriobacteriaceae, Bifidobacteriaceae (in particular Bifidobacterium longum and Bifidobacterium Pseudocatenulatum) | Decreased abundance in IBD (UC and CD) | Maukonen et al. [45] | Faecal samples |
| Bacteroides | Increased abundance in UC | ||
| Lactobacillus | Decreased abundance in UC | ||
| Bacteroidetes, Eubacterium, Prevotella, Alistipes (Alistipes finegoldii, Alistipes putredinis) | Decreased abundance in IBD (UC and CD) | de Meij et al. [46] | Faecal samples |
| Akkermansia muciniphila | Decreased abundance in UC | ||
| Escherichia coli | Increased abundance in IBD (UC and CD) | ||
| Prevotella | Increased abundance in IBD (UC and CD) and symptomatic non-IBD | Olbjørn et al. [29] | Faecal samples |
| Eubacterium rectale, Eubacterium biforme/Streptococcus agalactiae, Parabacteroides, Bifidobacterium | Decreased abundance in IBD (UC and CD) compared with symptomatic non-IBD controls | ||
| Bifidobacteriaceae | Decreased abundance in UC (active only) | Schwiertz et al. [42] | Faecal samples |
| Faecalibacterium prausnitzii, Bifidobacteriaceae | Decreased abundance in CD | ||
| Escherichia coli | Increased abundance in CD (active only) | ||
| B. Bacterial abundance differences between disease states in paediatric IBD | |||
| Ruminococcus gnavus | Increased in IBD patients with extensive disease (ileocolitis in CD or extensive colitis in UC) compared to CD patients with isolated colonic disease and UC patients with left-sided colitis or proctitis | Olbjørn et al. [29] | Faecal samples |
| Veillonella | Increased in CD patients with upper gastrointestinal involvement compared to those without upper gastrointestinal lesions | ||
| Proteobacteria | Increased abundance for CD patients with complicated disease behaviour, stricturing, or penetrating disease | ||
| Ruminococcaceae, Lachnospiraceae, Streptococcus anginosus (only in rectal biopsies), Veillonella dispar, Aggregatibacter segnis, Campylobacter, Lachnospiraceae, Veillonella parvula, Haemophilus parainfluenzae, Megasphaera | Decreased in severe disease in UC | Schirmer et al. [30] | Faecal samples and paired rectal biopsies (study found comparable abundances between stool faecal samples and biopsies) |
| Veillonella dispar, Veillonella parvula (additional OTU depletions also found) | Decreased in UC with extensive disease involvement or pancolitis compared to UC with proctosigmoiditis or left-sided colitis | ||
| Clostridiales, Veillonella dispar, Haemophilus parainfluenzae, Campylobacter | Increased in UC patients later requiring colectomy | ||
| Ruminococcaceae, Blautia, Dorea (additional OTU depletions also found) | Decreased in UC patients later requiring colectomy | ||
| C. Bacterial abundance in paediatric CD compared with UC | |||
| Akkermansia muciniphila | Decreased abundance in UC | de Meij et al. [46] | Faecal samples |
| Mycoplasma hominis | Decreased in CD (compared to UC) | Olbjørn et al. [29] | Faecal samples |