An Omics Study Of Gut Microbiota Characteristics In Patients With Systemic Lupus Erythematosus

Purpose:Systemic lupus erythematosus(SLE)is an autoimmune disease characterized by abnormal autoantibody production and chronic inflammation and leading to multi-organ damage.The pathogenesis of SLE has not yet been well elucidated.Recent studies have shown that the human gut microbiota may be involved in the occurrence and development of many autoimmune diseases,including SLE.However,current findings on the fecal microbiota of SLE patients have been limited by small sample size,low detection accuracy,and the influence of ongoing medications on microbiota.Integrating in-depth fecal shotgun metagenomic and metabolomic profiling,this study aims to reveal the gut microbiota characteristics of untreated SLE patients and their potential role in the development of SLE.Methods:We recruited 117 patients with untreated SLE,who had not received any steroids or immunosuppressive drugs for the last 3 months,and 1 15 sex-and age-matched healthy controls.We collected the clinical data,blood samples,and fecal samples,and 52 out of all SLE patients also provided samples after disease-relieving treatment.Metagenomic shotgun sequencing was performed to profile the fecal microbiota,and gas chromatography-mass spectrometer detection was employed to test the non-targeted fecal metabolome.We carried out multiple bioinformatic analyses to reveal changes in the diversity,taxonomical composition,and functional pathway of SLE patients.Using a single nucleotide polymorphism(SNP)-based clustering method,we assessed the homogeneity among the tested species from fecal and salivary samples,to determine whether the gut-enriched species in SLE patients were partly derived from the oral cavity or not.We also downloaded the sequences of confirmed SLE auto-epitopes from the immune epitope database,compared them with the genomic sequences of the SLE-related species found in our study,and used the enzyme-linked immunospot experiment to verify the autoimmunogenic properties of some of the mimicry microbial peptides.Finally,we also compared the gut microbiota of SLE patients with those of MRL/lpr lupus-prone mice and patients with primary Sjogren’s syndrome(pSS).Results:The gut microbiota of the untreated SLE patients had a lower richness and evenness in diversity and a disturbed taxonomical composition compared to healthy controls.Seven microbial species were found to increase in the gut microbiota of SLE patients and decrease after disease-relieving treatment.The SNP signatures of some SLE-enriched species from SLE feces and healthy saliva were very similar,suggesting that the increased abundance of these species in the gut of SLE patients was partly derived from their oral microbiota.We also found two bacterial peptides that mimic the auto-epitope of SLE patients.One of them mimics an epitope of the Smith antigen recognized by T cells,causing an increase in the number of cells expressing IFN-y and IL-17A in stimulated peripheral blood mononuclear cells of some SLE patients.The other mimics an epitope of the Fas antigen recognized by B cells and could bind to specific IgG secreted by the peripheral blood memory B cells of some SLE patients.Integrated analysis of the data from the fecal metagenome and metabolome showed significant abnormalities in the metabolic function of the SLE gut microbiota.In particular,we focused on analyzing the up-regulated "arginine-ornithine-proline" synthesis pathway and the down-regulated branched-chain amino acid synthesis pathway.Comparative analysis showed that SLE patients and lupus mice have much more common changes in gut microbial function than taxonomical composition.In addition,SLE patients and pSS patients also shared many common features in the gut microbiota.Conclusions:This study used multi-omic data to thoroughly analyze the compositional and functional changes in the gut microbiota of untreated SLE patients.We discovered several important correlations between gut microbial features and clinical indicators in SLE patients.We propose that some of the enriched species in the gut of SLE patients is partly a result of the translocation of oral microbiota.Furthermore,we have identified two potentially pathogenic microbial peptides involved in SLE pathogenesis via molecular mimicry.The findings of this study provide substantial information regarding the SLE-characteristic gut microbiota for follow-up mechanistic studies and offer new clues to the effective diagnosis and therapeutics of SLE.