2. Gut Microbiota and Autoimmune DiseasesIn this review, we will be expanding on the effects that the GM has on the more prevalent autoimmune diseases, with special focus on rheumatoid arthritis, systemic lupus erythematosus and multiple sclerosis.2.1 Rheumatoid ArthritisRheumatoid arthritis (RA) is an autoimmune disorder characterised by a chronic immune response, leading to damage to the joints (Horta-Baas et al., 2017). A feature found in RA patients even before any indication of joint inflammation is manifested is the presence of the rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPAs) in the blood (Malmstr¶m, Catrina & Klareskog, 2017).
Another interesting component of the disease is that bacterial and viral antibodies have been thought to be triggers for RA (Espinoza & Garca-Valladares, 2013).Various studies have shown that there is a marked difference between the components of GM in healthy patients in relation to RA patients. It has been found that there are lower amounts of Bifidobacterium and Bacteroides species whilst elevated levels of Prevotella bacteria in RA patients (Cenit-Laguna, 2015; Vaahtovuo, Munukka, Korkeamaki, Luukkainen & Toivanen, 2008; Bernard, 2014).
Other studies have shown that injecting cell wall fragments sourced from several species of intestinal bacteria proved to be arthritogenic. This concept has been further proved by this model as it has been suggested that arthritis failed to develop in GF mice (Bernard, 2014; Scher et al., 2013). 2.1.1 Molecular Insight on the Pathogenesis of Rheumatoid ArthritisDysregulation of the immune system is distinguished through the abundance of autoantibodies and autoreactive T cells. In addition, an aspect that is detected prior to the presentation of RA symptoms is the dysregulated production of autoreactive B cells (Sanmart & Gіmez-Puerta, 2011; Lee & Kim, 2017). A unique aspect in the initiation of the autoimmune reaction in RA is that the bacteria associated with the mucosa of the body would be the ones to strike and damage the leukocytes, leading to inflammation. Moving forward, the steps involved would be similar to the ones seen in other autoimmune conditions. After the leukocytes have been damaged, there is the release and distribution of cytokines through the blood. The antigens would then be presented by antigen presenting cells to the T cells. This leads to the activation of the T cells. These activated T cells would mediate the activation of the B cells. These cascade of events would result in the formation of autoantibodies, leading to the autoimmune condition (Malmstr¶m, Catrina & Klareskog, 2017; Catrina, Joshua, Klareskog & Malmstr¶m, 2016; Holers, 2013; Lee, Taneja & Vassallo, 2012) Posttranslational modifications (PTMs) are crucial in determining protein function and the development of antigens. The main PTM involved in RA is citrullination. Citrullination is the conversion of arginine to citrulline which is catalysed by the enzyme peptidyl arginine deiminases (PAD). This process causes conformational changes in proteins, causing the generation of new epitopes linked with the creation of ACPAs. ACPAs found in RA patients present varying degrees of cross-reactivity which may be linked to the proteins being affected through citrullination (Lourido, Blanco & Ruiz-Romero, 2017; Klareskog, Amara & Malmstr¶m, 2014). It has been suggested that citrullinated proteins may become autoantigens and can give rise to an autoimmune response in the RA-prone population (Sakkas, Bogdanos, Katsiari & Platsoucas, 2014). ACPAs’ are involved in the transition between the preclinical phase of the condition and the clinical presentation of RA. An analysis was done for ACPAs before a clinical presentation of the condition is evident, revealing that there is epitope spreading (Pratesi et al., 2013; Deane & El-Gabalawy, 2014; van de Stadt et al., 2011; Sokolove et al., 2012). Epitope spreading is when there is an immune reaction against an epitope which is not associated with the disease-causing epitope (Powell & Black, 2001). In RA, epitope spreading is linked to citrullination. Epitope spreading would be linked to a single antigen, however, the antigen in question might not be the same in different RA patients (Vaahtovuo, Munukka, Korkeamaki, Luukkainen & Toivanen, 2008; van de Stadt et al., 2011). Along the progression of the condition, there is an increase in ACPAs’ epitope variation