Table 1 Alteration of gut microbiome in human diseases

Irritable bowel syndrome

Increased ratio of the Firmicutes to Bacteroidetes

(Rajilić-Stojanović, Biagi et al. 2011) [70]

Crohn’s disease

Increased Clostridium species, Ruminococcus torques, and E. coli

(Martinez‐Medina, Aldeguer et al. 2006) [53]

Gastric cancer

H. pylori induces production of pro-inflammatory cytokines

(Tsuji, Kawai et al. 2003) [88]

Colorectal cancer

Abundance of Fusobacteria and Coriobacteria

(Castellarin, Warren et al. 2012) [9]

Obesity

Reduced ratio of Bacteroidetes to Firmicutes

(Ley, Bäckhed et al. 2005) [44]

Type 1 diabetes

Altered gut permeability to mannitol and lactulose

(Kuitunen, Saukkonen et al. 2002) [41]

Atherosclerosis

Metabolism of phospholipids by gut microbiota to trimethylamine-N-oxide

(Loscalzo 2011) [48]

Rheumatoid arthritis

Less Bifidobacteria and bacteria of the Bacteroides-Porphyromonas-Prevotella

(Vaahtovuo, Munukka et al. 2008) [90]

Autism

Higher number of Clostridium species known to produce tetanus neurotoxin (TeNT)

(Parracho, Bingham et al. 2005) [64]

(Bolte 1998) [4]

Chronic fatigue syndrome

Lower levels of Bifidobacteria and small-intestinal bacterial overgrowth

(Logan, Venket Rao et al. 2003) [47]

Alzheimer’s disease

Excess ammonia production by gut microbiota

(Samsel and Seneff 2013) [76]