Table 3.

Gut microbiome-associated human diseases and their respective dysbiotic features.

Disease categories	Specific diseases	Associated dysbiotic features	Reference
Immune-mediated/autoimmune diseases	inflammatory bowel disease (IBD)	Increase in virulent gut microbes (Enterobacteriaceae species, Bacteroides fragilis) and mucolytic Ruminococcus sp. Decrease in butyrate-producing Firmicutes (such as Faecalibacterium prausnitzii, Roseburia hominis)	Sokol et al., 2008; Png et al., 2010; Willing et al., 2010; Machiels et al., 2014
	Irritable bowel syndrome (IBS)	Increase in Escherichia coli Decrease in Clostridium leptum group of bacteria and Bifidobacterium. Decrease in bile acid biotransformation	Duboc et al., 2012
	Celiac disease	Increase in Bacteroides–Prevotella group Decrease in Bifidobacterium Varying observation (decrease or no change) in Clostridium histolyticum, C. lituseburense, and Faecalibacterium prausnitzii Alteration in SCFAs composition, but overall increase in total SCFA	Tjellström et al., 2005; Nadal et al., 2007; De Palma et al., 2010
	Systemic lupus erythematosus (SLE)	Increase in Blautia sp. and Gram-negative bacteria such as Proteobacteria. Decrease in gut microbiota diversity, Odoribacter sp., Alistipes sp. Increase in serum endotoxin	Shi et al., 2014; Luo et al., 2018
	Type-1 diabetes	Increase in Bacteroidetes Decrease in Actinobacteria, Firmicutes, and Firmicutes/Bacteroidetes ratio	Murri et al., 2013
	Rheumatoid arthritis (RA)	Increase in Prevotella copri and decrease in Bacteroides sp. In new-onset RA Increase in microbiota diversity of Lactobacillus genus in early RA	Liu et al., 2013; Scher et al., 2013
	Atopic disease (E.g., childhood allergic asthma)	Increase in fecal burden of Clostridium difficile, and C. difficile/Bifidobacteria ratio	Kalliomäki et al., 2001
Metabolic disorders/cardiovascular disorders	Obesity	Increase in Firmicutes, Actinobacter Varying observation (decrease, no change, increase) in Bacteroidetes Increase in glycoside hydrolase and SCFAs (butyrate and acetate)	Turnbaugh et al., 2006, 2009a; Koliada et al., 2017
	Type-2 diabetes	Increase in Lactobacillus Decrease in Clostridium coccoides, Atopobium cluster, and Prevotella Decrease in butyrate biosynthesis	Qin et al., 2012; Sato et al., 2014
	Hypertension	Increase in the Firmicutes/Bacteroidetes ratio, lactate-producer Decrease in microbiota diversity, acetate- and butyrate-producers	Yang et al., 2015
	Atherosclerosis	Increase in metabolites TMAO, endotoxin level (risk factor for early atherosclerosis)	Wiedermann et al., 1999; Koeth et al., 2013
Cancer	Colorectal cancer (CRC)	Increase in enterotoxigenic Bacteroides fragilis, and pathobionts Fusobacterium and Campylobacter sp. Decrease in butyrate-producer (Faecalibacterium and Roseburia)	Wang et al., 2012; Wu et al., 2013
Neurop sy chi atri c	Autism spectrum disorder (ASD)	Increase in Clostridium sp., Bacteroidetes, Lactobacillus, Desulfovibrio Decrease in Bifidobacteria	Song et al., 2004; Adams et al., 2011
	Alzheimer’s disease	Possible connection between gut microbiota-synthesized amyloids, LPS, γ-aminobutyric acid (GAB A – major inhibitory neurotransmitter), and the increased permeability of gut barrier and blood brain barrier with age	Pistollato et al., 2016
	Depression	Increase in genus Eggerthella, Holdemania, Gelria, Turicibacter, Paraprevotella, Anaerofilum Decrease in gut microbiota diversity, Prevotella and Dialister	Kelly et al., 2016
	Parkinson’s Disease	Increase in anti-inflammatory butyrate-producers from genus Blautia, Coprococcus, and Roseburia in patient fecal sample, pro-inflammatory Proteobacteria in patient mucosa Increased gene expression in LPS biosynthesis and microbial type III secretion system	Keshavarzian et al., 2015
Infectious disease	Clostridium difficile infection (CDI)	Increase in Clostridium difficile; Decrease in gut microbiota diversity and secondary bile acids-producing Clostridium scindens	Theriot et al., 2014
Uremic disease	Chronic kidney disease	Increase in Firmicutes, Proteobacteria, and Actinobacteria Decrease in Lactobacilli	Vaziri et al., 2013