Table 3.

Summary table of key findings.

Disease group	Specific disease	Gut microbes	Main findings
Autoimmune diseases	Rheumatoid arthritis	Prevotella copri.,	Increased in abundance [12, 13]
		Collinsella sp.,	Increased in abundance [13]
		Faecalibacterium sp.	Decreased in abundance, links to SCFA production [25]
	Type-1 diabetes	Dialister invisus., Gemella sanguinis., Bifidobacterium longum	Increased in abundance (children), gut permeability [25]
		F. prausnitzii	Decreased in abundance (children), butyrate (SCFA) production [28]
	Atopic eczema	Clostridium difficile	Increased in abundance [37]
		Escherichia coli	Increased in abundance, eosinophilic inflammation [37]
		Staphylococcus aureus	Increased in abundance [37]
		Bifidobacteria spp.	Decreased in abundance [37]
		Bacteroidetes spp.	Decreased in abundance [38, 39]
		Coprococcus eutactus	Decreased (in children), linked to butyrate production [39]
		F. prausnitizii	Increased in abundance, SCFA production [41]
	Atopic asthma	Various—Clostridium, Pediococcus, Escherichia, Klebsiella, Morganella, and Proteus spp.	Increased in abundance, increased bioamine (histamine) production [55]
		Enterococcus faecalis, Streptococcus spp., Bifidobacterium bifidum., Lactobacillus spp.	Increased in abundance, increased bioamine (histamine) levels, increased epoxide hydrolase production of oxylipins (12,13-diHOME) [55, 56]
Gut inflammation disorders	Irritable bowel syndrome	Ruminococcus spp., Clostridium spp., Dorea spp.	Increased in abundance [62]
		Bifidobacterium spp.	Decreased significantly in abundance (all IBS subtypes) [62, 68]
		Faecalibacterium spp.	Decreased in abundance, anti-inflammatory, butyrate production [62, 64, 65]
		Enterobacteriaceae spp.	Increased, links to previous intestinal infection and pathogen byproducts [63]
		Lactobacillaceae spp., Bacteroides spp.	Increased in abundance [63]
	Inflammatory bowel disease	Ruminococcaceae spp., Lachnospiraceae spp.	Decreased in microbiome, butyrate production [78–81]
		Faecalibacterium prausnitzii, Roseburia sp.	Decreased in microbiome, butyrate production [83]
Cardiometabolic diseases	Cardiovascular disease (including hypertension)	Lactobacillus plantarum, Lactobacillus rhamnosus	Improved ventricular function and attenuated heart failure after myocardial infarction [90, 107]. Improved blood pressure [110]
		Akkermansia muciniphila	Protected against atherosclerosis in mice [111]
	Type-2 diabetes	Bifidobacterium, Bacteroides, Faecalibacterium Akkermansia and Roseburia spp.	Negative association [112, 113]
		Ruminococcus, Fusobacterium, and Blautia	Positive association [112, 113]
		Lactobacillus spp.	Enriched in control microbiome, butyrate production [112, 114, 115], insulin sensitivity through GLP-1 [116–120]
		Clostridium spp.	Increased, opportunistic pathogen
NAFLD		Collinsell spp.	Increased in abundance [128]. Increased intestinal permeability and lipopolysaccharide release through metabolism of bile-acids to oxo-bile [144, 145]
		Escherichia spp., Dorea spp.	Increased in abundance [131, 135, 136]
		Coprococcus spp., Eubacterium spp., Faecalibacterium spp., Prevotella spp.	Decreased in abundance [131, 135, 137]
Chronic kidney disease		Bifidobacterium, Lactobacillaceae, Prevotellaceae	Decreased in abundance, SCFA producers associated with anti-inflammatory cytokines [148, 149]
		Enterobacter	Increased in abundance [149]
		Klebsiella	Increased in abundance, pathogen associated with inflammatory disease states including Crohn’s [148, 149]
		Clostridium perfringes	Increased in abundance, pathogen associated with intestinal diseases [148]
Mental health disorders	SCZ, ADHD	Lactobacillus spp, Bifidobacterium	Increased in abundance in specific disorders such as SCZ and ADHD [157, 158]
	General anxiety disorder (GAD)	Bacteriodetes, Ruminococcus gnavus, and Fusobacterium Bacteroidaceae, Enterobacteriaceae, and Burkholderiaceae	Decreased in abundance in general anxiety disorder (GAD) [170]. Increased in abundance in GAD [171, 172]
	Post- traumatic stress disorder (PTSD)	Actinobacteria, Lentisphaerae, and Verrucomicrobia	Decreased in abundance in post-traumatic stress disorder (PTSD) [173]
	Depression	Eggerthella., Holdemania, Turicibacter, Paraprevotella Prevotella, Dialister	Increased in abundance amongst individuals with depression [174, 175]. Decreased in abundance amongst individuals with depression [176]
	Dementia	Escherichia, Blautia, Bifidobacterium, Streptococcus, Lactobacillus, Dorea spp Actinobacteria, Bacteroides	Increased in abundance amongst individuals with dementia [177]. Decreased in abundance amongst individuals with dementia [177]