Skip to main content
SpringerLink
Log in

The Influence of the Microbiome and Genetic Associations on Immune Functions and on Autoimmune and Autoinflammatory Diseases

  • Chapter
  • First Online:
Role of Microorganisms in Pathogenesis and Management of Autoimmune Diseases

  • 260 Accesses

Abstract

Autoimmune and autoinflammatory diseases are different ends of several common genetic traits and pathways ending in chronic inflammation, which depends on adaptive and innate immunity, respectively. Autoimmune but not autoinflammatory diseases are strongly associated with major histocompatibility class II alleles, which define the target antigen for T and/or antibody-dependent tissue damage. Both types of diseases can be triggered and maintained by internal or external factors. Among the latter, dysbiosis of the microbiota, which profoundly influences the nature of the immune-mediated inflammation and immune tolerance, has received a great deal of interest over the past two decades. Here we discuss the recent advances in the knowledge of the immune system and the mechanisms leading to autoimmunity or autoinflammation. Moreover, we revise some of the most recent information about the possible roles of the microbiota on these processes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Akira S, Uematsu S, Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124:783–801

    Article  CAS  Google Scholar 

  • Arrieta MC, Finlay B (2014) The intestinal microbiota and allergic asthma. J Infect 69(Suppl 1):S53–S55

    Article  Google Scholar 

  • Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y et al (2011) Induction of colonic regulatory T cells by indigenous clostridium species. Science 331:337–341

    Article  CAS  Google Scholar 

  • Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, Saito T, Narushima S, Hase K et al (2013) Treg induction by a rationally selected mixture of clostridia strains from the human microbiota. Nature 500:232–236

    Article  CAS  Google Scholar 

  • Atarashi K, Tanoue T, Ando M, Kamada N, Nagano Y, Narushima S, Suda W, Imaoka A, Setoyama H, Nagamori T et al (2015) Th17 cell induction by adhesion of microbes to intestinal epithelial cells. Cell 163:367–380

    Article  CAS  Google Scholar 

  • Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T et al (2017) Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science 358:359–365

    Article  CAS  Google Scholar 

  • Belot A, Cimaz R (2012) Monogenic forms of systemic lupus erythematosus: new insights into SLE pathogenesis. Pediatr Rheumatol Online J 10:21

    Article  Google Scholar 

  • Bennett CL, Christie J, Ramsdell F, Brunkow ME, Ferguson PJ, Whitesell L, Kelly TE, Saulsbury FT, Chance PF, Ochs HD (2001) The immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) is caused by mutations of FOXP3. Nat Genet 27:20–21

    Article  CAS  Google Scholar 

  • Billington SG, Crabbe S (1924) Etiology and treatment of rheumatoid arthritis and allied diseases. Br Med J 1:1087–1089

    Article  CAS  Google Scholar 

  • Brewerton DA, Hart FD, Nicholls A, Caffrey M, James DC, Sturrock RD (1973) Ankylosing spondylitis and HL-A 27. Lancet (7809):904–907. PMID: 4123836. https://doi.org/10.1016/s0140-6736(73)91360-3

  • Bunker JJ, Bendelac A (2018) IgA responses to microbiota. Immunity 49:211–224

    Article  CAS  Google Scholar 

  • Butler TD, Gibbs JE (2020) Circadian host-microbiome interactions in immunity. Front Immunol 11:1783

    Article  CAS  Google Scholar 

  • Chen B, Miller AL, Rebelatto M, Brewah Y, Rowe DC, Clarke L, Czapiga M, Rosenthal K, Imamichi T, Chen Y et al (2015) S100A9 induced inflammatory responses are mediated by distinct damage associated molecular patterns (DAMP) receptors in vitro and in vivo. PLoS One 10:e0115828

    Article  Google Scholar 

  • Clatza A, Bonifaz LC, Vignali DA, Moreno J (2003) CD40-induced aggregation of MHC class II and CD80 on the cell surface leads to an early enhancement in antigen presentation. J Immunol 171:6478–6487

