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Immune adaptations that maintain
homeostasis with the intestinal
microbiota
Lora V. Hooper* and Andrew J. Macpherson‡
Abstract | Humans harbour nearly 100 trillion intestinal bacteria that are essential for
health. Millions of years of co-evolution have moulded this human–microorganism
interaction into a symbiotic relationship in which gut bacteria make essential contributions
to human nutrient metabolism and in return occupy a nutrient-rich environment.
Although intestinal microorganisms carry out essential functions for their hosts,
they pose a constant threat of invasion owing to their sheer numbers and the
large intestinal surface area. In this Review, we discuss the unique adaptations of
the intestinal immune system that maintain homeostatic interactions with a diverse
resident microbiota.
Microbiota
The microorganisms that are
harboured by normal, healthy
individuals. These
microorganisms live in the
digestive tract and at other
body sites.
*The Howard Hughes
Medical Institute and The
Department of Immunology,
The University of Texas
Southwestern Medical Center,
Dallas, Texas 75390, USA.
‡
The Department of Clinical
Research (DFK), Maurice
Müller Laboratories,
Universitätsklinik für Viszerale
Chirurgie und Medizin
(UVCM), University of Bern,
3008 Bern, Switzerland and
Farncombe Family Digestive
Health Research Institute,
McMaster University,
Hamilton, Ontario L8S 4L8,
Canada.
e‑mails: lora.hooper@
utsouthwestern.edu;
[email protected]
doi:10.1038/nri2710
The mammalian intestine contains a dynamic community of trillions of microorganisms. These microorganisms establish symbiotic relationships with their
hosts, making essential contributions to mammalian
metabolism while occupying a protected, nutrientrich environment. Despite the symbiotic nature of
this relationship, the close association of a dense bacterial community with intestinal tissues poses serious
health challenges. The sheer number of intestinal bacteria presents a persistent threat of microbial breach,
and the single-cell epithelial layer and huge intestinal
surface area (~200 m2 in humans) further compounds
this threat. Such opportunistic invasion of host tissue
by resident bacteria can result in breakdown of the
symbiotic host–microorganism relationship and contribute to pathologies such as bacteraemia or chronic
inflammation.
The intestinal immune system has an essential role in
limiting tissue invasion by the resident microbiota, and is
thus fundamentally important for preserving the symbiotic nature of these interactions. However, this system
faces challenges unlike those faced by any other organ
system, as it must continuously cope with an enormous
microbial load, a high degree of microbial diversity, a vast
surface area and frequent challenges from pathogenic
microorganisms ingested in food and water 1. At the same
time, the intestinal immune system must avoid potentially
harmful overreactions that could unnecessarily damage
intestinal tissues or alter the crucial metabolic functions
of the microbiota.
Despite these challenges, the intestinal immune system is remarkably effective at minimizing adverse health
effects from the microbiota, as shown by the fact that sepsis
and inflammation are rare in immunologically healthy
hosts. In this Review, we discuss the unique adaptations
of the intestinal immune system that allow it to limit
opportunistic invasion by the resident microbiota while
responding appropriately to bacterial pathogens. These
include immune mechanisms that limit direct bacterial
contact with epithelial cell surfaces, promote rapid detection and killing of penetrant bacteria, and minimize exposure of resident bacteria to the systemic immune system.
We explore how these immune mechanisms cooperate to
maintain the symbiotic nature of the host–microorganism
relationship, and how these mechanisms can become
dysregulated in disease. In doing so, our intention is not
to provide a comprehensive catalogue of all mucosal
immune mechanisms, but instead to offer a conceptual
framework for understanding how the intestinal immune
system manages its high bacterial load.
The intestinal microbiota
The human intestinal microbial community is complex and is composed of at least 1,000 distinct bacterial
species (BOX 1). This diverse microbiota makes several
essential contributions to human physiology and health.
A primary function of intestinal bacteria is to enhance
host digestive efficiency by degrading dietary polysaccharides2–4. It is this function that is thought to be the
driving force behind the evolution of the mammalian
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Sepsis
A systemic response to severe
infection or tissue damage,
leading to a hyperactive and
unbalanced network of
pro-inflammatory mediators.
Vascular permeability, cardiac
function and metabolic balance
are affected, resulting in tissue
necrosis, multi-organ failure
and death.
Metagenome
All the genetic material present
in a population of
microorganisms, consisting of
the genomes of many
individual organisms.
