Immunology and Cell Biology (2014) 92, 49–56; doi:10.1038/icb.2013.54; published online 8 October 2013

Gut TFH and IgA: key players for regulation of bacterial communities and immune homeostasis

Lucia M Kato1,2, Shimpei Kawamoto1,2, Mikako Maruya1 and Sidonia Fagarasan1

1Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences IMS-RCAI, RIKEN Yokohama Institute, Yokohama, Japan

Correspondence: Dr S Fagarasan or Dr LM Kato, Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences IMS-RCAI, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. E-mail: or

2These authors contributed equally to this work.

Received 14 August 2013; Revised 27 August 2013; Accepted 28 August 2013
Advance online publication 8 October 2013



The main function of the immune system is to protect the host against pathogens. However, unlike the systemic immune system, the gut immune system does not eliminate, but instead nourishes complex bacterial communities and establishes advanced symbiotic relationships. Immunoglobulin A (IgA) is the most abundant antibody isotype in mammals, produced mainly in the gut. The primary function of IgA is to maintain homeostasis at mucosal surfaces, and studies in mice have demonstrated that IgA diversification has an essential role in the regulation of gut microbiota. Dynamic diversification and constant adaptation of IgA responses to local microbiota require expression of activation-induced cytidine deaminase by B cells and control from T follicular helper and Foxp3+ T cells in germinal centers (GCs). We discuss the finely tuned regulatory mechanisms for IgA synthesis in GCs of Peyer’s patches and emphasize the roles of CD4+ T cells for IgA selection and the maintenance of appropriate gut microbial communities required for immune homeostasis.


Foxp3; gut; IgA; microbiota; TFH

The intestine is colonized by a large number of microorganisms that are establishing mutualistic relationships with the host. These microorganisms—mainly composed of bacteria and commonly referred as the gut microbiota—not only serve as a natural competitor for pathogens, but also are essential for nutrient processing, development and regulation of the host immune system.1 Gut microbiota, which are separated from the host by a single layer of epithelial cells, appear to stimulate constitutively the host mucosal immune system. To control the threshold of such stimulation, mammals evolved very sophisticated regulatory immune mechanism in the gut.2, 3, 4, 5

The gut immune system has some peculiarities when compared with the systemic immune system. These become obvious when considering that it is important not to eliminate but to peacefully coexist with gut microbiota to prevent the expansion of harmful bacteria yet to retain helpful and diversified bacteria. Gut immune system uniquely and constitutively produces large amounts of immunoglobulin A (IgA) in response to the interaction with gut microbiota. Most of these immune responses are generated in gut-associated lymphoid tissues. In this review, we dissect the uniqueness of gut immune responses, focusing on the characteristics of T follicular helper (TFH) cells in gut and their association with IgA selection and control of gut microbiota.


Gut-associated lymphoid tissues

Gut-associated lymphoid tissues are usually divided into two functional compartments: inductive and effector sites.6, 7 The primary inductive sites include organized follicular structures that are present along the wall of intestine, such as Peyer’s patches (PPs) and isolated lymphoid follicles. These follicular structures are enriched in B cells interacting with T cells. The lamina propria (LP), particularly of the small intestine (SI), is the main mucosal effector site where many of IgA-producing cells generated in the PPs relocate and reside. The IgAs are secreted in large quantities, mainly as dimers or larger polymers, after incorporation of J chain and association with polymeric Ig receptor.7

Recent studies have shown that IgA responses in gut are generated by multiple pathways, within or outside the follicular structures, with or without help from cognate T cells. Nevertheless, IgA production in T–cell-deficient mice is less efficient (takes longer times to develop)8 and effective (natural type of IgAs with few mutations) than in wild type (WT) mice (our unpublished data). This indicates that in normal conditions, the majority of IgAs are induced with the help of T cells.