    Article  CAS  Google Scholar 

  • Dai Y, Pei G, Zhao Z, Jia P (2019) A convergent study of genetic variants associated with Crohn's disease: evidence from GWAS, gene expression, methylation, eQTL and TWAS. Front Genet 10:318

    Article  CAS  Google Scholar 

  • de Vos WM, Tilg H, Van Hul M, Cani PD (2022) Gut microbiome and health: mechanistic insights. Gut 71(5):1020–1032

    Article  Google Scholar 

  • Duar RM, Henrick BM, Casaburi G, Frese SA (2020) Integrating the ecosystem services framework to define Dysbiosis of the breastfed infant gut: the role of B. infantis and human milk oligosaccharides. Front Nutr 7:33

    Article  Google Scholar 

  • Edwards V, Smith DL, Meylan F, Tiffany L, Poncet S, Wu WW, Phue JN, Santana-Quintero L, Clouse KA, Gabay O (2021) Analyzing the role of gut microbiota on the onset of autoimmune diseases using TNF(DeltaARE) murine model. Microorganisms 10:73

    Article  Google Scholar 

  • Edye ME, Lopez-Castejon G, Allan SM, Brough D (2013) Acidosis drives damage-associated molecular pattern (DAMP)-induced interleukin-1 secretion via a caspase-1-independent pathway. J Biol Chem 288:30485–30494

    Article  CAS  Google Scholar 

  • Fiorillo MT, Paladini F, Tedeschi V, Sorrentino R (2017) HLA class I or class II and disease association: catch the difference if You can. Front Immunol 8:1475

    Article  Google Scholar 

  • Fontenot JD, Gavin MA, Rudensky AY (2003) Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat Immunol 4:330–336

    Article  CAS  Google Scholar 

  • Friman V, Nowrouzian F, Adlerberth I, Wold AE (2002) Increased frequency of intestinal Escherichia coli carrying genes for S fimbriae and haemolysin in IgA-deficient individuals. Microb Pathog 32:35–42

    Article  CAS  Google Scholar 

  • Galli SJ, Borregaard N, Wynn TA (2011) Phenotypic and functional plasticity of cells of innate immunity: macrophages, mast cells and neutrophils. Nat Immunol 12:1035–1044

    Article  CAS  Google Scholar 

  • Gibson TJ, Ramu C, Gemund C, Aasland R (1998) The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor. Trends Biochem Sci 23:242–244

    Article  CAS  Google Scholar 

  • Gonzalez-Serna D, Ochoa E, Lopez-Isac E, Julia A, Degenhardt F, Ortego-Centeno N, Radstake T, Franke A, Marsal S, Mayes MD et al (2020) A cross-disease meta-GWAS identifies four new susceptibility loci shared between systemic sclerosis and Crohn's disease. Sci Rep 10:1862

    Article  CAS  Google Scholar 

  • Goodnow CC (2007) Multistep pathogenesis of autoimmune disease. Cell 130:25–35

    Article  CAS  Google Scholar 

  • Gordon S (2002) Pattern recognition receptors: doubling up for the innate immune response. Cell 111:927–930

    Article  CAS  Google Scholar 

  • Gregersen PK (1989) HLA class II polymorphism: implications for genetic susceptibility to autoimmune disease. Lab Investig 61:5–19

    CAS  Google Scholar 

  • Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R et al (2017) A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med 9:103

    Article  Google Scholar 

  • Harsha Krovi S, Zhang J, Michaels-Foster MJ, Brunetti T, Loh L, Scott-Browne J, Gapin L (2020) Thymic iNKT single cell analyses unmask the common developmental program of mouse innate T cells. Nat Commun 11:6238

    Article  CAS  Google Scholar 

  • Hornung V, Ablasser A, Charrel-Dennis M, Bauernfeind F, Horvath G, Caffrey DR, Latz E, Fitzgerald KA (2009) AIM2 recognizes cytosolic dsDNA and forms a caspase-1-activating inflammasome with ASC. Nature 458:514–518