Goblet cell
A mucus-producing cell found
in the epithelial cell lining of
the intestine and lungs.
host–microorganism relationship5. Recruitment of a
complex and dynamic bacterial community has allowed
mammals to acquire an adaptable ‘metagenome’ that
harbours a diversity of saccharolytic enzymes that complement the limited saccharolytic diversity encoded in
the host genome. commensal microorganisms such as
Bacteroides thetaiotaomicron are uniquely adapted for
harvesting luminal nutrients, as shown by the presence of
an unusually large number of genes in these microorganisms that encode carbohydrate-degrading enzymes6.
millions of years of co-evolution have led to a fundamental intertwining of mammalian and microbial biology that extends well beyond this metabolic function.
For example, intestinal microorganisms provide instructive signals for several aspects of intestinal development,
including epithelial cell maturation7,8, angiogenesis9 and
lymphocyte development 10–12. Intestinal bacteria also
have an important role in protecting their hosts against
pathogenic infections. Two distinct factors contribute
to this protective effect. First, many intestinal bacterial
pathogens are poorly adapted to compete with commensal microorganisms for dietary nutrients, restricting their luminal colonization13. Second, symbiotic
microorganisms stimulate immune responses against
pathogens. For example, invasion and dissemination of
Salmonella enterica subsp. enterica serovar Typhimurium
are limited by immune responses induced by the stimulation of epithelial Toll-like receptors (TlRs) by symbiotic
bacteria25. Intestinal commensal microorganisms also
direct a protective immune response against the protozoan parasite Toxoplasma gondii by activating cytokine
production by dendritic cells (Dcs)15.
Box 1 | Characterizing the intestinal microbiota
For decades, our understanding of the composition of intestinal microbial communities
was based on the enumeration and characterization of culturable organisms. However,
this approach left substantial gaps in the catalogue of intestinal bacterial species, as
most gut organisms are resistant to culture by available methods. The recent
development of molecular profiling methods, including high-throughput sequencing
of microbial 16S ribosomal RNA genes, has revolutionized the understanding of the
intestinal microbiota through culture-independent analyses of microbial community
composition. These methods have allowed unprecedented insight into the make-up
and diversity of intestinal microbial communities, and have even led to the
identification of new bacterial species97.
Molecular profiling of the human intestinal microbiota has revealed a high level of
variability between individuals at the bacterial species level. This argues against the
hypothesis that the human microbiota comprises a ‘core’ group of bacterial species
that is common among all individuals. Nevertheless, common patterns emerge when
microbial communities are compared at higher-level taxa. Firmicutes and
Bacteroidetes are the predominant intestinal phyla across all vertebrates5. The
intestinal Firmicutes are Gram-positive bacteria, dominated by species belonging to
the Clostridia class, but also include Enterococcaceae and Lactobacillaceae families
and Lactococcus spp.97. Intestinal Bacteroidetes are Gram-negative bacteria comprised
of several Bacteroides species, including Bacteroides thetaiotaomicron,
Bacteroides fragilis and Bacteroides ovatus97. The remaining intestinal bacteria,
accounting for less than 10% of the total population, belong to the Proteobacteria,
Fusobacteria, Actinobacteria, Verrucomicrobia and Spirochaetes phyla and a bacterial
group that is closely related to Cyanobacteria5,97. The species variability among
individuals has important implications for understanding intestinal immune system
function, as it indicates that the mucosal immune system must be able to flexibly and
rapidly adapt to a microbiota, the composition of which may change in unpredictable
ways as a function of host diet or other interactions with the external environment.
Being a member of the resident intestinal microbial
community does not necessarily imply that a particular species has an entirely benign disposition towards
its host. Although many gut microorganisms establish
mutually beneficial relationships with their hosts, specific members of the microbiota may exist at different points on the continuum between mutualism and
pathogenicity. For example, Enterococcus faecalis is a
Gram-positive bacterial species that is a prominent
member of the human intestinal microbiota, but it can
opportunistically invade mucosal tissues to cause bacteraemia and endocarditis14. Similarly, Bacteroides fragilis
is a prominent Gram-negative member of the microbiota that closely associates with mucosal surfaces and
opportunistically invades intestinal tissues16. Although
both E. faecalis and B. fragilis are controlled in healthy
people, they pose a serious threat of invasion and disease
in immunodeficient individuals.