and its titers, especially before the clinical presentation of the condition . Dendritic cells are responsible for the distinction in the development of immature CD4+ lymphocytes. This differentiation can be modulated by the GM. Meanwhile, dendritic cells regulate antigenic presentation (Luckey, Gomez, Murray, White & Taneja, 2013; Vaahtovuo, Munukka, Korkeamaki, Luukkainen & Toivanen, 2008; Hitchon & El-Gabalawy, 2011). This means that lengthy presentations of arthritogenic antigens to dendritic cells favour the exacerbation of inflammation in autoimmunity (Scher & Abramson, 2011). A number of cell types have been found to be associated with the pathogenesis of RA. Dendritic cells have been found in the rheumatoid synovium and its peripheral vessels, suggesting that they have originated from the peripheral blood. Circulating Treg cells have been found to be defective in RA patients. In addition, elevated levels of Th17 cells have been found in the plasma and synovial fluid of these patients (Lourido, Blanco & Ruiz-Romero, 2017; Scher & Abramson, 2011). Moreover, the disbalance within the components of the gut microbiota can lead to autoimmune ailments through the disproportionate production of T cell subpopulations eg Th1, Th2 and Treg cells. In addition, dysbiosis in a number of mucosal sites results in immune alterations and the development of immunity against citrullinated autoantigens (Lee & Kim, 2017; Holers, 2013). Different phyla and genera of bacteria act and interact with different receptors of the body depending on their biochemistry. In this case, due to the presence of lipopolysaccharide A on Gram-negative bacteria, they are able to interact with TLR-4. Meanwhile, peptidoglycans, which are mainly found on the surface of Gram-positive bacterial cell wall, interact with the TLR-2. This activation allows for the identification of pathogen-associated molecular patterns, which would lead to activation of the MyD88 coupling protein. Its signalling would then initiate the inflammatory response and the formation of proinflammatory cytokines including tumour necrosis factor-alpha, IL-6 or IL-1І (Scher & Abramson, 2011; Walker, 2013). Dysbiosis is able to modulate the degree at which TLRs are expressed on antigen presenting cells and may contribute to a disbalance between the Th17 cells and Treg cells population (Stone, Fortin, Pacheco-Tena & Inman, 2003; Lee & Kim, 2017).Bacteroides fragilis polysaccharide A is an immunomodulator. It can induce the production of IL-10 via the IL-2 dependent mechanism when the bacteria stimulate the CD4+ Treg cells (Luckey, Gomez, Murray, White & Taneja, 2013).188.8.131.52 Role of gut commensals in rheumatoid arthritisIn the previous section, it has been demonstrated that the shift in the composition of the GM can kickstart Th17 cell maturation through a number of pathways, which is concordant with the elevated level results in the circulation of Th17 cells in RA patients (Zhang, Li, Lv, Yin & Wang, 2015). Therefore, the disbalance within the bacterial populations making up the GM in RA is thought to be linked with the increased susceptibility of evolving debilitating conditions in RA patients .This disbalance in GM components has been observed in the differences in the faecal fatty acid profile studied by Eerola et al. (1994). This study has shown that there is a significant difference between the faecal fatty acid profile of a patient with RA and a normal person. One study has found that the amount of Bifidobacteria, Bacteroides and lactose-positive E.coli bacteria has been reduced in RA patients. Moreover, the copiousness of opportunistic Enterobacteriaceae and Staphylococcus bacteria is significant (Gul’ neva & Noskov, 2011). In addition, another group of bacteria that had been diminished in RA patients is Haemophilus spp., while Lactobacillus salivarius was present in elevated amounts. These changes in GM composition have been linked to an increase in autoantibody titers and disease severity, respectively (Sprouse, Bates, Felix & Wu, 2018). 