Intestinal dysbiosis and probiotic applications in autoimmune diseases

Summary

In humans, a complex interaction between the host immune system and commensal microbiota is required to maintain gut homeostasis. In this symbiotic relationship, the microbiota provides carbohydrate fermentation and digestion, vitamin synthesis and gut‐associated lymphoid tissue development, as well as preventing colonization by pathobionts, whereas the host offers a niche and nutrients for the survival of the microbiota. However, when this mutualistic relationship is compromised and an altered interaction between immune cells and microorganisms occurs, the gut microbiota may cause or contribute to the establishment of infectious diseases and trigger autoimmune diseases. Researchers have made efforts to clarify the role of the microbiota in autoimmune disease development and find new therapeutic approaches to treat immune‐mediated diseases. However, the exact mechanisms involved in the dysbiosis and breakdown of the gut epithelial barrier are currently unknown. Here, we provide a general overview of studies describing gut microbiota perturbations in animal models of autoimmune diseases, such as type 1 diabetes, multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus. Moreover, we include the main studies concerning dysbiosis in humans and a critical discussion of the existing data on the use of probiotics in these autoimmune diseases.

Abbreviations

CIA

collagen‐induced arthritic mice

CNS

central nervous system

DAS28

disease activity score calculator for rheumatoid arthritis

EAE

experimental autoimmune encephalomyelitis

GF

germ‐free mice

IFN‐γ

interferon‐γ

IL‐17

interleukin‐17

MS

multiple sclerosis

NOD

non‐obese diabetic mice

NZB

New Zealand black mice

RA

rheumatoid arthritis

RRMS

relapsing–remitting multiple sclerosis

SFB

segmented filamentous bacteria

SLE

systemic lupus erythematosus

T1D

type 1 diabetes

Th1

T helper type 1

TLR

Toll‐like receptors

Treg

regulatory T

Introduction

The skin surface and mucous membranes in vertebrates are colonized by a high number of microorganisms, mainly bacteria, representing commensal microbiota.1, 2, 3 In humans, approximately 30–400 trillion microorganisms (3 × 10¹³ to 40 × 10¹³) colonize the healthy human intestinal tract, and the vast majority reside in the distal portion.4, 5, 6 The gut bacteria have co‐evolved in a symbiotic relationship with the human host, and their composition depends on immunogenetic and environmental factors.7, 8

From birth, gut microbiota colonization depends on several factors, including age, mode of delivery (vaginal or caesarean section), mothers' microbiota composition, early use of antibiotics and feeding regimen (breastfeeding or formula).9, 10 The mode of delivery and mode of feeding in the first years of life strongly influence the establishment of gut microbiota composition and may affect the development of autoimmune diseases.10 Additionally, caesarean delivery and formula use have been associated with higher incidence of infectious diseases and increased susceptibility to allergic diseases.10, 11

In humans, the intestinal microbiota tends to stabilize and reaches greater diversity at approximately 3 years of age, and these microorganisms collaborate with many host physiological processes; in turn, the host contributes to their growth and survival by offering a niche, substrates and nutrients.10, 11, 12, 13 The main contributions of the microbiota to the host include carbohydrate fermentation and digestion, vitamin synthesis, gut‐associated lymphoid tissue development, the polarization of specific immune responses, and the prevention of colonization by pathobionts.14, 15, 16, 17, 18

The two predominant bacterial phyla in the healthy human gut are Firmicutes and Bacteroidetes. Also present are Proteobacteria, Actinobacteria, Fusobacteria and Verrucomicrobia phyla but to a lesser extent.19, 20 The most prevalent genera in the adult human gut are represented by Gram‐positive bacteria, such as Clostridium, Bifidobacterium, Lactobacillus, Ruminococcus, Streptococcus, and Gram‐negative bacteria, such as Bacteroides and Escherichia.21

A complex interaction between the host immune system and the microbiota is required to maintain gut homeostasis.14, 15, 16, 17, 18 However, when this mutualistic relationship is compromised, with alterations in bacterial function and diversity, a process called dysbiosis, the gut microbiota may cause or contribute to the establishment of infectious diseases and to autoimmune disease development.22