Intestinal homeostasis
The relationship of the microbiota and the intestinal
immune system is often described as ‘homeostatic’. In
other physiological contexts, homeostasis refers to an
equilibrium set point (such as blood sugar level) that is
maintained by positive and negative biological feedback
processes in the face of changing conditions. Similarly,
intestinal host–microorganism homeostasis involves
minimizing the adverse health effects of intestinal
microorganisms, even during environmental perturbations such as shifts in microbial community structure,
changes in host diet or overt pathogenic challenge. This
involves ensuring that resident bacteria breach the barrier
as rarely as possible; those that do invade are killed rapidly and do not penetrate to systemic sites. In this Review,
we suggest that intestinal homeostasis is maintained by a
hierarchy of three immunological barriers, each of which
encompasses a distinct set of immune mechanisms. First,
there are immune mediators that limit direct contact
between the intestinal bacteria and the epithelial cell
surface, decreasing the likelihood of tissue invasion. A
second layer of immune protection involves the rapid
detection and killing of bacteria that manage to penetrate
intestinal tissues. Finally, a third set of immune responses
minimizes exposure of resident bacteria to the systemic
immune system. This occurs by distinctive anatomical
adaptations that contain penetrant bacteria within the
mucosal immune compartment and help to maintain
systemic immune ‘ignorance’ towards the microbiota.
Minimizing bacteria–epithelial cell contact
A key element of the mammalian intestinal strategy for
maintaining homeostasis with the microbiota is to minimize contact between luminal microorganisms and the
intestinal epithelial cell surface. This is accomplished by
enhancing the physical barrier through the production
of mucus, antimicrobial proteins and IgA (FIG. 1).
The mucus layer. Goblet cells are specialized epithelial cells that secrete mucin glycoproteins. These
mucins assemble into a viscous gel-like layer that
extends up to 150 μm from the intestinal epithelial cell
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surface, forming two structurally distinct strata17 (FIG. 1).
visualization of spatial relationships between mucus,
bacteria and the epithelium indicates that the inner
mucus layer delineates a protected zone at the apical
epithelial cell surface, whereas the outer mucus layer
contains large numbers of bacteria17. Thus, the inner
layer is resistant to bacterial penetration, limiting direct
bacterial contact with epithelial cells. mice engineered
to lack the mucin glycoprotein muc2 do not have this
bacteria-free zone and suffer from spontaneous intestinal inflammation17,18, emphasizing the importance of
the mucus barrier in maintaining a symbiotic relationship with the microbiota.
Several pathogens have evolved specific strategies for
penetrating mucus in order to gain access to the epithelial
cell surface. For example, Helicobacter pylori uses urease
to increase the pH in its immediate microenvironment,
which in turn lowers mucus viscosity allowing the organism to propel itself through the mucus layer that coats the
stomach wall19. other pathogens, such as Campylobacter
jejuni and Salmonella spp., use their flagella to penetrate
intestinal mucus20. However, it is important to note that
flagella and mucus penetration are not sufficient for pathogenicity, as most commensal intestinal Firmicutes also
have flagella, and some also penetrate the mucus layer to
colonize the intestinal surface21.
Defensin
A class of antimicrobial peptide
that has activity against
Gram-positive and
Gram-negative bacteria, fungi
and viruses. α-defensins are
produced by intestinal Paneth
cells and neutrophils, and
β-defensins are expressed by
most epithelial cells.
C-type lectin
An animal receptor protein
that binds to carbohydrates,
frequently in a Ca2+-dependent
manner. The binding activity of
C-type lectins is based on the
structure of the carbohydraterecognition domain, which is
highly conserved among
members of this family.
Paneth cells
A specialized epithelial cell
lineage that produces most of
the antimicrobial proteins in
the small intestine.
Antimicrobial proteins. A second immune mechanism
that limits bacteria–epithelial cell contact is the secretion of antimicrobial proteins by gut epithelial cells
(FIG. 1). epithelial cell-derived antimicrobial proteins are
members of diverse protein families, including defensins,
cathelicidins and C-type lectins. most of these proteins
kill bacteria directly through enzymatic attack of the
bacterial cell wall or by disrupting the bacterial inner
membrane. In addition, a limited subset of antimicrobial
proteins, including lipocalin 1, function by depriving
bacteria of essential heavy metals such as iron22.
Antimicrobial proteins are produced by virtually
all intestinal epithelial cell lineages, including enterocytes, goblet cells and Paneth cells. The expression of
different subsets of antimicrobial proteins is regulated
by distinct mechanisms (FIG. 2). Several antimicrobial
proteins, including most α-defensins, are expressed
constitutively and do not require bacterial signals for
their expression23. However, the expression of a key
subset of antimicrobial proteins is controlled by bacterial signals through the activation of pattern recognition receptors, which recognize molecular patterns that
are unique to bacteria and other microorganisms. For
example, epithelial TlRs govern the expression of the
antimicrobial c-type lectin regenerating islet-derived
protein 3γ (ReG3γ) in the small intestine24,25. likewise,
nucleotide-binding oligomerization domain-containing
protein 2 (noD2) controls the expression of a distinct
subset of α-defensins and defensin-related cryptdins by
Paneth cells26.