    Article  CAS  Google Scholar 

  • Huus KE, Petersen C, Finlay BB (2021) Diversity and dynamism of IgA-microbiota interactions. Nat Rev Immunol 21:514–525

    Article  CAS  Google Scholar 

  • Hviid A, Svanstrom H, Frisch M (2011) Antibiotic use and inflammatory bowel diseases in childhood. Gut 60:49–54

    Article  Google Scholar 

  • Irons EE, Gomez EC, Andersen VL, Lau JTY (2022) Bacterial colonization and TH17 immunity are shaped by intestinal sialylation in neonatal mice. Glycobiology 32(5):414–428

    Article  CAS  Google Scholar 

  • Jacobse J, Li J, Rings E, Samsom JN, Goettel JA (2021) Intestinal regulatory T cells as specialized tissue-restricted immune cells in intestinal immune homeostasis and disease. Front Immunol 12:716499

    Article  CAS  Google Scholar 

  • Janeway CA Jr, Medzhitov R (1998) Introduction: the role of innate immunity in the adaptive immune response. Semin Immunol 10:349–350

    Article  Google Scholar 

  • Janeway CA Jr, Medzhitov R (2002) Innate immune recognition. Annu Rev Immunol 20:197–216

    Article  CAS  Google Scholar 

  • Jin H, You L, Zhao F, Li S, Ma T, Kwok LY, Xu H, Sun Z (2022) Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome. Gut Microbes 14:2021790

    Article  Google Scholar 

  • Jochum L, Stecher B (2020) Label or concept—what is a pathobiont? Trends Microbiol 28:789–792

    Article  CAS  Google Scholar 

  • Kagan JC, Barton GM (2014) Emerging principles governing signal transduction by pattern-recognition receptors. Cold Spring Harb Perspect Biol 7:a016253

    Article  Google Scholar 

  • Kalbus M, Fleckenstein BT, Offenhausser M, Bluggel M, Melms A, Meyer HE, Rammensee HG, Martin R, Jung G, Sommer N (2001) Ligand motif of the autoimmune disease-associated mouse MHC class II molecule H2-a(s). Eur J Immunol 31:551–562

    Article  CAS  Google Scholar 

  • Katz DH, Paul WE, Goidl EA, Benacerraf B (1970) Carrier function in anti-hapten immune responses. I. Enhancement of primary and secondary anti-hapten antibody responses by carrier preimmunization. J Exp Med 132:261–282

    Article  CAS  Google Scholar 

  • Kawai T, Akira S (2010) The role of pattern-recognition receptors in innate immunity: update on toll-like receptors. Nat Immunol 11:373–384

    Article  CAS  Google Scholar 

  • Kawamoto S, Maruya M, Kato LM, Suda W, Atarashi K, Doi Y, Tsutsui Y, Qin H, Honda K, Okada T et al (2014) Foxp3(+) T cells regulate immunoglobulin a selection and facilitate diversification of bacterial species responsible for immune homeostasis. Immunity 41:152–165

    Article  CAS  Google Scholar 

  • Kharlamova N, Jiang X, Sherina N, Potempa B, Israelsson L, Quirke AM, Eriksson K, Yucel-Lindberg T, Venables PJ, Potempa J et al (2016) Antibodies to Porphyromonas gingivalis indicate interaction between Oral infection, smoking, and risk genes in rheumatoid arthritis etiology. Arthritis Rheumatol 68:604–613

    Article  CAS  Google Scholar 

  • Klaus SJ, Pinchuk LM, Ochs HD, Law CL, Fanslow WC, Armitage RJ, Clark EA (1994) Costimulation through CD28 enhances T cell-dependent B cell activation via CD40-CD40L interaction. J Immunol 152:5643–5652

    CAS  Google Scholar 

  • Laforest-Lapointe I, Arrieta MC (2017) Patterns of early-life gut microbial colonization during human immune development: an ecological perspective. Front Immunol 8:788