The major site for T-cell-dependent IgA induction is represented by PPs. These are larger lymphoid structures consisting of multiple B-cell follicles built on a network of follicular dendritic cells (FDCs),9 and separated by interfollicular areas containing T cells and dendritic cells. PPs are already present at birth, because they develop independently of the gut microbiota. However, after colonization with bacteria, PPs form germinal centers (GCs), unique microenvironments where B cells activated by antigens interact with a subset of CD4+ T cells known as TFH cells10, 11 and generate IgAs with the required specificities. As the GC matures two main compartments, called dark zone (DZ) and light zone (LZ), are formed. The LZ is occupied by FDCs loaded with antigen in the format as immune complex, whereas DZ are occupied by proliferating B cells that move from the LZ after antigen stimulation.12 Therefore, the DZ and LZ of GCs were classically thought to be the sites of clonal expansion and selection of GC B cells, respectively.


Characteristics of PP GCs

Unlike in the systemic immune system, where the presence of GCs is related either with systemic infections or with deliberate vaccination, PP GCs are constantly induced by gut bacteria and thus are non-synchronized GCs triggered by various and variable antigens. Germ-free mice have few if any GCs.3, 4 Reversely, the spontaneous PP GC formation, and the size of PPs drastically decrease after reduction and/or elimination of gut bacteria by antibiotics.13, 14, 15 These observations clearly indicate that GCs in PPs are set ‘in motion’ by the bacterial communities in the gut. Formation of GCs in PPs was thought to be an antigen-specific reaction, rather than just a polyclonal B-cell expansion triggered by stimulation through pattern-recognition receptors, such as Toll-like receptors. However, studies of knock-in mice for LMP2A, a membrane protein encoded by Epstein–Barr virus that acts as a B-cell receptor (BCR) surrogate, apparently challenged this view.14 LMP2A transgenic mice lacking antigen-specific recognition through BCRs, but having constitutive CD40-like signaling in all B cells, developed GCs in PPs (and partially in mesenteric lymph nodes) but not in spleen. This result led to an alternative model in which the mucosal B cells can be driven into GCs independent of BCR specificity, through the interaction of Toll-like receptors on B cells with bacterial components.16

GC B cells express activation-induced cytidine deaminase (AID), a key enzyme necessary for two genetic alterations of the Ig heavy chain that are essential for B-cell maturation after antigen stimulation: class switch recombination (CSR) and somatic hypermutation.17 The first AID-induced modification produces antibodies with different effector functions by switching the BCR class from IgM to IgA; the second introduces non-templated point mutations in the Ig variable region genes (VH), resulting in incremented antigen receptor diversity and affinity.18 The absence of AID expression leads to a significant accumulation of B cells and T cells and hyperplasia of GCs.13, 17 Within GCs, B cells compete for TFH cell help, so that highly mutated B cells (presumably with higher affinity to the antigen) have advantage over their low-mutated counterparts.12, 19 Thus, a proper interaction between B cells and TFH cells within GCs guarantees the appropriate selection of presumably high-affinity IgAs (see later discussion). The selection process may be also regulated directly by the antibodies deposited on the FDCs, as recently proposed for the peripheral GCs.20 The lack of antibody feedback regulation, combined with reduced B-cell apoptosis (because of lack of deleterious mutations) may also explain the B-cell intrinsic hyperplasia of GCs in AID-deficient mice. How IgA antibody feedback contributes to regulation of GC reaction in the gut remains to be elucidated.

Another characteristic that distinguishes GC in PPs is that B cells in GC of PPs preferentially switch to IgA. In contrast, in GCs induced upon immunization in peripheral lymph nodes (pLNs) or spleen, B cells switch to various IgG isotypes, depending on the cytokine milieu.4, 21 The preferential switching to IgA is partly explained by the fact that bacterial and food-derived products present in the gut, such as lipopolysaccharide and retinoic acid, condition PP FDCs and facilitate the activation of transforming growth factor (TGF)-β1 and secretion of large amounts of B-cell activating factor (BAFF),22 the two essential cytokines that direct switching toward IgA23 and survival of recently switched IgA+ B cells,24 respectively. Besides the FDCs, Foxp3+ T cells by secreting TGF-β125, 26 and generating an anti-inflammatory milieu27 also contribute to IgA generation in PP GCs.28


GC T cells

The majority of T cells located within the GCs are CD4+ T cells, although a small fraction of CD8+ T cells were also reported to be present in the GCs.29, 30 More recently, invariant natural killer T cells were shown to differentiate into natural killer TFH cells and to support a distinct type of antibody response in GCs.31