Biochemical measurements of antimicrobial activity
indicate that antimicrobial proteins secreted by epithelial
cells are retained in the mucus layer and are virtually
absent from the luminal content27. This suggests that the
Lumen
Outer
mucus
layer
Inner
mucus
layer
Bacterium
Mucin glycoproteins
(assemble to form
mucus layers)
IgA
Antimicrobial
proteins
Transcytosis
Lamina
propria
Enterocyte Goblet
cell
IgA-secreting
plasma cell
Figure 1 | Immune mechanisms
that limit bacteria–
Nature Reviews | Immunology
epithelial cell interactions. Several immune
mechanisms work in concert to limit contact between
the dense luminal microbial community and the
intestinal epithelial cell surface. Goblet cells secrete
mucin glycoproteins that assemble into a thick, stratified
mucus layer. Bacteria are abundant in the outer mucus
layer, whereas the inner layer is resistant to bacterial
penetration. Epithelial cells (such as enterocytes, Paneth
cells and goblet cells) secrete antimicrobial proteins that
further help to eliminate bacteria that penetrate the
mucus layer. Plasma cells secrete IgA that is transcytosed
across the epithelial cell layer and secreted from the
apical surface of epithelial cells, limiting numbers of
mucosa-associated bacteria31 and preventing bacterial
penetration of host tissues32,33.
mucus layer protects the epithelial cell surface in at least
two ways: first, by limiting the access of luminal bacteria
to the epithelium, and second, by forming a diffusion
barrier that concentrates antimicrobial proteins near the
epithelial cell surface. This probably increases the effectiveness of antimicrobial proteins in protecting the apical
surfaces of epithelial cells from microbial colonization.
The suggestion that epithelial cell-derived antimicrobial proteins function primarily to protect this surface
niche is supported by in vivo genetic studies of Paneth
cells. Genetic ablation of these cells through Paneth cellspecific expression of a diphtheria toxin transgene 20
results in increased penetration of the epithelial cell
barrier by both symbiotic and pathogenic bacteria.
However, the number of luminal bacteria is not altered
by the loss of Paneth cells, suggesting that Paneth cellderived antimicrobial factors do not reach bacteria that
are confined to the intestinal lumen25.
Several gastrointestinal pathogens have evolved
specific resistance mechanisms against antimicrobial
proteins that facilitate the invasion of these organisms
across the epithelial cell barrier. For example, Listeria
monocytogenes deacetylates its peptidoglycan, allowing it to evade enzymatic attack by lysozyme, a cellwall degrading enzyme secreted by intestinal epithelial
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Constitutive expression TLR-dependent expression
NOD2-dependent expression
Bacteria
Bacterial
killing
α-defensins
Microorganismassociated
molecular
pattern
TLR
REG3γ
MYD88
Muramyl
dipeptide
Subset of
α-defensins
NOD2
Paneth cell
Enterocyte
Figure 2 | Regulation of antimicrobial protein expression. Antimicrobial proteins are
produced by virtually all intestinal epithelial cell lineages. Several
antimicrobial
proteins,
Nature
Reviews | Immunology
including most α-defensins, are expressed constitutively and do not require bacterial
signals for their expression23,26. The expression of the antimicrobial C-type lectin
regenerating islet-derived protein 3γ (REG3γ) is controlled by microorganism-associated
molecular patterns that activate Toll-like receptors (TLRs) and is dependent on the
common TLR signalling adaptor molecule myeloid differentiation primary-response
protein 88 (MYD88)24,25. REG3γ expression is activated in both enterocytes and Paneth
cells25. The expression of a subset of α-defensins and defensin-related cryptdins is
controlled by nucleotide-binding oligomerization domain-containing protein 2
(NOD2)26,90. NOD2 localizes to the cytoplasm of Paneth cells98 and recognizes muramyl
dipeptide99, a constituent of bacterial peptidoglycan.
Peyer’s patches
Groups of lymphoid nodules
present in the small intestine
(usually the ileum). They occur
massed together on the
intestinal wall, opposite the
line of attachment of the
mesentery. Peyer’s patches
consist of a dome area, B cell
follicles and interfollicular T cell
areas. High endothelial venules
are present mainly in the
interfollicular areas.
Lamina propria
Connective tissue that
underlies the epithelium of the
mucosa and contains various
myeloid and lymphoid cells,
including macrophages,
dendritic cells, T cells and
B cells.
Plasma cell
A non-dividing, terminally
differentiated, immobile
antibody-secreting cell of the
B cell lineage.
cells28. Similarly, S. Typhimurium evades the membrane
disruptive activity of some antimicrobial peptides by
modifying the lipid A moiety of lipopolysaccharide,
which is present in the Gram-negative outer membrane29. S. Typhimurium also expresses specific factors
(from the iroBCDEN gene cluster) that allow it to evade
lipocalin 2 (also known as nGAl), an epithelial antimicrobial protein that functions by blocking bacterial
iron acquisition30.