184.108.40.206 Bacteria that exacerbate the diseaseAs can be shown in Table 1, the gut microbiota has been considered to be occupied mainly by Prevotella copri during the early stages of RA (Maeda et al., 2016). This has occurred to the extent that it has taken up niches previously occupied by more beneficial bacteria. In turn, it has led to the suppression of the immune system (Bernard, 2014; Scher et al., 2013; Pianta et al., 2017). This bacterium has been linked to new-onset rheumatoid arthritis (NORA) patients (Liu, Zou, Zeng, Fang & Wei, 2013; Scher et al., 2013). Being a gram-negative bacterium, P.copri has lipopolysaccharides (LPS) attached to its wall, making it able to interact with TLR-4. This interaction would then lead to the production of molecules that have an activating effect on antigen presenting cells (APCs). These molecules would be able to cause T cell activation and also partakes in the differentiation of T-cell subtypes through the production of cytokine cascades. Since the LPS found on the cell membrane of P.copri is the ligand for TLR-4, its detection by the receptor might be responsible for induction of pro-inflammatory Table 1: A compilation of results showing the main alterations in gut microbiota found in RA patients relative to normal, healthy controlsName of bacterium The stage at which the bacterium is prevalent Change in its levels CitationPrevotella copri Early RA Increase 32Lactobacillus salivarius Very active RA Increase 35Gordonibacter pamelaeae, Clostridium asparagiforme, Eggerthella lenta and Lachnospiraeae bacterium, Bifidobacterium dentium and Ruminococcus lactaris n/a Increase 35Haemophilus spp. n/a Decrease 35Prevotella intermedia and Porphyromonas gingivalis Active RA Increase 38Bacteroides sp., Prevotella sp. and Porphyromonas sp. Early RA Decrease 39Collinsella sp. Active RA Increase 45This table details the bacteria found in various different studies regarding gut microbiota changes found in RA patients. This table would detail the bacteria, the stage at which it was found to be prevalent within the patient.molecules such as IL-17 and also mediates the T-cell mediated pathogenesis pathway in RA. In addition, LPS aids in platelet aggregation (Abdollahi-Roodsaz et al., 2008; Maeda et al., 2016; Scher et al., 2013; Tripathy et al., 2017; Zhang et al., 2009). Moreover, if the bacterium was administered orally, it would exacerbate a local inflammatory response in the colitis murine model. This leads to the conclusion that the bacterium has a role in modulating gut permeability (Scher et al., 2013). Segmented filamentous bacteria (SFB) make up a group of Clostridia-related gram-positive bacteria which closely associate to the Peyer’s plaques in the small intestine. They can initiate the immune response by inducing IgA secretion and B cell activation  (Stone, Fortin, Pacheco-Tena & Inman, 2003; Lee & Kim, 2017; Block, Zheng, Dent, Kee & Huang, 2016). Mm et al found that the monocolonisation of SFB in the gut of GF mice is enough to cause the production of pro-inflammatory cytokines such as IL-17 from Th17 cells, leading to the pathogenesis and clinical presentation of RA. The Th17 cells produced would act on B cells to induce their differentiation and production of antibodies, which leads to the initiation of RA pathogenesis (Luckey, Gomez, Murray, White & Taneja, 2013; Negi, Singh & Mukhopadhyay, 2017). SFBs are able to promote the formation of acute-phase isoforms of serum amyloid A in the ileum, which interacts with dendritic cells to cause differentiation of immature CD4+ T cells into Th17 cells (Ivanov et al., 2009; Wu et al., 2010). Block et al. have added that the GM contributes to the differentiation of T follicular helper cells as this could be modulated through the use of antibiotics (Block, Zheng, Dent, Kee & Huang, 2016; Teng et al., 2016; Onuora, 2016). Pathogens that colonise the periodontal regions such as Prevotella intermedia and Porphyromonas gingivalis have been detected in the synovial fluid of RA patients. These bacterial species have been thought to partake in either the initiation or the persistence of the chronic inflammatory state. Collinsella sp. has been found to exacerbate the disease severity in the humanised mouse model. On a genetic level, development of RA can occur in relation to the bacterium through molecular mimicry since the bacterium shares sequences with DRB1*0401, which is a pro-arthritogenic gene. It can contribute to the pathogenesis of RA by increasing the gut permeability since it would attenuate the number of tight junction proteins being expressed. Additionally, the bacteria is able to modulate the formation of IL-17 from the epithelium. It has been found that Collinsella sp., along with Eggerthella sp., levels normalise through disease-modifying antirheumatic drugs (Chen et al., 2016). Apart from having distinct species of bacteria that can exacerbate RA, there is an exception to this concept. Xx et al found that RA patients can be divided into 2 groups: those that are positive for RF and those that are negative. The former group were commonly colonised with phylogenetic group D-type E.coli whereas the latter group were colonised with phylogenetic group B2 E.coli (Newkirk, Zbar, Baron & Manges, 2010). 