In the PPs of major histocompatibility complex class II (MHCII)-deficient mice, we detected very few GCs and those we did detect were small in size, an observation indicating that the CD4+ T cells are likely the main players for the GC reaction in PPs.8 Two major kinds of CD4+ T cells are located inside GCs: TFH cells, defined as CXCR5+PD-1hiFoxp3 cells, and T follicular regulatory (TFR) cells, defined as CXCR5+PD-1hiFoxp3+ cells, collectively termed GC-CD4+ T cells. The generation of both, TFH and TFR cells, depends on the induction of Bcl6 protein.32, 33, 34, 35, 36, 37


GC TFH cells

The characteristics of TFH cells are their positioning within the GCs, the high expression of co-stimulatory molecules (CD40L, inducible co-stimulator, programmed cell death-1 (PD-1) and OX40) as well as the production of cytokines (interleukin (IL)-21 and IL-4) associated with regulatory and B helper function.11, 38 Indeed, TFH cells are essential for the formation and maintenance of GCs and for the generation of most memory B cells and plasma cells.39

The development of TFH cells starts when T cells primed by dendritic cells migrate to the border between the T zones and the B-cell follicles (T–B border). T cells migrate toward the B-cell follicle upon downregulation of CCR7 expression and upregulation of CXCR5, which direct TFH cells to B-cell follicles via gradients of the chemokine CXCL13 expressed by FDCs.38, 40 This interaction with B cells is modulated by SAP molecule and the expression of Bcl6, the major regulator of TFH differentiation, although other transcription factors, such as IRF4, c-Maf, Batf and STAT3/5, may be also involved after the activation events leading to TFH cell development.39, 41 After their encounter at the T–B border, B cells become GC B cells and proliferate extensively (this proliferation associated with AID induction, mutation and selection is essential for the GC response), whereas minimal GC T-cell proliferation has been reported.42 Using fluorescent ubiquitination-based cell-cycle indicator (Fucci) mice43 (in which the cells in S-G2-M phase of the cell cycle are fluorescently marked) we found that while 30% of DZ B cells and 15% of LZ B cells in the PP GCs expressed Fucci,44 only 2–3% of PP TFH cells were Fucci+ (our unpublished data). As discussed later, the high expression of PD-1 might provide an inhibitory signal to GC TFH cells preventing the excessive CD4+ T-cell proliferation in GCs. A ‘slow-down’ of proliferation might be required for appropriate cytokine production by TFH cells, as different cytokines may be produced during different stages of the T-cell cycle.45 The ‘imprinting’ of TFH characteristics such as cytokine production might happen before these cells become TFH cells. Indeed, increasing evidence suggest that different types of T cells can be the precursors of TFH cells. TFH cells in pLNs can differentiate from IL-4+ Th2 cells elicited in response to helminth antigens.46, 47 In the PP GCs, many TFH cells appear to be generated from CD4+ T cells induced in the context of gut antigens, such as the Foxp3+ T cells and Th17 cells—the two major regulatory/effector CD4+ T-cell subsets in the intestine.28, 48


Conversion of Foxp3+ T cells into TFH cells in PPs

Foxp3-expressing CD4+ T cells appear to be a heterogeneous and dynamic population that includes cells generated in different places (thymus vs gut), by distinct antigens (self- vs bacterial or food antigens), found in different stages of their ‘life’ (recently induced, nonactivated or activated) and capable to regulate immune responses in multiple ways.49, 50 Because it is difficult at present—if not impossible—to precisely distinguish between different Foxp3+ T-cell populations, we chose to refer to them simply as Foxp3+ T cells instead of ‘Treg cells’ used widely in the literature.