For several decades, researchers interested in enteroinfections and gut‐associated diseases have studied the gut microbiota. It has been evident that the microbiota plays an important role in immune homeostasis in the gut mucosa, and researchers are extensively investigating microbiota–immune system interactions and their role in the susceptibility or resistance to gut infections and in the triggering of autoimmune, allergic and chronic inflammatory diseases.23

Gut microbiota and immune system

Studies in germ‐free (GF) mice showed that the gut microbiota is required for normal immune system maturation, including gut‐associated lymphoid tissue development, which plays important roles in tolerance induction to autoantigens in the gut mucosa.24, 25, 26 These GF mice showed decreased numbers of CD4⁺ T cells, secreting IgA plasma cells and antimicrobial peptides, a thinner mucus layer and Peyer's patches.23 The spleen and lymph nodes are abnormally developed in GF mice, with decreased numbers of B and T cells in the germinal centres and parafollicular region, respectively.27, 28

In mice and humans, during equilibrium, intestinal dendritic cells and macrophages are hyporesponsive to pathogen‐associated molecular patterns.1, 29 However, when epithelial barrier breakdown occurs, the pattern recognition receptors, which are present in innate immune cells, recognize gut microbiota or pathobionts through toll‐like receptors, NOD‐like receptors, soluble retinoic acid‐inducible gene I, or melanoma differentiation‐associated protein 5, which triggers an inflammatory cascade, pro‐inflammatory cytokine secretion, and the activation of adaptive immune responses.29, 30

Gut microbiota and T cells

The resident microbiota regulates the development of specific subsets of lymphocytes in the gut. T helper type 17 (Th17) lymphocytes are essential in defence against bacterial and fungal infections and play roles in autoimmune disease development by producing pro‐inflammatory cytokines, such as interleukin‐17 (IL‐17) and IL‐22, and by the recruitment of neutrophils.31 Th17 cells accumulate in the intestine, suggesting that intrinsic processes in the gut mucosa could regulate the development of these cells. Moreover, studies have shown that the number of Th17 cells are reduced in GF mice or antibiotic‐treated adult mice, and it was observed that some particular species of Clostridia, called segmented filamentous bacteria (SFB), promote the generation of Th17 cells in the gut32, 33, 34, 35, 36 (Fig. 1).

Figure 1.

A schematic representation of the interaction between commensal microbiota and the immune system. Under eubiosis, there are microbiota diversity and immune homeostasis in the gut mucosa. Commensal microorganisms instruct dendritic cells to induce IgA‐secreting cell differentiation, and in turn, IgA regulates the composition of the gut microbiota. During dysbiosis, there are decreased diversity in commensal microbiota and deregulated interactions between immune cells and these microorganisms. Some specific bacteria, such as Bacteroides fragilis, induce regulatory T cell differentiation and the secretion of anti‐inflammatory cytokines, whereas segmented filamentous bacteria (SFB) promote T helper type 17 (Th17) cell differentiation and the secretion of pro‐inflammatory cytokines, which play roles in several autoimmune diseases.

Regulatory T (Treg) cells aggregate in the intestine and help with the maintenance of homeostasis.37, 38 Treg cell depletion induces an abnormal expansion of CD4⁺ T cells expressing T‐cell receptors against commensal microbiota, resulting in gut inflammation.1 Studies have shown that the Treg cell numbers were reduced in the lamina propria of GF mice and particular species of Clostridium are involved in the Treg induction in the gut.38, 39 In addition, the polysaccharide A, which is secreted by Bacteroides fragilis, can induce CD4⁺ T cells into Foxp3⁺ Treg cells, which secretes IL‐10, an anti‐inflammatory cytokine, and mediates mucosal tolerance40 (Fig. 1).

Gut microbiota and B cells

An important relationship exists between intestinal microbiota and the humoral immune responses. Secreted IgA protects us against enteroinfections and coats commensal bacteria by inhibiting their binding to the intestinal epithelium and the lamina propria invasion.41 Secreted IgA has barrier functions and shapes the microbiota composition through antibody‐mediated immunoselection.27

B cells differentiate into plasma cells by T‐helper‐dependent or T‐helper‐independent mechanisms. In Peyer's patches, T‐helper‐dependent responses occur with isotype switching, somatic hypermutation and affinity maturation, which induce the differentiation of IgA‐secreting plasma cells with a high affinity for antigens.41 T‐helper‐independent responses are mainly mediated by B1 cells that differentiate into polyclonal IgA‐secreting plasma cells with a low affinity for antigens.27 The T‐helper‐dependent and T‐helper‐independent immune responses in the gut have been extensively reviewed in the literature.41, 42, 43, 44, 45, 46

