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. Author manuscript; available in PMC: 2020 Jun 24.
Published in final edited form as: Dig Dis Sci. 2020 Mar;65(3):757–788. doi: 10.1007/s10620-020-06090-z

Table 1.

Representative dysbiotic microbiota in IBD

Ulcerative colitis Pouchitis Crohn's disease
Bacterial diversity Bacterial diversity ↓↑ Bacterial diversity
Proteobacteria Proteobacteria Proteobacteria
  Enterobacteriaceae   Enterobacteriaceae   Enterobacteriaceae ↑
   E. coli    E. coli    Adherent-invasive E. coli
   K. pneumoniae
  Pasteurellaceae ↑
   Haemophilus
  Neisseriaceae ↑
Fusobacteria Fusobacteria Fusobacteria
  F. varium   Fusobacterium   Fusobacteriaceae ↑
Bacteroidetes ↑↓ Bacteroidetes Bacteroidetes
  Bacteroides   Bacteroides   Bacteroiales ↓↑
  B. vulgatus
Firmicutes Firmicutes Firmicutes
  Clostridiales ↓   Clostridiales ↓
   clusters IV, XIVa, XVIII ↓    clusters IV, XIVa ↓
   F. prausnitzii    F. prausnitzii
   E. rectale    E. rectale    E. rectale
  Ruminococcaceae   Ruminococcaceae   Ruminococcaceae ↓
   R. gnavus    R. gnavus    R. gnavus
   clusters I, II, IX, XI ↑
   C. perfringens    C. perfringens
  Peptostreptococci ↑   Veillonellaceae ↑
  Lachnospiraceae   Lachnospiraceae ↓
   Roseburia hominis   Erysipelotrichaceae ↓
  Bacilli ↑   Bacilli   Bacilli ↑
   E. faecalis    Lactobacilli ↓    Lactobacillus ↓↑
Actinobacteria Actinobacteria
  Bifidobacteria ↓   Bifidobacteriaceae ↓
Viral diversity Viral diversity
Caudoviales bacteriopahge ↑
Fungal diversity Fungal diversity
Candida Candida

IBD: inflammatory bowel disease, ↑/↓: increase/decrease in IBD compared to healty, red: increased in IBD, blue: decreased in IBD. References [3,12, 13, 30-39, 60, 84].