We have recently shown that PP TFH cells could be generated from Foxp3+ T cells with IgA helper properties.28 Thus, in an adoptive transfer model of Foxp3+ T cells into T-cell-deficient (CD3/) mice, we found that some Foxp3+ T cells lose their Foxp3 expression and convert into TFH cells capable of inducing, very efficiently, GCs and IgA production in PPs. Interestingly, the conversion of Foxp3+ cells into TFH cells was only observed in PPs (and partially in the mesenteric lymph node), indicating this conversion being a gut-specific phenomenon. Indeed, the Foxp3+ cells could not differentiate into IgG- or IgA-inducing TFH cells in spleen even after repeated intravenous immunization with sheep red blood cells in the context of ‘gut molecular mimicry’ like lipopolysaccharide or peptidoglycan.28 In agreement with this, using Foxp3 fate-mapping mice, it was shown that the majority of TFH cells in pLNs after immunization with sheep red blood cells were derived from T cells that have never expressed Foxp3.35 Thus, in the gut there seems to be a connection between Foxp3+ T cells, GC and IgA, and bacteria. The existence of a Foxp3–IgA axis in gut is strengthened by the observation that the depletion of Foxp3+ T cells leads to a rapid loss of specific IgA responses in the gut.51, 52

Furthermore, it has been reported that a fraction of Foxp3+ cells that are negative for CD25 expression are prone to lose the Foxp3 expression and to differentiate into effector helper T cells.53 In agreement with this, we found that Foxp3+ T cells especially from the SILP and PPs expressed low levels of CD25 and these cells have slightly lower expression level of Foxp3.28 Furthermore, CD4+ T cells induced to express Foxp3 in vitro had a modest expression of microRNA, miR-10a, and could convert into TFH cells in the PPs upon their adoptive transfer.54 miR-10a is highly expressed in thymus-derived Foxp3+ T cells and appears to prevent the conversion into TFH cells by targeting Bcl6.54 Together, all these observations suggest that CD4+ T cells induced to express Foxp3 outside the thymus, probably by the gut antigens and in the context of TGF-β1, can more easily convert into TFH cells in PPs than thymus-derived Foxp3+ T cells (although the latter may also contain some unstable T cells, expressing Foxp3+ transiently).55 Interestingly, mice deficient in a regulatory region of the Foxp3 promoter (CNS1: an intronic Foxp3 enhancer stimulated by TGF-β1) and lacking a subset of Foxp3+ cells induced in organs other than the thymus, spontaneously developed Th2-type pathologies and had altered bacterial composition in gut, with overall decrease in the ratio of Firmicutes to Bacteroidetes.56 Therefore, Foxp3+ cells induced outside the thymus may have unique functions for preventing mucosal inflammatory reactions and controlling commensal bacteria,57 but the mechanisms by which peripherally induced Foxp3+ T cells achieve these functions remain unknown.


Conversion of Th17 cells into TFH cells in PPs

In addition to Foxp3+ T cells, Th17 cells were also reported recently to have the potential to convert into TFH cells in PPs and to support IgA production in the gut.48 Using an adoptive transfer model of Th17 cells (sorted as YFP+ cells from Il17aCreR26ReYFP) into T-cell-deficient mice, it was shown that Th17 cells converted into TFH cells and supported IgA induction in PPs. In the IL-17 fate-reporter mice, the fluorescent reporter (eYFP) permanently labels Il17aCre cells, which allows the identification of cells that have switched on the IL-17 program. Because a sizeable fraction (16% and 10%) of YFP+ cells did not express IL-17 and RORγt (the critical transcription factor of Th17 cells),58 respectively, this system likely marked cells with alternative effector programs that might have been activated together with IL-17.

Nevertheless, it is quite likely that some CD4+ T cells induced to express the transcription factor RORγt (which better define the Th17 cells) can downregulate the RORγt expression and convert into TFH cells. It may be possible that some of the converting RORγt+ Th17 cells might have previously expressed Foxp3, as one in four RORγt+ T cells were found to have expressed previously Foxp3.59 However, the capabilities of RORγt+ Th17 T cells to relocate from the SILP (where they are almost exclusively induced in homeostatic conditions) to the PPs where they would convert into TFH cells remain to be determined.

In a few infectious or inflammatory conditions, some CD4+ T cells express concomitantly IL-17 and interferon-γ,60 but whether these double expressers might become TFH cells and how they impact GCs remain to be explored in future studies.