IgA. A third mechanism for sequestering symbiotic bacteria involves IgA (FIG. 1). Secreted IgA limits bacterial
association with the intestinal epithelial cell surface31
and restricts the penetration of symbiotic bacteria across
the gut epithelium32. IgA specific for intestinal bacteria
is produced with the aid of Dcs that sample bacteria at
various mucosal sites (FIG. 3; BOX 2). Dcs located beneath
the epithelial dome of Peyer’s patches sample bacteria
that penetrate the overlying epithelium33. Lamina propria
Dcs also actively sample the small numbers of bacteria
that are present at the apical surfaces of epithelial cells,
allowing them to monitor bacteria that associate with
the mucosal surface34,35. The bacteria-laden Dcs induce
B cells to differentiate into plasma cells that produce
IgA specific for intestinal bacteria. Although these Dcs
migrate from the Peyer’s patches and lamina propria
to the mesenteric lymph nodes, they do not penetrate
further into the body 33. IgA+ plasma cells translocate
from lymphoid sites to the intestinal lamina propria and
secrete IgA, which is transcytosed across the epithelial
cell layer. The transcytosed IgA binds to bacteria on the
luminal side of the epithelial cell barrier, limiting bacterial association with the epithelium31 and preventing
bacterial penetration of host tissues32. The exact mechanisms by which IgA carries out these functions remain
unclear but may involve trapping of bacteria in the
mucus layer or promoting rapid phagocytic clearance
of organisms that penetrate the epithelial cell barrier 36.
Immune responses to penetrant bacteria
Although mucus, antimicrobial proteins and secretory
IgA work together to protect intestinal epithelial cell barriers from direct bacterial contact, the vast numbers of
intestinal bacteria means that occasional breaches of this
barrier are inevitable. A second crucial layer of intestinal
immune protection relies on the rapid detection and killing of bacteria that penetrate beyond the epithelial cells.
This occurs by several distinctive immune mechanisms,
including bacterial uptake and phagocytosis by innate
immune cells and T cell-mediated responses.
Phagocytic killing. commensal microorganisms that
breach the intestinal epithelial cell barrier typically
succumb to rapid phagocytosis and elimination by
lamina propria macrophages. macrophages are present
in high numbers in the mammalian gastrointestinal
tract and are frequently in close contact with the epithelium37. These cells rapidly phagocytose bacteria
and kill the ingested organisms through mechanisms
that include antimicrobial proteins and reactive oxygen
species38. Although macrophages from many tissue sites
(such as the bone marrow) secrete pro-inflammatory
mediators that recruit neutrophils and activate T cells,
intestinal macrophages do not mediate strong proinflammatory responses following bacterial recognition, despite retaining efficient phagocytic and
bactericidal functions33,39. This probably reflects an
evolutionary adaptation by these cells to the high bacterial load in the gut, preventing potentially damaging
pro-inflammatory responses from being activated
under normal, homeostatic conditions.
Although, typically, penetrant commensal microorganisms are rapidly killed by phagocytic cells, evasion or suppression of phagocytic killing is a virulence
strategy that is frequently used by intestinal pathogens,
allowing them to escape the intestinal lumen where
they are poorly adapted to compete with commensal
microorganisms for luminal nutrients. Salmonella spp.
and Shigella spp., for example, actively downregulate
the microbicidal mechanisms of macrophages, allowing the pathogens to survive and replicate in host
tissues 40. The susceptibility of commensal microorganisms to the antimicrobial mechanisms of macrophages is probably important for promoting mutually
beneficial relationships with their hosts, as evasion of
phagocytic killing could damage host tissues and perhaps compromise the microorganisms’ own intestinal
niche. Susceptibility to macrophage antimicrobial mechanisms may thus reflect an evolutionary co-adaptation to
the host that increases the overall evolutionary fitness of
symbiotic bacteria41.
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Lumen
Bacteria
Epithelial cell
M cell
Transcytosis
T cell
Lamina
propria
DC
IgA
B cell
IgA+
B cell
Peyer’s patch
Migrating DCs can
induce B and T cell
activation in the
mesenteric lymph nodes
IgA+
B cell
IgA+
plasma
cell
Recirculation of
B cells through
lymph and blood
Mesenteric lymph node
DCs do not
recirculate through
lymph and blood
Figure 3 | Production of IgA directed against intestinal bacteria. Dendritic
cells (DCs) sample bacteria at various sites. DCs located beneath
the epithelial
Nature Reviews
| Immunology
dome of Peyer’s patches take up bacteria that penetrate the overlying epithelium33.