The gut microbiota also induces the expression of factors involved in the induction of IgA⁺ B cells, such as B‐cell activating factor and a proliferation‐inducing ligand (known as APRIL) in dendritic cells in the lamina propria.46 Therefore, the microbiota instructs dendritic cells and follicular dendritic cells to induce IgA‐secreting plasma cells, and in turn, IgA regulates the composition and function of the gut microbiota (Fig. 1).46 To confirm the essential role of this mutualistic relationship, studies have shown that GF mice and mice deficient in activation‐induced cytidine deaminase have decreased plasma cells and alterations in the gut microbiota composition, respectively.42, 43, 44, 45, 46

Gut microbiota and autoimmune diseases

Evidence from animal models has implied the direct involvement of gut microbiota in disease development, and some intestinal microbiota are associated with autoimmune diseases.24, 25, 26

Intestinal dysbiosis observed in autoimmune diseases is associated with decreased bacterial function and diversity, impaired gut barrier function, increased inflammation and decreased Treg cells in the gut.47, 48 Additionally, the hypotheses proposed to link intestinal dysbiosis with autoimmune diseases include molecular mimicry, bystander T‐cell activation, and the amplification of autoimmunity by pro‐inflammatory milieu, which is elicited by altered gut microbiota.49 Finally, a more recent hypothesis proposed by Lerner et al. implicated the post‐translational modification of luminal proteins, promoted by enzymes from dysbiotic microbiota, which modify substrates in a different way from that performed under eubiotic conditions.49 The defective post‐translational modification of luminal proteins may induce neo‐epitope generation that could become immunogenic and may induce systemic autoimmunity and trigger autoimmune diseases.49

Here, we describe several reports concerning alterations in the intestinal microbiota in some autoimmune diseases, such as type 1 diabetes, multiple sclerosis, rheumatoid arthritis and systemic lupus erythematosus. Additionally, we provide a critical discussion concerning the data from the use of probiotics in autoimmune diseases.

Type 1 diabetes

Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by the immune destruction of insulin‐secreting pancreatic β‐cells, resulting in exogenous insulin dependence to control blood glucose levels.50 The aetiopathogenesis may involve the interaction of predisposing HLA genes and environmental factors, such as viral enteroinfections and intestinal dysbiosis.51 According to the International Diabetes Federation, 79 100 children under the age of 15 will develop T1D annually worldwide.52

The role of the gut microbiota in T1D aetiology has been the subject of research over the last decade to clarify its role in disease development and determine preventive approaches, such as diet manipulation and probiotic administration.51

One of the first studies in non‐obese diabetic mice (NOD) showed that the composition of the intestinal microbiota modulates innate and adaptive immune functions and enhances the disease in MyD88^−/− NOD mice. However, protection against diabetes in these mice is abrogated by the administration of antibiotics and GF conditions, suggesting that commensal bacteria may be important to reduce disease susceptibility in these mice.53 Additionally, Emani et al. reported that NOD mice treated with a conventional diet presented impaired tolerance to gut microbes, an altered barrier permeability, an increased number of peritoneum macrophages and a decreased abundance of Firmicutes.54

An imbalance among Th1, Th17 and Treg cell differentiation in the gut was reported in GF NOD mice and is associated with insulitis and pancreas inflammation.55 Interestingly, the SFB, which are associated with the exacerbation of the Th17 responses in other autoimmune diseases, are involved in protection against diabetes in NOD mice.56

In biobreeding diabetes‐prone rats, increased percentages of Bacteroides, Ruminococcus and Eubacterium reads in stool samples were observed, and there was a higher abundance of Bifidobacterium and Lactobacillus in stool samples from biobreeding diabetes‐resistant rats.57 The altered gut microbiota, such as the increased abundance of Bacteroidetes, could promote increased intestinal permeability and precede the clinical onset of T1D in animal models and pre‐diabetic and diabetic patients.58, 59, 60, 61 In fact, the role of the gut microbiota in T1D has been suggested since 1987, and the first study in humans was performed in Finland by using stool samples from four T1D children and four matched controls.62 They observed that children with T1D had decreased microbiota diversity compared with controls and had a reduction in the Firmicutes : Bacteroidetes ratio62, 63 (Fig. 2). Additionally, recent studies showed that the composition of the intestinal microbiota is altered in children with pre‐diabetes with genetic susceptibility and autoantibodies against β‐cells.64, 65, 66

Figure 2.