    Article  Google Scholar 

  • Langan D, Rose NR, Moudgil KD (2020) Common innate pathways to autoimmune disease. Clin Immunol 212:108361

    Article  CAS  Google Scholar 

  • Lanz TV, Brewer RC, Ho PP, Moon JS, Jude KM et al (2022) Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. Nature 603(7900):321–327. https://doi.org/10.1038/s41586-022-04432-7. Epub 2022 Jan 24. PMID: 35073561

    Article  CAS  Google Scholar 

  • Li J, Xue H, Ma Q, He X, Ma L, Shi B, Sun S, Yao X (2020) Heterogeneity of CD4(+)CD25(+)Foxp3(+)Treg TCR beta CDR3 repertoire based on the differences of symbiotic microorganisms in the gut of mice. Front Cell Dev Biol 8:576445

    Article  Google Scholar 

  • Li Y, Zhang SX, Yin XF, Zhang MX, Qiao J, Xin XH, Chang MJ, Gao C, Li YF, Li XF (2021) The gut microbiota and its relevance to peripheral lymphocyte subpopulations and cytokines in patients with rheumatoid arthritis. J Immunol Res 2021:6665563

    Article  Google Scholar 

  • Liu YJ (2001) Dendritic cell subsets and lineages, and their functions in innate and adaptive immunity. Cell 106:259–262

    Article  CAS  Google Scholar 

  • Lv L, Jiang H, Yan R, Xu D, Wang K, Wang Q, Chen X, Li L (2021) The salivary microbiota, cytokines, and metabolome in patients with ankylosing spondylitis are altered and more proinflammatory than those in healthy controls. mSystems 6:e0117320

    Article  Google Scholar 

  • Margulies DH (2014) The in-betweeners: MAIT cells join the innate-like lymphocytes gang. J Exp Med 211:1501–1502

    Article  CAS  Google Scholar 

  • Mariathasan S, Newton K, Monack DM, Vucic D, French DM, Lee WP, Roose-Girma M, Erickson S, Dixit VM (2004) Differential activation of the inflammasome by caspase-1 adaptors ASC and Ipaf. Nature 430:213–218

    Article  CAS  Google Scholar 

  • Marietta E, Mangalam AK, Taneja V, Murray JA (2020) Intestinal dysbiosis in, and enteral bacterial therapies for, systemic autoimmune diseases. Front Immunol 11:573079

    Article  CAS  Google Scholar 

  • Matzinger P (2002) The danger model: a renewed sense of self. Science 296:301–305

    Article  CAS  Google Scholar 

  • Matzinger P (2012) The evolution of the danger theory. Interview by Lauren constable, Commissioning Editor. Expert Rev Clin Immunol 8:311–317

    Article  CAS  Google Scholar 

  • Medzhitov R, Janeway CA Jr (1998) Innate immune recognition and control of adaptive immune responses. Semin Immunol 10:351–353

    Article  CAS  Google Scholar 

  • Medzhitov R, Janeway C Jr (2000) Innate immune recognition: mechanisms and pathways. Immunol Rev 173:89–97

    Article  CAS  Google Scholar 

  • Medzhitov R, Janeway CA Jr (2002) Decoding the patterns of self and nonself by the innate immune system. Science 296:298–300

    Article  CAS  Google Scholar 

  • Mills RH, Dulai PS, Vazquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K et al (2022) Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. Nat Microbiol 7:262–276

    Article  CAS  Google Scholar 

  • Mirza AH, Kaur S, Brorsson CA, Pociot F (2014) Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci. PLoS One 9:e105723

    Article  Google Scholar 

  • Mocanu V, Rajaruban S, Dang J, Kung JY, Deehan EC, Madsen KL (2021) Repeated fecal microbial transplantations and antibiotic pre-treatment are linked to improved clinical response and remission in inflammatory bowel disease: a systematic review and pooled proportion meta-analysis. J Clin Med 10:959