Lamina propria DCs actively sample the small numbers of bacteria that are present
at the apical surfaces of epithelial cells by extending their dendrites between the
epithelial cells34,35. The bacteria-laden DCs migrate to Peyer’s patches and
mesenteric lymph nodes where they induce B cells to differentiate into IgA+ plasma
cells. IgA+ plasma cells home to the lamina propria and secrete dimeric IgA that is
transcytosed across the epithelial cell layer and binds to intestinal bacteria, limiting
bacterial association with the epithelium31 and preventing bacterial penetration of
host tissue32. M cell, microfold cell.
Transcytosis
Process of transport of
material across a cell
monolayer by uptake on one
side of the cell into a coated
vesicle, which might then be
sorted through the trans-Golgi
network and transported to the
opposite side of the cell.
Germ-free mouse
A mouse that is born and
raised in isolators, without
exposure to microorganisms.
Intestinal macrophages have a second important
role in maintaining symbiotic relationships with the
intestinal microbiota by helping to restore the physical
integrity of the epithelial cell barrier following injury.
The presence of a dense resident microbiota means that
gut epithelial cell damage can quickly lead to bacterial
penetration, inflammation and sepsis. mouse models of intestinal epithelial cell damage have revealed
that bacteria that penetrate damaged areas trigger the
expression of a specific repair pathway in macrophages,
inducing them to migrate to the damaged areas and
produce growth factors42. These growth factors interact with the epithelium, triggering vigorous enterocyte
proliferation that fuels the replacement of damaged epithelium with new cells. Bacteria activate this pathway by
engaging TlRs expressed by macrophages42,43, although it
is not yet clear whether internalization of the bacteria is
required or whether the repair pathway can be activated
by detection of extracellular bacteria.
CD4 + T cells. Studies that compare germ-free mice
and bacterially colonized mice show that the adaptive
immune system, in particular the mucosal compartment, is profoundly shaped by the presence of the commensal intestinal microbiota. This includes increases
in the size and number of germinal centres in Peyer’s
patches44 and in the numbers of IgA-secreting plasma
cells45, lamina propria cD4+ T cells and αβ T cell receptor (TcR)-expressing intraepithelial cD8αβ+ T cells46,47.
In addition, the presence of commensal microorganisms
in the intestine is tolerated without an acute neutrophil inflammatory infiltrate in both healthy mice and
humans. cD4+ regulatory T (TReg) cells are an essential
component of this mutualism.
The two main subtypes of TReg cells are cD4+FoXP3+
TReg cells that are found in the colon and small intestinal
lamina propria and cD4+FoXP3–Il-10+ TReg cells that are
found in the small intestinal intraepithelial and lamina
propria compartments48. evidence for the key role of TReg
cells in intestinal immune regulation against commensal
microorganisms came originally from two types of mouse
model, and in both cases immune regulation is only
necessary when mice are colonized with intestinal
microorganisms. First, there is spontaneous intestinal inflammation in mice with specific deficiencies in
regulatory cytokines (such as interleukin-10 (Il-10)49
and transforming growth factor-β (TGFβ)50) or in factors that determine TReg cell thymic selection (such as
autophagy-related gene 5 (ATG5)), differentiation
and/or function (such as forkhead box P3 (FoXP3) or
αvβ8 integrin)51. Second, there are mouse models in which
chronic intestinal inflammation is induced — for example, by the transfer of naive colitogenic cD45RBhicD4+
T cells into recombination-activating gene (Rag) deficient or
severe combined immunodeficient (ScID) mice, which are
lymphopenic — and is rescued by the co-transfer of TReg
cell populations. The TReg cell-mediated rescue verifies the
in vivo requirements for TReg cell-derived factors (such as
Il-10 (ReFs 52–54) or TGFβ55) by analysing the suppressive ability of TReg cells from genetically targeted and conditioned mice in chronic intestinal inflammation. There
is also evidence that TReg cell populations are induced
by intestinal bacteria56 or their molecular products,
such as the polysaccharide A carbohydrate expressed by
B. fragilis 57 and the non-culturable clostridia-related
segmented filamentous bacteria58. The expression of regulatory cytokines such as TGFβ and Il-10 is not restricted
to TReg cells, but the induction of TReg cells by commensal
microorganisms and the occurrence of intestinal inflammation in their absence indicate that TReg cells determine
the threshold between non-inflammatory homeostasis
and intestinal inflammation. The difference between
these two states is important functionally: during intestinal inflammation there is a dramatic infiltrate of neutrophils and lymphocytes into the intestinal mucosa
with increased epithelial cell proliferation and enhanced
secretion of mucus and electrolytes. These inflammatory changes are necessary to eliminate invasive mucosal
pathogens, but must usually be avoided if the intestine
is to function properly in the presence of non-invasive
luminal commensal microorganisms.