Together, the results strongly suggest that TFH cells in PP GCs are a heterogeneous population. However, what appears to distinguish mucosal TFH from non-mucosal TFH cells might be their provenance from unique CD4+ T-cell subsets induced in the gut. Future studies should address the functional difference of TFH cells derived from different CD4+ T-cell subsets and their contribution to GC responses and IgA production in PPs.


GC TFR cells

TFR cells share several features with TFH cells, such as high expression of CXCR5 and PD-1, as well as their location within the GCs.35, 36, 37 Similar to TFH cells, the differentiation of TFR cells also depends on Bcl6 expression, requires the presence of B cells and intact SAP signaling, suggesting that T–B interaction is required for their entry into the GCs. Yet, unlike TFH cells, TFR cells express the transcription factor Foxp3, GITR and CTLA-4 but lack the CD40L expression and the potential to secrete B-helper cytokines other than IL-10.35, 36, 37 In the GCs in spleen or pLNs, TFR cells seem to be derived from thymic Foxp3+ T cells. In the GCs in PPs, the origin of TFR is yet unknown, although it is possible that they could be derived from Foxp3+ T cells generated either in the gut or in the thymus. It may be also possible that TFR cells and ex-Foxp3 TFH cells could be derived from Foxp3+ T cells induced in the thymus and in the gut, respectively, but this possibility remains to be tested in future studies.

Clearly the TFR-cell function is to control the GC responses by limiting the number and the quality of TFH cells and selection of GC B cells. Thus, the lack of TFR cells leads to an increased number of TFH cells in GCs, associated with an increase in GC B cells producing polyspecific/polyreactive rather than specific antibodies.35, 36 The TFR cells may also act directly on B cells, as indicated by the initial studies performed in vitro.61, 62 In their culture system, CD4+CD25+CD69 cells (mainly Foxp3+ cells) upregulated CXCR5 upon antigen priming and directly suppressed B-cell Ig production induced by TFH cells. This direct B-cell suppression by Foxp3+ cells required cell–cell interaction. Interestingly, at least for peripheral GCs, the number of TFR cells increased later in the GC response and their presence coincided with the decline of TFH cell number when they appear to prevent the GC reaction to become chronic.37 Therefore, the TFH/TFR ratio may be a marker to determine GC maturation and longevity.11 In agreement with this idea, the TFH/TFR ratio in PP GCs is much higher than in peripheral GCs (our unpublished data), where GC are constantly induced by ever-changing bacterial antigens. Further studies are required to establish the mechanisms by which TFR cells regulate the GC reaction in general, and the IgA synthesis in PP GCs in particular.


Role of PD-1 in regulation of GCs

PD-1, which is highly expressed on TFH cells, is an inhibitory receptor found on the surface of activated T cells and some B cells.63, 64 PD-1 has a critical role in shutting down ineffective immune responses and maintaining immune tolerance.65, 66, 67 Interestingly, PD-1-deficient mice developed species-specific and antibody-mediated autoimmune disease.63 PD-1 belongs to the CD28-CTLA4 Ig super family and interacts with two ligands: PD-L1 and PD-L2. In PP GCs, PD-L1 expression seems downregulated on GC B cells, but is re-induced on IgA+ B cells and further upregulated on plasma cells. In contrast, PD-L2 is expressed by both GC B cells and IgA+ B cells located predominantly in the LZ of GCs.19 Thus, PD-1 on TFH cells is mostly engaged by PD-L2 expressed on GC B cells, and this interaction would probably modulate in situ the GC reaction. Indeed, B-cell intrinsic expression of PD-L2 was shown to be required for optimal generation of antibody-producing cells in systemic immune system.68 However, the phenotype of the PD-L1/PD-L2/ and PD-1/ mice were more pronounced than those of the PD-L2/ mice after systemic immunization68 and PD-L1/ mice also showed a similar phenotype with PD-1/ mice such as TFH expansion after helminth infection.69 Thus, constitutive PD-L1 expression on B cells also probably contributes to PD-1 signaling and affects GC responses in systemic immune system, but the function of PD-L1 in gut immune system is still unknown.

