Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJ. Role of the microbiome in human development. Gut. 2019;68(6):1108–14. https://doi.org/10.1136/gutjnl-2018-317503.

Article  CAS  PubMed  Google Scholar 

Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–14. https://doi.org/10.1038/nature11234.

Kishikawa T, Maeda Y, Nii T, Motooka D, Matsumoto Y, Matsushita M, et al. Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population. Ann Rheum Dis. 2020;79(1):103–11. https://doi.org/10.1136/annrheumdis-2019-215743.

Article  CAS  PubMed  Google Scholar 

Chen BD, Jia XM, Xu JY, Zhao LD, Ji JY, Wu BX, et al. An autoimmunogenic and proinflammatory profile defined by the gut microbiota of patients with untreated systemic lupus erythematosus. Arthritis Rheumatology (Hoboken, NJ). 2021;73(2):232–43. https://doi.org/10.1002/art.41511.

Article  CAS  Google Scholar 

Kishikawa T, Ogawa K, Motooka D, Hosokawa A, Kinoshita M, Suzuki K, et al. A metagenome-wide association study of gut microbiome in patients with multiple sclerosis revealed novel disease pathology. Front Cell Infect Microbiol. 2020;10:585973. https://doi.org/10.3389/fcimb.2020.585973.

Article  PubMed  PubMed Central  Google Scholar 

Cano-Ortiz A, Laborda-Illanes A, Plaza-Andrades I, Membrillo Del Pozo A, Villarrubia Cuadrado A, Rodríguez Calvo de Mora M, et al. Connection between the gut microbiome, systemic inflammation, gut permeability and FOXP3 expression in patients with primary Sjögren’s syndrome. International Journal of Molecular Sciences. 2020;21(22). https://doi.org/10.3390/ijms21228733.

Fanouriakis A, Tziolos N, Bertsias G, Boumpas DT. Update οn the diagnosis and management of systemic lupus erythematosus. Ann Rheum Dis. 2021;80(1):14–25. https://doi.org/10.1136/annrheumdis-2020-218272.

Article  PubMed  Google Scholar 

Woo JMP, Parks CG, Jacobsen S, Costenbader KH, Bernatsky S. The role of environmental exposures and gene-environment interactions in the etiology of systemic lupus erythematous. J Intern Med. 2022;291(6):755–78. https://doi.org/10.1111/joim.13448.

Article  CAS  PubMed  Google Scholar 

Li Y, Wang HF, Li X, Li HX, Zhang Q, Zhou HW, et al. 2019 Disordered intestinal microbes are associated with the activity of systemic lupus erythematosus. Clinical science (London, England : 1979) 133(7):821–38. https://doi.org/10.1042/cs20180841.

Zhou HY, Cao NW, Guo B, Chen WJ, Tao JH, Chu XJ, et al. Systemic lupus erythematosus patients have a distinct structural and functional skin microbiota compared with controls. Lupus. 2021;30(10):1553–64. https://doi.org/10.1177/09612033211025095.

Article  CAS  PubMed  Google Scholar 

Liu F, Ren T, Li X, Zhai Q, Xu X, Zhang N, et al. Distinct microbiomes of gut and saliva in patients with systemic lupus erythematous and clinical associations. Front Immunol. 2021;12:626217. https://doi.org/10.3389/fimmu.2021.626217.

Article  CAS  PubMed  PubMed Central  Google Scholar 

James WA, Ogunrinde E, Wan Z, Kamen DL, Oates J, Gilkeson GS, et al. A distinct plasma microbiome but not gut microbiome in patients with systemic lupus erythematosus compared to healthy individuals. J Rheumatol. 2022;49(6):592–7. https://doi.org/10.3899/jrheum.210952.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gomaa EZ. Human gut microbiota/microbiome in health and diseases: a review. Antonie Van Leeuwenhoek. 2020;113(12):2019–40. https://doi.org/10.1007/s10482-020-01474-7.

Article  PubMed  Google Scholar 

Heintz-Buschart A, Wilmes P. Human gut microbiome: function matters. Trends Microbiol. 2018;26(7):563–74. https://doi.org/10.1016/j.tim.2017.11.002.