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Box 2 | Intestinal dendritic cells
Dendritic cells (DCs) are immune cells with characteristic projections (dendrites) acquired during development
and are specialized for antigen presentation to B and T cells. For this they load peptide antigens onto MHC class II
molecules that engage with the T cell receptor and provide co-stimulatory signals through, for example,
B7 molecules on the DC and CD28 on the T cell. DCs can also stimulate T cells indirectly; for example, by secreting
interleukin-12 (IL-12) to promote the differentiation of the CD4+ T helper 1 (TH1) cell subset. DCs also stimulate
B cells through expression of tumour necrosis factor family ligands, including a proliferation-inducing ligand
(APRIL) and B cell-activating factor (BAFF). Conversely, when loaded with food proteins, in the absence of
activating molecules (such as Toll-like receptor ligands from microorganisms), intestinal DCs promote the
peripheral tolerance of B and T cells.
Intestinal DCs constitutively produce retinoic acid, which promotes mucosal IgA class switch recombination
(in B cells) or FOXP3– CD4+ regulatory T cell differentiation and programmes intestinal B and T cells to express
CC-chemokine receptor 9 (CCR9), which in turn regulates their homing from the blood back into the mucosa.
In the intestine, DCs are present in the lymphoid follicles (such as Peyer’s patches) adjacent to the epithelial cell layer
and in the lamina propria beneath the epithelial cell layer. They can be separated into different classes depending on
surface marker expression (classically CD11chiCD11b+CD8α–, CD11chiCD11b–CD8α+ and CD11chiCD11b–CD8α– DCs)
with distinct histological distributions and functional responses. CCR6 regulates DC homing to Peyer’s patches and a
large proportion of intestinal DCs express surface CD103 (also known as αE integrin).
It has been shown that intestinal DCs can extend dendrites between contiguous epithelial cells to sample
the external luminal milieu. Activated DCs show CCR7-dependent migration to draining lymph nodes, and, in the
case of intestinal DCs, there is a constant traffic of cells from the mucosa to the mesenteric lymph nodes. Most
CD103+ DCs in the mesenteric lymph nodes have probably trafficked from the lamina propria.
In contrast to macrophages, DCs have poor biocidal activity, so after sampling commensal microorganisms the live
bacteria are not immediately killed but persist within the DCs and can be transported to the mesenteric lymph
nodes. Because DCs have a short lifespan, bacteria-laden DCs, and therefore bacteria, do not reach central systemic
lymphoid structures. This is a mechanism that limits the induction of mucosal immunity by commensal microorganisms
to the mucosal immune system, with the mesenteric lymph nodes functioning as a type of immune ‘firewall’.
Germinal centre
Located in peripheral lymphoid
tissues (for example, the
spleen), these structures are
sites of B cell proliferation and
selection for clones that
produce antigen-specific
antibodies of higher affinity.
Recombination-activating
gene
(Rag). A gene expressed by
developing lymphocytes. Mice
that are deficient for either
Rag1 or Rag2 fail to produce
B or T cells owing to a
developmental block in the
gene rearrangement that is
necessary for antigen receptor
expression.
Severe combined
immunodeficiency
(sCID). A phenotype of mice
with a defect in DNA
recombination. sCID mice lack
B and T cells and do not reject
tissue grafts from allogeneic
and xenogeneic sources.
A balance between the function of TReg cells and the
cD4+ effector T cells in the intestinal mucosa is also
crucial for homeostasis. Based on the signalling molecules and transcription factors responsible for their
differentiation and their signature cytokines59, the characteristics of T helper 1 (TH1), TH2, TH17 and TReg cells
are summarized in FIG. 4. The differentiation of both
TH17 and FoXP3+ TReg cells requires TGFβ, although
Il-6 produced by Dcs and macrophages in response
to bacterial molecules, including cpG-containing
oligodeoxynucleotides, drives the differentiation of the
TH17 cell lineage. In the colon, FoXP3+ TReg cells can
express Il-10, which reciprocally inhibits TH17 and TH1
cells. In the small intestine, another FoXP3– regulatory
T cell subset, referred to as TR1 cells, is also stimulated
by Il-6 to express Il-10 (FIG. 5).
