Table 3. Association of diseases with characteristics of the microbiome.

Microbiome	Disease or Condition	Relevant Characteristics
Cutaneous	Psoriasis	Significantly increased ratio of Firmicutes to Actinobacteria in lesions4
	Acne	Propionibacterium acnes infection of pilosebaceous units4
	Chronic skin ulcers	Increased Pseudomonadaceae following antibiotic treatment4
	Diabetic skin ulcers	Increased Streptococcaceae4
Gastric	Increased risk of peptic ulcer disease, gastric mucosa-associated lymphoid tissue tumors, and non-cardia gastric adenocarcinomas Decreased risk of reflux esophagitis and childhood-onset asthma	Presence of H. pylori in gastric microbiota4
	Increased risk for childhood-onset asthma, reflux esophagitis, gastroesophageal reflux disease, Barrett's esophagus, and esophageal and gastric cardia adenocarcinomas	Absence of H. pylori in gastric microbiota2
	Reflux esophagitis	Esophageal microbiota dominated by Gram negative anaerobes; gastric microbiota has low or absent H. pylori4
	Childhood-onset asthma	Absence of H. pylori in gastric microbiota4
	Age-related gastric atrophy	Enhanced by presence of H. pylori in gastric microbiota3
Upper GI	Obesity	Reduced ratio of Bacteroidetes to Firmicutes; enrichment of genes related to lipid and carbohydrate metabolism; risk significantly increased with antibiotic use prior to 6 months of age4 Successful weight loss associated with higher levels of Bacteroides fragilis, Lactobacilli, and Bifidobacteria5
	Cardiovascular disease	Gut-microbiota-dependent metabolism of phosphatidylcholine4
	Diseases of the liver: non-alcoholic fatty liver disease, alcoholic steatosis, hepatocellular carcinoma	Exposure to metabolic products of microbiome: acetaldehyde; phenols; ammonia4
	Cirrhosis	Substantially altered microbiome; with enrichment of Proteobacteria and Fusobacteria phyla, and Enterobacteriaceae, Veillonellaceae, and Streptococcaceae families4
	ASD	Significantly increased presence of Clostridium bolteae8
	Small intestine bacterial overgrowth	Associated with recurrent antibiotics, gastric acid inhibitors, Crohn's disease, cirrhosis, chronic pancreatitis, end stage renal disease12
Colonic	Inflammatory bowel disease	Host polymorphisms in bacterial sensor genes (NOD2; CARD15; TLR4); symptoms may improve with antibiotic treatment4 Bacterial sensor genes (NOD2, TLR4, CARD8, CARD9, NLRP3) and autophagy genes (ATG16L1, IRGM, LRRK2)5 Reduced butyrate, acetate, methylamine, trimethylamine; elevated amino acids; metabolites from arachidonic acids and bile acids were most affected3 Impaired production of α-defensin40
	Functional bowel diseases	Larger populations of Veillonella and Lactobacillus4
	Ulcerative colitis	Large populations of Enterobacteriaceae, increased proportions of Actinobacteria and Proteobacteria4 Increased taurine and cadaverine3
	Crohn's disease	Increased risk with early childhood exposure to antibiotics; Significantly diminished microbial diversity; Large populations of Enterococcus faecium and several Proteobacteria4 Genes involved in epithelial barrier integrity (IBD5, DLG5, PDGER4, DMBT1, XBPI); decreased Faecalibacterium prausnitzii and Roseburia hominis5 Linked to disruption of duodenal microbiota12 Higher amounts of bacteriophages3
	Colorectal cancer	Larger populations of Fusobacterium spp.; significantly lower Desulfovibrio spp.4, 5, 8 Invasive CRC associated with Escherichia coli NC1015 Lower butyrate and acetate, higher proline and cysteine3
	Irritable bowel syndrome	Distinctive alterations in Coprococcus, Collinsella, and Coprobacillus genera5 Higher levels of Pseudomonas aeruginosa and lower levels of Bifidobacterium catenulatum in upper GI12 Higher bile acid concentration, lower levels of branched chain fatty acids3 May follow infection by Campylobacter enteritis, Shigella, or Salmonella40

The presence or absence of certain human diseases is associated with and influenced by genetic and bacterial conditions of the relevant microbiome.