Article  CAS  PubMed  Google Scholar 

Hevia A, Milani C, López P, Cuervo A, Arboleya S, Duranti S, et al. 2014 Intestinal dysbiosis associated with systemic lupus erythematosus. mBio (5):01548–14. https://doi.org/10.1128/mBio.01548-14.

Xiang K, Wang P, Xu Z, Hu YQ, He YS, Chen Y, et al. Causal effects of gut microbiome on systemic lupus erythematosus: a two-sample mendelian randomization study. Front Immunol. 2021;12:667097. https://doi.org/10.3389/fimmu.2021.667097.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu Q, Ni JJ, Han BX, Yan SS, Wei XT, Feng GJ, et al. Causal relationship between gut microbiota and autoimmune diseases: a two-sample Mendelian randomization study. Front Immunol. 2021;12:746998. https://doi.org/10.3389/fimmu.2021.746998.

Article  CAS  PubMed  Google Scholar 

He Z, Shao T, Li H, Xie Z, Wen C. Alterations of the gut microbiome in Chinese patients with systemic lupus erythematosus. Gut pathogens. 2016;8:64. https://doi.org/10.1186/s13099-016-0146-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang Y, Wei J, Zhang W, Doherty M, Zhang Y, Xie H, et al. Gut dysbiosis in rheumatic diseases: a systematic review and meta-analysis of 92 observational studies. EBioMedicine. 2022;80:104055. https://doi.org/10.1016/j.ebiom.2022.104055This article conducted a systematic review in various rheumatic diseases and identified similarities and differences among these diseases

Azzouz D, Omarbekova A, Heguy A, Schwudke D, Gisch N, Rovin BH, et al. Lupus nephritis is linked to disease-activity associated expansions and immunity to a gut commensal. Annals of the rheumatic diseases. 2019;78(7):947-56. https://doi.org/10.1136/annrheumdis-2018-214856The article revealed that Ruminococcus gnavus contributes to the pathogenesis of lupus nephritis by molecular mimicry.

Wen M, Liu T, Zhao M, Dang X, Feng S, Ding X, et al. Correlation Analysis between gut microbiota and metabolites in children with systemic lupus erythematosus. J Immunol Res. 2021;2021:5579608. https://doi.org/10.1155/2021/5579608.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Santiago-Rodriguez TM, Hollister EB. Human virome and disease: high-throughput sequencing for virus discovery, identification of phage-bacteria dysbiosis and development of therapeutic approaches with emphasis on the human gut. Viruses. 2019;11(7). https://doi.org/10.3390/v11070656.

Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498. https://doi.org/10.1038/ncomms5498.

Article  CAS  PubMed  Google Scholar 

Chen C, Yan Q, Yao X, Li S, Lv Q, Wang G, et al. Alterations of the gut virome in patients with systemic lupus erythematosus. Front Immunol. 2022;13:1050895. https://doi.org/10.3389/fimmu.2022.1050895.

Article  CAS  PubMed  Google Scholar 

Tomofuji Y, Kishikawa T, Maeda Y, Ogawa K, Nii T, Okuno T, et al. Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease. Annals of the rheumatic diseases. 2022;81(2):278-88. https://doi.org/10.1136/annrheumdis-2021-221267This article filled the gap in the study of viruses in the autoimmunity associated gut microbiome.

d'Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, et al. The impact of the fungus-host-microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS microbiology reviews. 2021;45(3). https://doi.org/10.1093/femsre/fuaa060.

Lapiere A, Richard ML. Bacterial-fungal metabolic interactions within the microbiota and their potential relevance in human health and disease: a short review. Gut microbes. 2022;14(1):2105610. https://doi.org/10.1080/19490976.2022.2105610.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guinan J, Wang S, Hazbun TR, Yadav H, Thangamani S. Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans. Sci Rep. 2019;9(1):8872. https://doi.org/10.1038/s41598-019-45467-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doron I, Mesko M, Li XV, Kusakabe T, Leonardi I, Shaw DG, et al. Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease. Nat Microbiol. 2021;6(12):1493–504. https://doi.org/10.1038/s41564-021-00983-z.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li BZ, Wang H, Li XB, Zhang QR, Huang RG, Wu H, et al. Altered gut fungi in systemic lupus erythematosus - a pilot study. Front Microbiol. 2022;13:1031079. https://doi.org/10.3389/fmicb.2022.1031079.

