Table 1

Alterations in gut microbiota associated with immune-mediated diseases

Associated microbes

Microbiota changes


IBD - Crohn's disease

Reduction in microbial diversity when compared with controls


Gut microbiome

Bacteroides ovatus

Bacteroides vulgatus

Bacteroides uniformis


Associated with overall community shift and dysbiosis


Gut microbiome

Bacteroidetes ↓

Lachnospiraceae ↓

Actinobacteria ↑

Proteobacteria ↑

Clostridium ↓

Firmicutes/Bacteroidetes ratio ↓

Bifi dobacteria ↓

Celiac disease

Overall higher diversity of microbes in patients with celiac disease compared with controls


Gut microbiome

Bacteroides vulgatus

Escherichia coli

Clostridium coccoides


Overrepresentation of Firmicutes and an underrepresentation of Actinobacteria and Proteobacteria when compared with controls


Skin microbiome

Firmicutes ↑

Bacteroidetes ↑

Actinobacteria ↓

Proteobacteria ↓

Rheumatoid arthritis

Dysbiosis and increased diversity


Oral microbiome

Porphyromonas gingivalis

IBD, inflammatory bowel disease.

Costello et al. Arthritis Research & Therapy 2013 15:214   doi:10.1186/ar4228