Table 1.

Microbiome alterations in different autoimmune conditions respect to healthy subjects.

Autoimmune Conditions	Microbiome Alterations in Autoimmunity Respect to Healthy Subjects	References
Type I diabetes	↓ bacterial diversity in high-risk children	[35,42,43]
	↑ Bacteroidetes/Firmicutes ratio	[36,44,51]
	↑ Bacteroidetes, Clostridium, and Veillonella; ↓ Bifidobacterium, Lactobacillus, Blautia coccoides/Eubacterium rectale group, and Prevotella	[37]
	↑ Bacteroides dorei in high-risk children	[39]
	↑ Bacteroides and ↓ Prevotella in newly diagnosed T1D patients	[40]
	↓ Bifidobacterium	[36,41]
	↑ Bacteroides and Clostridium cluster XVa and cluster IV; ↓ Bifidobacterium	[47]
	↑ Candida albicans and Enterobacteriaceae	[41]
Rheumatoid arthritis	↑ of the pathobiont Prevotella (Prevotella copri) in new-onset RA subjects	[107]
	Gut and oral microbiome dysbiosis; ↓ Haemophilus spp. and ↑ Lactobacillus salivarius	[56]
	↓ gut bacterial diversity and expansion of rare lineage intestinal microbes	[57]
	Association between periodontal infection due to Porphyromonas gingivalis and RA	[54,108]
	↑ Fretibacterium, Selenomonas and Prevotella nigrescens	[55]
	↑ Bacilli and Lactobacillales; ↓ genus Faecalibacterium and the specie Faecalibacterium prausnitzii; Absence of the genus Flavobacterium and the species Blautia coccoides in RA patients present instead in controls	[62]
	↑ Prevotella copri and ↓ Bacteroides in new-onset untreated RA patients	[107]
Systemic lupus erythematosus	↑ Bacteroidetes/Firmicutes ratio	[65]
	Association between SLE and periodontal disease; Dysbiosis of the subgingival microbiota; ↑ subgingival bacterial load; ↓ subgingival microbial diversity at diseased sites	[67]
	↑ Fretibacterium, Selenomonas, and Prevotella nigrescens;	[109]
	Association with periodontal pathogens (Treponema denticola, Porphyromonas gingivalis, Fretibacterium fastidiosum and Tannerella forsythia	[109,110]
Behcet’s disease	↓ Roseburia and Subdoligranulum genera	[79]
	↑ Bifidobacterium and Eggerthella genera and ↓ Megamonas and Prevotella genera	[81]
	↑ Bilophila spp. and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.); ↓ butyrate-producing bacteria Clostridium spp. and methanogens (Methanoculleus spp. and Methanomethylophilus spp.).	[82]
Inflammatory bowel disease	↓ gut bacterial diversity	[68]
	↓ diversity in the bacterial phylum Firmicutes faecal; ↓ Clostridium leptum phylogenetic group	[70]
	↑ Proteobacteria phylum including Escherichia coli; ↓ Firmicutes phylum was reduced	[69,70,73,111]
	↓ Faecalibacterium prausnitzii is associated with an ↑ risk of postoperative recurrence of ileal CD	[72]
	↓ in several butyrate-producing bacteria species	[74,76]
	↓ of the genera Bacteroides, Eubacterium, Faecalibacterium and Ruminococcus; ↑ genera Actinomyces and Bifidobacterium; ↓ butyrate-producing bacterial species, as Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis, and Faecalibacterium prausnitzii	[76]
	Dysbiosis	[112]
	↑ Caudovirales bacteriophages and fungal composition	[113]
Vitiligo	↑ Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes	[83,114]
	↓ bacterial diversity	[83]
Psoriasis vulgaris	↑ Proteobacteria; ↓ Staphylococci and Propionibacteria	[85]
	↓ bacterial diversity; ↑ Corynebacterium, Propionibacterium, Staphylococcus, and Streptococcus; ↓ Cupriavidus, Flavisolibacter, Methylobacterium, and Schlegelella genera. Association between lesion samples with Firmicutes-associated microbiota	[86]
	↓ diversity and ↑ Staphylococcus in psoriatic ear sites	[87]
	↑ diversity and ↑ heterogeneity ↑ Staphylococcus aureus; ↓ Staphylococcus epidermidis and Propionibacterium acnes	[88]
Atopic dermatitis	↑ Faecalibacterium prausnitzii subspecies	[93]
	↑ Staphylococcus aureus	[94]
	↓ Propionibacterium acnes and Lawsonella clevelandensis; ↑ Staphylococcus aureus in non-lesional relative to lesional AD patients	[95]
Autoimmune neurological diseases	↓ species belonging to Clostridia XIVa and IV Clusters	[101]
	↑ Pseudomonas, Mycoplana, Haemophilus, Blautia, and Dorea in relapsing remitting MS patients; ↓ Parabacteroides, Adlercreutzia, and Prevotella genera	[102]
	↑ Methanobrevibacter and Akkermansia; ↓ Butyricimonas	[103]
	↑ Akkermansia muciniphila and Acinetobacter calcoaceticus; ↓ Parabacteroides distasonis	[106]