Although it was reported that PD-1 expression on TFH cells impact IgG antibody production,68 the effect of PD-1 on PP TFH cells for IgA production was unknown. Recently we showed that PD-1/ mice had higher frequency and number of TFH cells in PPs.44 Furthermore, the properties of PP TFH cells in PD-1/ mice differed from those in WT mice, in the sense that they had reduced surface expression of inducible co-stimulator, expressed more Bcl6 and less IRF4, and produced more pro-inflammatory cytokines (interferon-γ and tumor necrosis factor-α) but less IL-21. These changes in numbers and properties of TFH cells in the absence of PD-1 associated with impaired selection of GC B cells in PPs (Figure 1). Indeed, PD-1/ mice had worsened B-cell responses, at least in terms of quality, rather than enhanced B-cell responses.69 Although the frequency and absolute number of GC and IgA+ B cells were higher in PPs of PD-1/ mice compared with WT mice, the frequency of clonally related sequences (with identical VH-DH-JH and junctions) was reduced in PD-1/ mice. Moreover, compared with WT mice, the turnover of GC B cells in PPs was enhanced and the apoptosis slightly reduced in PD-1/ mice. These data suggest that GC B cells are not selected well in PD-1/ mice because of less clonal expansion and the quicker passage of GC B cells through PPs in PD-1/ mice when compared with WT mice (Figure 1). In fact, PD-1/ mice showed reduced affinity maturation of IgA-producing plasma cells in SI, and less IgA binding capacity to commensal bacteria. These outcomes were partly due to the altered functionality of PD-1-deficient TFH cells with uncontrolled expansion and altered cytokine production in PPs, because T-cell-deficient mice (CD3/) transferred with PD-1/TFH cells (with or without the Foxp3-expressing TFR cells) have similar but worse phenotype than PD-1/ mice, namely more expansion of TFH cells in PPs and less IgA selection and production in the gut.44 Thus, PD-1 is required for GC-T-cell functionality, which contributes to antibody diversification that is important for maintaining gut homeostasis.

Figure 1.
Figure 1 - Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact or the author

Schematic representation of IgA selection within and outside the GCs. Discrimination of GC IgA B cells with different affinities for gut antigens requires BCR engagement and competition for TFH cell help. (Left) In WT mice, the limited number of TFH cells implies that only the B cells capable to present more antigens (high affinity) will receive TFH help, whereas B cells capturing less antigen (low affinity) undergo apoptosis. (Right) In PD-1/ mice, both high- and low-affinity B cells will receive help from the numerous TFH cells present within the GCs. This rapid passage through the GC produces less mutated (less selected) IgAs (represented in green). As a result, PD-1/ mice have skewed gut bacteria. In both cases, the IgA B cells generated in the PP GCs migrate out to the mesenteric lymph node where they further proliferate and differentiate into plasmablasts, which migrate to the SILP. In addition to selection in the GCs, IgAs appear to undergo a second, likely commensal-driven selection within the LP. In this way, the proliferating plasmablasts are reselected to fit the geographical distribution of bacteria along the intestine.

Full figure and legend (172K)

PD-1 is also highly expressed on TFR cells.35, 36, 37 In the case of non-mucosal GCs, PD-1 expression on TFR cells was shown to control their abundance and suppressive function for antibody production.70 Analysis of PD-1/ mice showed that they have increased frequency and number of TFR cells than WT mice, but equal number of TFH cells compared with WT mice. In contrast, in the case of mucosal GCs, the number of both TFR and TFH cells increased in PPs of PD-1/ mice, as PD-1 deficiency is associated also with an increased Foxp3+ T cells (our unpublished data). Therefore the function of TFR cells for GCs may be different between systemic and gut immune systems, because the environment, the activation and dynamics of GC is quite different in those systems. As mentioned before, in the IL-6 and IL-21 saturated GC environment, Foxp3 expression is downregulated71 and many TFR cells seem to become TFH cells in situ (our unpublished data). However, it remains an enigma how at the population level, the cells sense the microenvironment and adjust to it, as to always achieve the physiologic equilibrium, for example the Foxp3/Foxp3+ ratio in the case of CD4+ T cells, or TFH/TFR ratio for GC T cells. It seems that there exists a sort of ‘quorum sensing’ of lymphocytes similar to that of bacterial communities,72, 73 yet we understand almost nothing of this communication network between lymphocytes belonging to the same or to different lineages (i.e., B- and T-cell ratio, inside or outside GCs, in different lymphoid tissues or different phases of the immune response).