A schematic representation of the intestinal dysbiosis in organ‐specific autoimmune diseases in humans.

Studies from the De Goffau group showed that children with autoantibodies against β‐cells exhibit an increased number of Bacteroidetes and decreased abundance of lactate and butyrate‐producing bacteria in faeces.63, 65 In agreement with this study, Brown et al. showed a decreased number of mucin‐degrading and butyrate‐producing bacteria in T1D patients compared with healthy controls.67 Butyrate has anti‐inflammatory activity, induces Treg cell differentiation in the gut and enhances the gut barrier via tight junctions.64

Endesfelder et al. did not observe significant differences in gut microbiota diversity in 22 children with positive‐islet autoantibodies compared with 22 children with negative ones.68 Additionally, children with T1D have decreased numbers of lactate‐producing bacteria, such as Bifidobacterium longum, subspecies infantis. Bifidobacteria members promote carbohydrate fermentation, generate acetate and lactate, release polyphenols and linoleic acids, and have antioxidant activities.68 They also play a role in gut‐associated lymphoid tissue development maturation during early life and guarantee protection against pathobionts by bacteriocin release, causing decreases in the luminal pH and the inhibition of adhesion to epithelial cells.69 In addition, Bifidobacteria species synthesize B‐group vitamins, which can induce Treg cells in the gut mucosa70, 71 (Fig. 2).

Murri et al. evaluated the gut microbiota in a cohort of 16 children with T1D and 16 controls and showed an increased abundance of Clostridium, Bacteroides and Veillonella in patients compared with controls. Furthermore, the Firmicutes : Bacteroidetes ratio and levels of Lactobacillus, Bifidobacterium and Prevotella were decreased in these patients.72

Davis‐Richardson et al. evaluated stool samples isolated from 29 patients with seroconverted T1D disease and 47 healthy controls and observed a high abundance of Bacteroides dorei and Bacteroides vulgatus in seroconverted patients with T1D 8 months before β‐cell autoimmunity. These data suggest that early dysbiosis may be relevant to predict T1D in genetically predisposed individuals.73

Kostic et al. evaluated stool samples from 33 children genetically predisposed to T1D and reported alterations in microbiota α‐diversity between and within the children over time. They also observed a decrease in the number of Gram‐negative members and an inverse correlation between Lachnospiraceae and Ruminococcaceae with Enterobacteriaceae, a Gram‐negative aerobe. In addition, they reported that early commensals are aerobic, whereas later microbes appear to be anaerobic.74

A more complex study with 35 patients newly diagnosed with T1D, 21 first‐degree relatives with β‐cell autoimmunity, 32 relatives with negative autoantibodies, and 23 controls showed that the numbers of Lactobacillus and Staphylococcus reads were decreased in patients and in first‐degree relatives when compared with controls. Furthermore, the gut microbiota from subjects with negative and positive autoantibodies grouped together but in a different cluster from newly diagnosed patients.75 This study and the work performed by Meiía‐León et al. support the hypothesis that there is an intestinal microbiota signature associated with T1D development in seropositive children.76

Even though studies have shown that intestinal dysbiosis can affect gut permeability via their metabolites and play a role in T1D development, there is no evidence for the real role of intestinal microbiota in the development of autoimmunity to β‐cells and in tissue damage in humans. Additional studies are needed to find the specific microbial ligands that signal through immune cells in the gut and might be involved in the autoreactivity to β‐cells.77

Multiple sclerosis

Multiple sclerosis (MS) is a chronic and inflammatory disease that affects the central nervous system (CNS) and is characterized by autoimmune reactions against myelin proteins. Susceptible HLA alleles and environmental factors, such as virus infection, a hypercaloric diet, vitamin D deficiency and dysbiosis, have been implicated in triggering MS.78 MS promotes disability in young adults and affects twice as many women as men. According to the Multiple Sclerosis International Federation and World Health Organization (WHO), the prevalence of MS increased from 2·1 million in 2008 to 2·3 million in 2013.79