    Article  Google Scholar 

  • Monteiro M, Graca L (2014) iNKT cells: innate lymphocytes with a diverse response. Crit Rev Immunol 34:81–90

    Article  CAS  Google Scholar 

  • Moreno J (2015) Prevotella copri and the microbial pathogenesis of rheumatoid arthritis. Reumatol Clin 11:61–63

    Article  Google Scholar 

  • Moreno J, Lipsky PE (1986a) Differential ability of fixed antigen-presenting cells to stimulate nominal antigen-reactive and alloreactive T4 lymphocytes. J Immunol 136:3579–3587

    CAS  Google Scholar 

  • Moreno J, Lipsky PE (1986b) Functional heterogeneity of human antigen-presenting cells: presentation of soluble antigen but not self-Ia by monocytes. J Clin Immunol 6:9–20

    Article  CAS  Google Scholar 

  • Moreno J, Adorini L, Hammerling GJ (1990) Co-dominant restriction by a mixed-haplotype I-A molecule (alpha k beta b) for the lysozyme peptide 52-61 in H-2k x H-2b F1 mice. J Immunol 144:3296–3304

    CAS  Google Scholar 

  • Moreno J, Vignali DA, Nadimi F, Fuchs S, Adorini L, Hammerling GJ (1991) Processing of an endogenous protein can generate MHC class II-restricted T cell determinants distinct from those derived from exogenous antigen. J Immunol 147:3306–3313

    CAS  Google Scholar 

  • Muramatsu M, Nagaoka H, Shinkura R, Begum NA, Honjo T (2007) Discovery of activation-induced cytidine deaminase, the engraver of antibody memory. Adv Immunol 94:1–36

    Article  CAS  Google Scholar 

  • Murdaca G, Greco M, Borro M, Gangemi S (2021) Hygiene hypothesis and autoimmune diseases: a narrative review of clinical evidences and mechanisms. Autoimmun Rev 20:102845

    Article  CAS  Google Scholar 

  • Nakajima A, Vogelzang A, Maruya M, Miyajima M, Murata M, Son A, Kuwahara T, Tsuruyama T, Yamada S, Matsuura M et al (2018) IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J Exp Med 215:2019–2034

    Article  CAS  Google Scholar 

  • Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M et al (2018) Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease. J Gastroenterol 53:95–106

    Article  Google Scholar 

  • Oh SF, Praveena T, Song H, Yoo JS, Jung DJ, Erturk-Hasdemir D, Hwang YS, Lee CC, Le Nours J, Kim H et al (2021) Host immunomodulatory lipids created by symbionts from dietary amino acids. Nature 600:302–307

    Article  CAS  Google Scholar 

  • Oldstone MB (1987) Molecular mimicry and autoimmune disease. Cell 50:819–820

    Article  CAS  Google Scholar 

  • Osgood JA, Knight JC (2018) Translating GWAS in rheumatic disease: approaches to establishing mechanism and function for genetic associations with ankylosing spondylitis. Brief Funct Genomics 17:308–318

    CAS  Google Scholar 

  • Pabst O, Izcue A (2022) Secretory IgA: controlling the gut microbiota. Nat Rev Gastroenterol Hepatol 19:149–150

    Article  CAS  Google Scholar 

  • Pabst O, Slack E (2020) IgA and the intestinal microbiota: the importance of being specific. Mucosal Immunol 13:12–21

    Article  CAS  Google Scholar 

  • Paul WE (2011) Bridging innate and adaptive immunity. Cell 147:1212–1215

    Article  CAS  Google Scholar 

  • Paul WE, Katz DH, Goidl EA, Benacerraf B (1970) Carrier function in anti-hapten immune responses. II. Specific properties of carrier cells capable of enhancing anti-hapten antibody responses. J Exp Med 132:283–299

    Article  CAS  Google Scholar 

  • Peterson P, Nagamine K, Scott H, Heino M, Kudoh J, Shimizu N, Antonarakis SE, Krohn KJ (1998) APECED: a monogenic autoimmune disease providing new clues to self-tolerance. Immunol Today 19:384–386