Role of IgA in gut

The common view is that IgA confers the first line of defense against pathogens in mucosal surfaces. Studies in IgA-deficient mice have shown that these mice are less resistant to infection.74, 75, 76 However, the secretory IgAs seem to have important roles also in homeostatic conditions, because AID-deficient mice, which lack IgAs, have deregulated bacterial communities in the gut.13, 77 Indeed, an abnormal expansion of uncultured anaerobes such as segmented filamentous bacteria (SFB) was observed in all gut segments, but particularly in the SI of these mice. The aberrant expansion of few species of Firmicutes caused an overactivation not only of the gut immune system, but also the whole systemic immune system. Reconstitution of AID-deficient mice with normal levels of IgA decreased the number of SFB and restored the normal composition of gut microbiota.77

More recently, it has been shown that not only the simple presence or absence, but also the quality of IgA is crucial for controlling gut (and host) homeostasis. AIDG23S is a mutant form of AID that has normal class switch recombination but impaired somatic hypermutation activity.78 Indeed, the knock-in mice expressing AIDG23S had a limited diversity of the Ig repertoire due to a severe defect in somatic hypermutation but the concentration of serum and fecal IgAs, as well as other Ig isotypes, was equivalent to those in WT mice.79 Nevertheless, AIDG23S mice showed signs of systemic activation like GC B-cell hyperplasia and were more susceptible to oral challenge with cholera toxin than WT animals. In addition, AIDG23S mice had an abnormal expansion of Proteobacteria and skewed bacterial composition toward Firmicutes over Bacteroidetes, suggesting that mutated (likely selected) IgAs are required to control the balance of gut microbiota.79

PD-1 deficiency, as discussed above, resulted in increased number of PP TFH cells and impaired selection of IgAs in PP GCs, leading to a reduction in fecal bacteria coated with IgA. Microbiota composition was also altered, because PD-1/ mice had a marked reduction in the number of ‘healthy’ bacteria, such as Bifidobacterium. In contrast, the Enterobacteriaceae, which are minor representatives in the SI of WT mice, were significantly increased in PD-1/ mice. Hyperactivation of the systemic immune system was also observed, with T- and B-cell hyperplasia and presence of serum IgGs against components of commensal bacteria, indicating a breach of normal mucosal–systemic compartmentalization. This hyperactivation of the systemic immune system can be rescued by antibiotic treatment of PD-1/ mice.19, 44

It is known that IgA can control bacterial infection by coating pathogenic bacteria and preventing their physical contact to the epithelium, a process called immune exclusion.76 However, other mechanisms might be involved, such as changes in the bacterial gene expression by binding of IgA.80, 81 The mechanisms by which specific binding of IgA control gut bacterial expansion and diversification—not only of pathogens, but of commensals as well—remain to be solved.

So, IgA is not only necessary to defend the host against pathogens, but also it is an important player in the communication between gut commensal bacteria and the host immune system.1, 82 Interestingly, recent genetic analyses for IgA and PD-1 revealed signatures of local adaptations to pathogen diversification in the last 175 million years, with IgA deficiency having higher frequency in regions where microbial load was lower (i.e., Europe).83 Reversely, PD-1 and PD-L1 variants were associated with regions where pathogen load was high (i.e., Asia), indicating that PD-1–PD-L axis has an important role in the resistance to infectious agents and adapted in such a way to avoid the hijacking by pathogens while keeping its immuno-inhibitory function.83

Paradoxically, the IgA deficiency is the most common immune deficiency found in humans and until recently, it was thought to cause no clinical manifestations.84 For this reason there was a persisting question as to whether the secretory IgAs have an important role in humans. However, recent studies indicate a higher rate of manifestations in IgA-deficient patients, consisting of multiple episodes of gastrointestinal and respiratory infections,85 and the development of autoimmune diseases.86 Conversely, it is also possible that autoimmune mechanisms may contribute to the pathogenesis of IgA deficiency. Hammarström and colleagues performed a genome-wide association study and found a significant association between autoimmunity risk alleles and selective IgA deficiency but the mechanistic link is not known.87 Given the obvious link between microbiota and the host metabolism,88, 89 it will be important to study the role of IgA contribution to the almost ‘epidemic’ metabolic disorders observed only recently,90, 91, 92 and its association with diversity and composition of the bacterial communities in the gut.