Studies have shown that gut microbiota can affect the development of MS, and these works implicated intestinal dysbiosis as one of the possible causes of extraintestinal disease development.80 The colonization of GF mice with SFB promotes an increase in the number of Th17 cells in the lamina propria and CNS, worsening disease severity in experimental autoimmune encephalomyelitis (EAE), an MS animal model.81 Likewise, the colonization of the same mice with Bacteroides fragilis and polysaccharide A, which induces Foxp3⁺ Treg cell differentiation, decreases symptoms in EAE mice.82

The immune response in EAE is mediated mainly by Th1 and Th17 cells. The gut SFB induces Th17 cells in EAE mice. To validate the influence of the intestinal microbiota in the development of EAE, mice were treated with antibiotics, and they exhibited a reduction in clinical score, suggesting the role of the microbiota in the induction of inflammatory cells in these models. The attenuation of the clinical score was accompanied by decreased interferon‐γ (IFN‐γ), macrophage inflammatory protein 1α, monocyte chemoattractant protein 1, IL‐17 and IL‐6 and increased IL‐10 and IL‐13 secretion.83

The colonization of EAE mice with Bacteroides fragilis and polysaccharide S resulted in decreased clinical scores and the protection of mice from disease.84 This effect was achieved because of the induction of Treg cells, increased IL‐10 and reduced IL‐17, suggesting the use of these microorganisms as probiotics in humans.85 Some of the tested probiotics seemed to have an effect on the autoimmunity of EAE mice. Oral administration of Lactobacillus spp. and Bifidobacterium bifidum showed a significant decrease in the clinical score and increase in the Treg cell number in treated mice.86

Recently, it was also demonstrated that the gut microbiota could affect the permeability of the blood–brain barrier.86 The defective tight‐junctions at the blood–brain barrier of GF mice are restored after they are colonized with conventional microbiota.86 The use of GF mice also demonstrated the importance of intestinal microbiota in the development of EAE. The induction of EAE in GF mice resulted in the reduction of IFN‐γ and IL‐17A in the CNS, accompanied by an increase in the number of Treg cells in the gut.81

In patients, recent studies have evaluated seven individuals with relapsing–remitting MS (RRMS) and found a reduction in Firmicutes, Bacteroidetes and Proteobacteria members.87, 88 Jhangi et al. evaluated 22 untreated MS patients and observed an increase in Methanobrevibacter smithii and reduction in Firmicutes, as well as Butyricimonas, which are butyrate‐producing members of the microbiota.88 A Japanese study found altered intestinal microbiota in RRMS patients, with decreased Clostridia XIVa and IV groups and Bacteroidetes members.89 Another study, including 15 RRMS patients with an Expanded Disability Status Score ≤ 3·0 showed a decreased amount of Faecalibacterium and increased amounts of Akkermansia, Coprococcus and Faecalibacterium after vitamin D supplementation90 (Fig. 2).

A recent study investigated 60 RRMS patients, 28 untreated patients, and 43 healthy controls and showed increased amounts of Methanobrevibacter and Akkermansia and decreased amounts of Butyricimonas in untreated patients.90 Methanobrevibacter is involved in inflammatory conditions by recruiting macrophages and activating dendritic cells.91 Akkermansia species have immunoregulatory effects by converting mucin into short‐chain fatty acids; however, they could play a role in degrading the mucus layer and promoting inflammation.92, 93 Butyricimonas species are butyrate‐producing bacteria and have immunomodulatory properties by inducing Treg cells in the gut.71 In treated patients (IFN‐β and glatiramer acetate), there was an increased number of Prevotella compared with untreated patients.94 This genus is associated with high‐fibre ingestion and has regulatory roles via butyrate generation95 (Fig. 2).

Chen et al. also reported dysbiosis in RRMS patients after comparing stool samples from 31 patients and 36 controls. They observed an increased abundance of the Pseudomonas, Mycoplasma, Haemophilus, Blautia and Dorei genera in patients compared with healthy counterparts, which showed a prevalence of Prevotella and Parabacteroides.96

Available findings on dysbiosis in animal models and patients with MS point to the gut–brain axis connection. The relationship between immunity in the gastrointestinal mucosa and commensal bacteria seems to promote important physiological homeostasis for the host.97 However, future studies are required to determine the real role of the gut microbiota in CNS demyelinating diseases.