    Article  CAS  Google Scholar 

  • Peterson DA, McNulty NP, Guruge JL, Gordon JI (2007) IgA response to symbiotic bacteria as a mediator of gut homeostasis. Cell Host Microbe 2:328–339

    Article  CAS  Google Scholar 

  • Pulendran B, Ahmed R (2006) Translating innate immunity into immunological memory: implications for vaccine development. Cell 124:849–863

    Article  CAS  Google Scholar 

  • Qiu CC, Caricchio R, Gallucci S (2019) Triggers of autoimmunity: the role of bacterial infections in the extracellular exposure of lupus nuclear autoantigens. Front Immunol 10:2608

    Article  CAS  Google Scholar 

  • Rosen CE, Palm NW (2017) Functional classification of the gut microbiota: the key to cracking the microbiota composition code: functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease. BioEssays 39

    Google Scholar 

  • Sakaguchi S, Sakaguchi N, Shimizu J, Yamazaki S, Sakihama T, Itoh M, Kuniyasu Y, Nomura T, Toda M, Takahashi T (2001) Immunologic tolerance maintained by CD25+ CD4+ regulatory T cells: their common role in controlling autoimmunity, tumor immunity, and transplantation tolerance. Immunol Rev 182:18–32

    Article  CAS  Google Scholar 

  • Sakaguchi S, Ono M, Setoguchi R, Yagi H, Hori S, Fehervari Z, Shimizu J, Takahashi T, Nomura T (2006) Foxp3+ CD25+ CD4+ natural regulatory T cells in dominant self-tolerance and autoimmune disease. Immunol Rev 212:8–27

    Article  CAS  Google Scholar 

  • Sanna S, Kurilshikov A, van der Graaf A, Fu J, Zhernakova A (2022) Challenges and future directions for studying effects of host genetics on the gut microbiome. Nat Genet 54:100–106

    Article  CAS  Google Scholar 

  • Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB et al (2013) Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. elife 2:e01202

    Article  Google Scholar 

  • Shin NR, Whon TW, Bae JW (2015) Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol 33:496–503

    Article  CAS  Google Scholar 

  • Spits H, Bernink JH, Lanier L (2016) NK cells and type 1 innate lymphoid cells: partners in host defense. Nat Immunol 17:758–764

    Article  CAS  Google Scholar 

  • Spriggs MK, Fanslow WC, Armitage RJ, Belmont J (1993) The biology of the human ligand for CD40. J Clin Immunol 13:373–380

    Article  CAS  Google Scholar 

  • Steinman L (1995) Escape from "horror autotoxicus": pathogenesis and treatment of autoimmune disease. Cell 80:7–10

    Article  CAS  Google Scholar 

  • Stone M, Fortin PR, Pacheco-Tena C, Inman RD (2003) Should tetracycline treatment be used more extensively for rheumatoid arthritis? Metaanalysis demonstrates clinical benefit with reduction in disease activity. J Rheumatol 30:2112–2122

    CAS  Google Scholar 

  • Strasser D, Neumann K, Bergmann H, Marakalala MJ, Guler R, Rojowska A, Hopfner KP, Brombacher F, Urlaub H, Baier G et al (2012) Syk kinase-coupled C-type lectin receptors engage protein kinase C-delta to elicit Card9 adaptor-mediated innate immunity. Immunity 36:32–42

    Article  CAS  Google Scholar 

  • Swat W, von Boehmer H, Kisielow P (1994) Central tolerance: clonal deletion or clonal arrest? Eur J Immunol 24:485–487

    Article  CAS  Google Scholar 

  • Taniguchi M, Tashiro T, Dashtsoodol N, Hongo N, Watarai H (2010) The specialized iNKT cell system recognizes glycolipid antigens and bridges the innate and acquired immune systems with potential applications for cancer therapy. Int Immunol 22:1–6