Although much progress has been made to help us understand the complex interaction between the gut microbiota and the host immune system, many questions remain to be answered.

Increasing evidence suggest that in addition to the amount, the specificity and diversity of IgAs are important for keeping balanced and diversified bacterial communities in the gut. In this sense, it is not surprising that the composition and dynamics of the gut T-cell compartment have impact on the regulation of gut microbiota. Indeed, TFH cells, by controlling IgA selection in PP GCs, have a crucial role in the regulation of host–bacteria relationship.44 As discussed above, PP TFH cells can be generated from different T-cell subsets, but how TFH cells from distinct origins regulate IgA selection is still unknown (Figure 2).

Figure 2.
Figure 2 - Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, please contact or the author

Scheme of the regulatory loop between TFH cells, IgA and gut microbiota. Gut bacteria (such as Clostridia) or food antigens can induce the differentiation of CD4+ T cells to Foxp3+ T cells, which can migrate to the PP GC and become TFH cells, by losing the expression of Foxp3 or regulate the GC reaction acting as TFR cells. Other bacteria, like SFB, can promote the differentiation of Th17 cells, which are thought to generate TFH in PP. However, how and where Th17 cells become TFH cells is not known. Besides, TFH cells from distinct origins might generate IgAs with different affinity to the antigen, but how these IgAs regulate the gut microbiota remains unclear.

Full figure and legend (164K)

Gut microbiota, in its turn, also modulate the T-cell population in gut. Mono-colonization of germ-free mice with SFB can induce expansion Th17 cells and IgA plasma cells in LP.58, 93, 94 In addition, specific bacteria species such as Clostridium species belonging to cluster IV and XIVa95, 96 or Bacteroides fragilis97 were shown to induce the Foxp3 expression in naive CD4+ T cells, especially in the large intestine (Figure 2). Furthermore, recently it was shown that complex bacterial communities are also required for conversion of CD4+ T cells into cytotoxic yet protective CD8+ T cells in the intraepithelial cell compartment in gut.98

Another intriguing issue is whether the presence of certain species of bacteria is sufficient for effective IgA production (by ‘effective’ we understand IgAs capable to support complex and balanced bacterial communities in their specific location along the gut). Interestingly, some bacterial species present in the gut, even when abundant and persistent, do not appear to be able to induce detectable IgA responses,99 and mono-colonization, even with the most potent activators of immunity like SFB, does not stimulate IgA synthesis in PPs as efficiently as normal diversified bacterial colonization.93 These results suggest that a certain level of bacterial complexity is required for appropriate IgA responses. Similarly, colonization of germ-free mice with 17 strains of Clostridium was more efficient in inducing Foxp3+ T-cell expansion than colonization with one strain alone.96

The diversity of bacterial species that efficiently induce one or another subset of CD4+ or CD8+ T cells and effective IgAs, and how they achieve these effects—either directly through their structural components or indirectly through the metabolites they produce—will likely be uncovered by future studies. We will also need to obtain more information of biogeography of microbial communities, which is critical to understand how bacteria communicate with different components of the immune system. Clearly we are just beginning to dissect the feedback mechanisms between complex and dynamic bacterial communities to equally complex and dynamic immune cell populations. Further studies are also required to understand how the immune system modulates the host–microbe interactions and how all major regulatory networks of the body, namely immune, endocrine and neurologic systems integrate with microbiota to achieve homeostasis.



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We thank all members of Mucosal Immunity laboratory for the work cited and discussions. Supported in part by Grants-in-Aid for Scientific Research (SF) and for Young Scientist, the Naito Foundation, RIKEN special Postdoctoral Researchers Program (SK) and JSPS Postdoctoral Fellowship for Foreign Researchers (LMK).