Rheumatoid arthritis

Rheumatoid arthritis (RA) is a systemic autoimmune disorder characterized by chronic inflammation of multiple joints, bone erosion and cartilage destruction. Moreover, RA can affect internal organs such as the lungs, heart and kidneys. Anti‐cyclic citrullinated peptide and/or rheumatoid factor are the most important autoantibodies in RA and can be found before disease onset.98 The disease is three times more common in women, and according to WHO, the worldwide prevalence, which is between 0·3 and 1%, ranks the disease among the most common autoimmune disorders. The triggering of RA involves the interaction of HLA genes and environmental factors, such as smoking and infections.99 Among environmental factors, dysbiosis has been identified as a possible trigger factor for autoimmunity and RA development.100

Experiments in animal models suggest that the gut microbiota influences local and systemic immunity and might trigger joint inflammation.100, 101 Studies in mice with collagen‐induced arthritis (CIA) showed that the administration of antibiotics exacerbates the disease and increases the level of IL‐6, IFN‐γ and IL‐17 pro‐inflammatory cytokines.102 Further study showed differences in the gut microbiota composition between CIA‐susceptible and CIA‐resistant mice, with a prevalence of Desulfovibrio, Prevotella, Parabacteroides, Odoribacter, Acetatifactor, Blautia, Coprococcus and Ruminococcus genera in arthritic mice, in addition to increased levels of serum IL‐17 and CD4 Th17 cells in the spleen.102

Mice deficient in IL‐1RA signalling spontaneously develop arthritis; however, under GF conditions, RA is attenuated because of decreases in IL‐17 and IL‐1β secretion and decreased Toll‐like receptor 2 and Toll‐like receptor 4 stimulation.103, 104, 105 On the other hand, when these IL‐RA^−/− GF mice were colonized with Bifidobacterium bifidum, there was an increase in clinical scores compared with mice that were conventionally housed.104

Recent studies have investigated the gut microbiota of the genetically arthritis‐susceptible transgenic mice *0401 and in the genetically resistant transgenic mice *0402. Clostridia were prevalent in susceptible mice, whereas the Porphyromonadaceae and Bifidobacteriaceae families were dominant in resistant mice. Moreover, the authors observed increased intestinal permeability and a Th17 profile in susceptible mice, suggesting that genetic background influences the individual's microbiota profile.106

Similar to that observed in EAE mice, Th17 cells induced by SFB in the lamina propria induced autoantibodies involved in RA development in animal models.107 The correlation between intestinal dysbiosis and RA aetiology is not a new concept. The ‘toxaemic factor’ hypothesis was proposed in the twentieth century when it was suggested that the increase in the level of Gram‐negative bacteria in the intestinal lumen could induce an increase in toxic molecules/metabolites that enter the bloodstream, promoting systemic inflammation.100 Recent studies have shown that the intestinal microbiota of newly diagnosed RA patients was dominated by Gram‐negative Prevotella members, especially Prevotella copri, compared with healthy individuals.108, 109 In the work of Maeda et al., the gut microbiota transplant from RA patients to GF arthritis‐prone SKG mice induced an increase in the number of Th17 cells in the gut and severe arthritis. Additionally, the co‐culture of SKG dendritic cells with Prevotella copri increased IL‐17 secretion in response to RA autoantigens, suggesting that RA gut microbiota may induce autoreactive cells in the gut and promote joint inflammation109 (Fig. 3).

Figure 3.

A schematic representation of intestinal dysbiosis in rheumatic autoimmune diseases in humans.

Another study, which was performed by Liu et al., investigated the Lactobacillus community by quantitative real‐time PCR in faecal samples from 15 patients with RA and 15 healthy controls and reported increased absolute copy numbers of Lactobacillus salivarius, Lactobacillus iners and Lactobacillus ruminis in untreated RA patients that were recently diagnosed.110

Chen et al. identified the gut microbiota profile in patients with RA and found decreased species richness (α‐diversity) that positively correlated with increased rheumatoid factor levels and disease progression.111 The authors evaluated 40 patients with RA and 32 healthy controls and found increased Eggerthella, Actinomyces, Turibacter, Streptococcus and Collinsela reads in the gut microbiota of people with RA, with positive correlations with the pro‐inflammatory cytokine IL‐17. The rheumatoid factor, C‐reactive protein, disease progression and methotrexate treatment correlated with β‐diversity found in the gut microbiota of patients with RA, suggesting that these clinical data might a play role in gut microbiota modulation111 (Fig. 3).