220.127.116.11 Bacteria that attenuate the diseaseDespite the previous section discussing the contribution that Prevotella has to the pathogenesis of RA, there is another side to the story. Prevotella histicola has been shown to attenuate the clinical presentation of RA. Firstly, it has been noted to do so through its contribution to the expression of the tight junction protein zonula occludens-1. Therefore, there is a link between P.histicola and a decreased in intestinal permeability in all of the areas of the small bowel. Secondly, the bacterium can initiate the maturation of immature T cells into Treg cells and can also elevate the levels of anti-inflammatory cytokines being produced (Marietta et al., 2016). Another 2 groups of bacteria that have been demonstrated to diminish disease severity are elevated populations of the families Porphyromonadaceae and Bifidobacteriaceae. Bifidobacteriaceae have been linked with anti-inflammatory response in the intestinal mucosal immune system through the attenuation of T cell proliferation and creation of proinflammatory cytokines (Gomez et al., 2012; Taneja, 2014; Scher et al., 2013) 2.1.3 Management and Treatment in Rheumatoid Arthritis The management options available have a partial normalising effect on treated RA patients, when compared to treatment-naive patients. The associated microbiota depletion as a result of antibiotic intake has been found to reduce the disease severity by 40% when given before the induction of collagen-induced arthritis. In addition, it has been linked to the decreased production of pro-inflammatory cytokines including IL-17, IL-22 and IL-23 (Sprouse, Bates, Felix & Wu, 2018). This depletion of gut commensals allows for the proliferation of beneficial GM species. This has been linked to the improvement of disease symptoms rather than the microbial change being a result of the alleviation of symptoms (Xu et al., 2014). However, it has also been shown in mice that depletion of the GM through the use of antibiotics can aggravate RA symptoms. This would have been the result of the partial depletion of the beneficial gut flora (Doroјy”ska, Majewska-Szczepanik, Marci”ska & Szczepanik, 2014). Other drugs used to treat RA, which have antimicrobial effects, have been shown to normalise the disease-altered GM (Edwards, 2008; Ogrendik, 2009; Ogrendik & Karagoz, 2011; Stone, Fortin, Pacheco-Tena & Inman, 2003) Another mode of treatment being tested on is probiotics. The bacteria introduced via probiotic supplementation in RA patients had the opportunity to enrich the gut with immune-modulating molecules such as SCFAs. These have been shown to contribute their immune regulatory effects by reducing serum pro-inflammatory cytokines and elevating the serum level of anti-inflammatory cytokines. The introduction of Bifidobacterium, Lactobacillus and Faecalibacterium prausnitzii through probiotic administration, has been linked to protective effects in non-steroidal anti-inflammatory drug (NSAID)-treated animal models (Syer et al., 2015; So et al., 2008; Mazmanian, Round & Kasper, 2008; Smith et al., 2013). This finding is useful since NSAID intake in RA patient has been found to cause gut mucosal injury and enteropathy (Syer et al., 2015). Another mode of treatment being tested for RA is the introduction of specific species of bacteria. P.histicola attenuated arthritis progression by altering the immune response which results in the suppression of Th17 responses and decrease in proinflammatory cytokines such as IL-2 and IL-17. Contrary to this, giving P.melaninogenica gave neither significant changes in cytokine levels nor prevention of RA progression (Marietta, 2016). The inflammatory state linked with RA can be managed through a diet change. Skolstam et al. (2003) has shown diets consisting of plant-based foods, such as the Mediterranean and vegan diets, reduces inflammatory activity, enhances physical function and improves vitality.