The Dynamic Interplay between the Gut Microbiota and Autoimmune Diseases

Table 1

Autoimmune diseases and alteration of the gut microbiota composition.

Diseases	Species	Methods	Increasing microbiota species	Decreasing microbiota species	References
RA	Mouse	16S rRNA gene sequencing	Desulfovibrio; Mucispirillum; Helicobacter; Lachnospiraceae; Rikenellaceae_RC9	S24-7; Rikenella	[60]
	Human	16S rRNA sequencing		Euryarchaeota	[54]
	Human	16S ribosomal DNA	Collinsella	Actinobacteria	[53]
	Human	Denaturing gradient gel electrophoresis	Lactobacillus		[57]
	Mouse	16S rRNA sequencing	Bacteroidaceae; Lachnospiraceae; S24-7		[47]
SLE	Mouse, human	16S rDNA sequencing	Lactobacillus reuteri		[62]
	Human	16S rRNA sequencing	Proteobacteria	Ruminococcaceae	[61]
	Human	16S ribosomal RNA gene sequencing	Bacteroides	Firmicutes/Bacteroidetes ratio	[112]
	Human	16S rRNA sequencing	Streptococcus; Lactobacillus; S. anginosus; L. mucosae; Megasphaera	Faecalibacterium; F. prausnitzii; Cryptophyta; Roseburia; Bifidobacterium	[66]
	Human	16S rRNA sequencing	Ruminococcus gnavus		[67]
	Human	Metagenomic analyses		Firmicutes/Bacteroidetes ratio	[69]
	Mouse	16S rDNA sequencing	Lachnospiraceae	Lactobacillus spp.	[47]
SpA	Human	16S rRNA gene- and ITS2-based DNA sequencing	Escherichia-Shigella; Veillonella; Lachnospiraceae; NK4A136 group; Dothideomycetes	Prevotella strain 9; Megamonas; Fusobacterium; Agaricales	[79]
	Human	16S ribosomal RNA amplicon sequencing	Dialister		[83]
	Human	16S ribosomal RNA gene sequencing	Ruminococcus gnavus		[84]
IBD	Human	Metagenomic sequencing	Escherichia coli	Eubacterium rectale; Faecalibacterium prausnitzii	[101]
	Human	Tag-sequencing the 16S rRNA gene		Roseburia spp.	[93]
	Human	16S rRNA sequencing	Actinobacteria; Proteobacteria (Enterobacteriaceae)	Firmicutes (Clostridiales)	[94]
	Human	16S rRNA sequencing	Proteobacteria	Firmicutes; Actinobacteria	[95]
	Dog	16S rRNA gene next-generation sequencing	Paraprevotellaceae; Porphyromonas		[91]