Increasing evidence suggests an association between intestinal dysbiosis and rheumatic diseases and their role in disease progression and the inflammatory microenvironment. Future studies should demonstrate the role of gut inflammation as a trigger for the development of autoimmunity and RA. The determination of an intestinal dysbiotic signature will provide us with the means to develop therapeutic tools for the adjuvant treatment of immune‐mediated diseases.112, 113

Systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune and heterogeneous disease characterized by damage to the skin, kidneys, lungs, joints, heart and brain.114 The disease affects mainly females, and its worldwide prevalence varies from 30 to 60 per 100 000 in the UK and the USA.115 The pathogenesis of SLE may involve genetic and environmental factors, such as viral infections, defective apoptosis and solar exposure to ultraviolet‐B waves. Regarding immune response, it is known that autoantibodies bind mainly with nuclear and cytoplasmic antigens.116 Moreover, increased evidence has emerged that suggests the role of intestinal dysbiosis in SLE development.117

In female lupus‐prone mice, Zhang et al. reported a decrease in the relative abundance of Lactobacillus spp. and an increase in Lachnospiraceae members when compared with controls. Early disease onset and severe symptoms correlated with increased Lachnospiraceae reads in female lupus‐prone mice. Additionally, the number of Clostridiaceae and Lachnospiraceae reads increased at specific time‐points during disease progression.118 Another study reported that dietary intervention, such as caloric restriction, in NZB/W F₁ mice promoted changes in the gut microbiota and avoided disease progression in this animal model.119

Similarly, Johnson et al. reported that (SWR × NZB) F₁ mice given drinking water with a low pH have altered gut microbiota and decreased antinuclear antibodies, and develop nephritis more slowly, suggesting that gut microbiota modulation might influence disease progression.120 In addition, when examining GF lymphotoxin‐deficient mice, Van Praet et al. reported that the intestinal microbiota could play a role in antinuclear antibody induction and could be associated with SFB colonization and IL‐17 receptor signalling.121

Hevia et al. analysed human stool samples from 20 patients with SLE and 20 healthy controls, and the results showed decreased Firmicutes : Bacteroidetes ratios in the patients with SLE. Additionally, in silico analysis suggested that the intestinal dysbiosis observed in patients with SLE could be linked to an increase in oxidative phosphorylation and the glycan metabolism pathways induced by patients' intestinal microbiota.122 In this manner, another study evaluated stool samples from 45 patients with SLE and 48 control subjects and reported a decreased amount of Firmicutes members, an increased level of Bacteroidetes members, and a prevalence of Rhodococcus, Eggerthella, Klebsiella, Prevotella, Eubacterium, Flavonifractor and Incertae sedis genera in patients with SLE, suggesting a gut microbiota profile for patients with SLE123 (Fig. 3).

Based on these reports showing intestinal dysbiosis in patients with SLE, López et al. evaluated the role of microbes derived from stool samples from patients with SLE and controls in the in vitro differentiation of Treg, Th1 and Th17 cells. The authors showed that patients' samples induced Th17 differentiation and supplementation with Treg‐inducing bacteria significantly decreased the Th17/Th1 balance, supporting the use of these strains as therapeutic probiotics for autoimmune diseases.124

Probiotic applications in autoimmune diseases

According to the WHO, a probiotic is ‘a live organism, which provides a benefit to the host when provided in adequate quantities'.125 Studies suggest that probiotics influence systemic immune responses, ensure the homeostasis of the healthy microbiota in the intestinal mucosa and could, therefore, be used as adjuvant therapy to treat immune‐mediated diseases.125 The mechanisms proposed to achieve this include mucus secretion, antimicrobial peptide production, the maintenance of the function of the gastrointestinal–epithelial barrier, ensuring adequate interactions between the gut microbiota and the mucosal immune cells, and finally, helping the activation of the host immune system in response to pathobionts.126 Here, we reported the results of the main clinical trials concerning the applicability of probiotics in autoimmune diseases.