Article  PubMed  PubMed Central  Google Scholar 

Chen YF, Hsieh AH, Wang LC, Huang YJ, Yun-Chen T, Tseng WY, et al. Fecal microbiota changes in NZB/W F1 mice after induction of lupus disease. Sci Rep. 2021;11(1):22953. https://doi.org/10.1038/s41598-021-02422-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luo XM, Edwards MR, Mu Q, Yu Y, Vieson MD, Reilly CM, et al. Gut microbiota in human systemic lupus erythematosus and a mouse model of lupus. Applied and environmental microbiology. 2018;84(4). https://doi.org/10.1128/aem.02288-17.

Zhang H, Liao X, Sparks JB, Luo XM. Dynamics of gut microbiota in autoimmune lupus. Appl Environ Microbiol. 2014;80(24):7551–60. https://doi.org/10.1128/aem.02676-14.

Article  PubMed  PubMed Central  Google Scholar 

Zegarra-Ruiz DF, El Beidaq A, Iñiguez AJ, Lubrano Di Ricco M, Manfredo Vieira S, Ruff WE, et al. 2019 A diet-sensitive commensal Lactobacillus strain mediates TLR7-dependent systemic autoimmunity. Cell host & microbe. (1):113–27.6 https://doi.org/10.1016/j.chom.2018.11.009

Toumi E, Goutorbe B, Plauzolles A, Bonnet M, Mezouar S, Militello M, et al. Gut microbiota in systemic lupus erythematosus patients and lupus mouse model: a cross species comparative analysis for biomarker discovery. Front Immunol. 2022;13:943241. https://doi.org/10.3389/fimmu.2022.943241.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):1002533. https://doi.org/10.1371/journal.pbio.1002533.

Article  CAS  Google Scholar 

Ruff WE, Greiling TM, Kriegel MA. Host-microbiota interactions in immune-mediated diseases. Nat Rev Microbiol. 2020;18(9):521–38. https://doi.org/10.1038/s41579-020-0367-2.

Article  CAS  PubMed  Google Scholar 

Huang C, Yi X, Long H, Zhang G, Wu H, Zhao M, et al. Disordered cutaneous microbiota in systemic lupus erythematosus. J Autoimmun. 2020;108:102391. https://doi.org/10.1016/j.jaut.2019.102391.

Article  PubMed  Google Scholar 

Terui H, Yamasaki K, Wada-Irimada M, Onodera-Amagai M, Hatchome N, Mizuashi M, et al. Staphylococcus aureus skin colonization promotes SLE-like autoimmune inflammation via neutrophil activation and the IL-23/IL-17 axis. Sci Immunol. 2022;7(76):9811. https://doi.org/10.1126/sciimmunol.abm9811.

Article  Google Scholar 

Paetzold B, Willis JR, Pereira de Lima J, Knödlseder N, Brüggemann H, Quist SR, et al. Skin microbiome modulation induced by probiotic solutions. Microbiome. 2019;7(1):95. https://doi.org/10.1186/s40168-019-0709-3.

Article  PubMed  PubMed Central  Google Scholar 

Verma D, Garg PK, Dubey AK. Insights into the human oral microbiome. Arch Microbiol. 2018;200(4):525–40. https://doi.org/10.1007/s00203-018-1505-3.

Article  CAS  PubMed  Google Scholar 

Kudsi M, Nahas LD, Alsawah R, Hamsho A, Omar A. The prevalence of oral mucosal lesions and related factors in systemic lupus erythematosus patients. Arthritis Res Ther. 2021;23(1):229. https://doi.org/10.1186/s13075-021-02614-8.

Article  CAS  PubMed