    Article  CAS  Google Scholar 

  • Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hamalainen AM et al (2016) Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165:842–853

    Article  CAS  Google Scholar 

  • Vilchez-Vargas R, Salm F, Znalesniak EB, Haupenthal K, Schanze D, Zenker M, Link A, Hoffmann W (2022) Profiling of the bacterial microbiota along the murine alimentary tract. Int J Mol Sci 23:1783

    Article  CAS  Google Scholar 

  • Wang Q, Zhang SX, Chang MJ, Qiao J, Wang CH, Li XF, Yu Q, He PF (2022) Characteristics of the gut microbiome and its relationship with peripheral CD4(+) T cell subpopulations and cytokines in rheumatoid arthritis. Front Microbiol 13:799602

    Article  Google Scholar 

  • Wencker M, Turchinovich G, Di Marco Barros R, Deban L, Jandke A, Cope A, Hayday AC (2014) Innate-like T cells straddle innate and adaptive immunity by altering antigen-receptor responsiveness. Nat Immunol 15:80–87

    Article  CAS  Google Scholar 

  • Xu Q, Ni JJ, Han BX, Yan SS, Wei XT, Feng GJ, Zhang H, Zhang L, Li B, Pei YF (2021) Causal relationship between gut microbiota and autoimmune diseases: a two-sample Mendelian randomization study. Front Immunol 12:746998

    Article  CAS  Google Scholar 

  • Ye J, Gillespie KM, Rodriguez S (2018) Unravelling the roles of susceptibility loci for autoimmune diseases in the post-GWAS era. Genes (Basel) 9:377

    Article  Google Scholar 

  • Zhang H, Fu Q, Shi X, Pan Z, Yang W, Huang Z, Tang T, He X, Zhang R (2020) Human A-to-I RNA editing SNP loci are enriched in GWAS signals for autoimmune diseases and under balancing selection. Genome Biol 21:288

    Article  CAS  Google Scholar 

  • Zhang X, Borbet TC, Fallegger A, Wipperman MF, Blaser MJ, Muller A (2021) An antibiotic-impacted microbiota compromises the development of colonic regulatory T cells and predisposes to dysregulated immune responses. mBio 12:e03335-20

    Article  Google Scholar 

  • Zhu LY, Shao T, Nie L, Zhu LY, Xiang LX, Shao JZ (2016) Evolutionary implication of B-1 lineage cells from innate to adaptive immunity. Mol Immunol 69:123–130

    Article  CAS  Google Scholar 

  • Zuklys S, Balciunaite G, Agarwal A, Fasler-Kan E, Palmer E, Hollander GA (2000) Normal thymic architecture and negative selection are associated with Aire expression, the gene defective in the autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). J Immunol 165:1976–1983

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Direction of Research, Hospital Juárez de México, Mexico City, Mexico

    José Moreno

  2. Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Chihuahua, Chih, Mexico

    César Pacheco-Tena

Authors
  1. José Moreno
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. César Pacheco-Tena
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat, Gujarat, India

    Mitesh Kumar Dwivedi

  2. Department of Life Sciences, Sri Sathya Sai University for Human Excellence, Kalaburagi, Karnataka, India

    A. Sankaranarayanan

  3. Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK

    E. Helen Kemp

  4. Zabludowicz Center for Autoimmunity, Sheba Medical Center, Tel-Hashomer, Israel

    Yehuda Shoenfeld

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Moreno, J., Pacheco-Tena, C. (2022). The Influence of the Microbiome and Genetic Associations on Immune Functions and on Autoimmune and Autoinflammatory Diseases. In: Dwivedi, M.K., Sankaranarayanan, A., Kemp, E.H., Shoenfeld, Y. (eds) Role of Microorganisms in Pathogenesis and Management of Autoimmune Diseases. Springer, Singapore. https://doi.org/10.1007/978-981-19-4800-8_23

Download citation

Publish with us

Policies and ethics

Search

Navigation