In a recent study in NOD mice, the oral administration of a Lactobacillaceae‐enriched probiotic protects mice from T1D by suppressing IL‐1β expression and the release of immunomodulatory indoleamine 2,3‐dioxygenase and by promoting the differentiation of CD103⁺ tolerogenic dendritic cells in the gut.127

In humans, a TEDDY study group evaluated probiotic supplementation for children with genetic risk for T1D during their first year of life. This multicentre prospective cohort study (USA, Finland, Germany and Sweden) investigated 7473 children ranging from 4 to 10 years in age. Early probiotic administration was correlated with a decreased risk of islet autoimmunity when compared with the group that received probiotics after 27 days of life or no supplementation.128

Several studies in EAE mice demonstrated the immunoregulatory functions of probiotic administration. Treatment with Lactobacillus spp., Pediococcus acidolactici, Bifidobacterium bifidum, Bifidobacterium animalis and Bacteroides fragilis improved CNS inflammation through the induction of Treg cells in the gut mucosa by promoting the secretion of IL‐10 and transforming growth factor‐β,and inducing decreased Th1/Th17 inflammatory subsets.86, 129, 130, 131, 132, 133

In humans, Kouchaki et al. reported improved Expanded Disability Status Score, insulin resistance and a decrease in inflammatory markers in MS patients treated with probiotic supplementation containing Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus fermentum and Bifidobacterium bifidum. This randomized double‐blind placebo‐controlled clinical trial analysed probiotic intake for 12 weeks in 60 MS patients.134

In a recent study, the oral administration of Bacillus coagulans, which has an anti‐inflammatory effect, promoted a decrease in the level of serum amyloid A protein and decreased tumour necrosis factor serum levels in rat models of RA.134

Some performed studies evaluating the effect of probiotics as an adjuvant therapy for RA treatment have shown no significant results.135 Some of these conducted studies have smaller numbers of patients and a short period of treatment.136 In a double‐blind, placebo‐controlled trial, the oral administration of Lactobacillus rhamnosus and Lactobacillus reuteri for 3 months to 29 RA patients did not improve the disease, measured by the American College of Rheumatology criteria (ACR20). However, the authors reported functional improvement within the probiotic supplementation group compared with the placebo group.136

Vaghef‐Mehrabany et al. investigated the role of Lactobacillus casei intake in 46 RA patients for 8 weeks. This randomized, double‐blind placebo‐controlled trial showed improvement in disease activity score, increased levels of serum IL‐10, and decreased levels of tumour necrosis factor, IL‐6 and IL‐12 in treated patients.137 Another clinical trial with the same study design evaluated the administration of Lactobacillus acidophilus, Lactobacillus casei and Bifidobacterium bifidum for 8 weeks in 60 RA patients. Probiotic intake improved DAS28, decreased the level of serum C‐reactive protein, and promoted a decrease in the insulin levels.138

In a lupus‐like animal model, the administration of retinoic acid restored Lactobacillus spp. and improved lupus symptoms, suggesting the use of these species as a probiotic to diminish inflammation in patients with SLE.118 Some Lactobacillus species have been demonstrated to have immunomodulatory properties in the host gut mucosa, such as inhibiting neutrophil extracellular trap formation, improving antioxidant status and increasing the expression of adhesion molecules in the gut.139, 140 However, currently, there are no clinical trials reported at clinicaltrials.gov investigating the role of probiotics as an adjuvant therapy in the treatment of patients with SLE.

Future studies with higher numbers of patients and longer evaluation times are necessary to corroborate these results. Such confirmation may lead to the routine use of probiotics as an adjunctive therapy in the treatment of immune‐mediated diseases. However, these studies should take into consideration the patient's immunological status before probiotic introduction.

Conclusions

Emerging findings associate intestinal dysbiosis with autoimmune disease pathogenesis. Mucosal surfaces with impaired microbiota function and diversity, such as in the gut, could represent a trigger site of autoimmunity by neo‐antigen generation under dysbiotic conditions. If this hypothesis is validated, all the generated data could collaborate in the discovery of new probiotics, predictive biomarkers and therapeutic approaches for use in clinical settings for the adjuvant treatment of autoimmune diseases.

Disclosures

The authors report no conflict of interest.