TReg cell-mediated regulation of effector T cells is
important, as there is a substantial population of TH1
cells in the mucosa, where they are induced by the intestinal microbiota, notably by polysaccharides produced
by Bacteroides spp.60,61. The differentiation of TH17
cells in the mucosa also depends on the microbiota11;
however, this differentiation is driven only by a limited subset of commensal bacterial species, including
mucosa-adherent segmented filamentous bacteria21,58.
constitutive expression of the p40 subunit of Il-12 or
Il-23, which are involved in the differentiation of TH1
and TH17 cells, respectively, by lower-small-intestinal
cD8α–cD11b–cD11c+ lamina propria Dcs has also
been shown to be triggered by the uptake of intestinal
microorganisms62. These results are consistent with
the hypothesis that T H1 and T H17 cells are needed
for the elimination of the small numbers of commensal
microorganisms that penetrate the surface epithelial cell
layer. Indeed, mice deficient in T cells have increased
persistence of translocated commensal bacteria in the
mucosal tissues63.
Another key function of mucosal T cells is to enhance
the antimicrobial functions of phagocytic cells and epithelial cells. As discussed above, efficient microbicidal
activity by phagocytic cells is essential to avoid opportunistic infections from those commensal organisms
that penetrate the epithelial cell layer. The production
of interferon-γ (IFnγ) by TH1 cells enhances macrophage activation. macrophages and Dcs that have been
activated by microbial products secrete Il-12, which has
a positive feedback effect on TH1 cell-dependent IFnγ
expression. Similarly, TH17 cells secrete Il-22, which
limits commensal antigen exposure by enhancing the
expression of antimicrobial proteins. TH17 cells also
produce Il-17A and Il-17F (which promote neutrophil
recruitment and activation) (FIG. 5) and Il-21 (which
inhibits TReg cell generation)64. mucosal TH2 cells are not
frequently found in healthy humans and in animals that
do not harbour parasites, probably owing to limited Il-4
production in the normal mucosa and antagonism from
TH1 cell-derived IFnγ. A further twist in the complex
interactions between TH cell subsets is shown by observations that these subsets are not necessarily terminally
differentiated but that there can be conversion from
TH17 to TH1 cells and TReg to TH17 cells65,66.
We have discussed homeostasis between T cell subsets in the mucosa as if all commensal microorganisms
are completely benign. In fact, asymptomatic carriage of
potential intestinal pathogens is seen in both mice and
humans; for example Clostridium difficile-associated
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Naive T cell
CD4+
FOXP3–
IL-12
TGFβ
IL-6
IL-4
IL-6
TGFβ
No IL-6
T-bet
GATA3
RORγt
MAF
FOXP3–
FOXP3+
TH1 cell
TH2 cell
TH17 cell
TR1 cell
TReg cell
IFNγ
IL-4
IL-5
IL-13
IL-17A
IL-17F
IL-6
IL-10
TGFβ
Figure 4 | CD4+ T cell subset differentiation. CD4+ T cells differentiate in response to
Nature Reviews | Immunology
cytokine-induced signals mediated by characteristic transcription
factors. Each subset of
+
CD4 T cells produces the characteristic cytokine profile shown. Interleukin-23 (IL-23)
enhances effector function of the T helper 17 (TH17) cell subset, but it does not determine
TH17 cell differentiation per se (not shown). The two classes of CD4+ regulatory T cells,
conventional regulatory T (TReg) cells and TR1 cells, are characterized by the presence or
absence of expression of the transcription factor forkhead box P3 (FOXP3), respectively.
Although CD4+ T cell subsets have traditionally been seen as terminally differentiated
cells, evidence for conversion from TH17 cells to TH1 cells and possibly from TReg cells to
TH17 cells suggests plasticity between the subsets65,66. GATA3, GATA-binding protein 3;
MAF, macrophage-activating factor; RORγt, retinoic acid receptor-related orphan
receptor-γt; TGFβ, transforming growth factor-β.
Intraepithelial CD8αα+ T cell
A type of T cell that is found in
the intestinal epithelium. The
CD8 molecule that they
express is a homodimer of
CD8α, rather than the CD8αβ
heterodimer that is expressed
by conventional CD8+ T cells in
the lymph nodes. It has been
proposed that these cells are
self-reactive T cells that have
regulatory properties.
colitis can be triggered by antibiotic usage. Therefore, it
is important to briefly consider the differences between
the murine models in which most of the mechanisms of
mucosal immune regulation have been investigated and
the ‘real life’ situation. To standardize the colonies and to
eliminate pathogens, mice and rats can be maintained
with a highly restricted ‘modified Schaedler’ microbiota,
which is limited to eight fastidious culturable bacterial
species introduced into a germ-free colony by inoculation from a pure culture. The ideal of having a fixed
microbiota in this way is rarely achieved, as other species become established in most colonies through human
handling. nevertheless, the simple microbiota in most
immunological studies is completely different from a
‘wild’ or ‘human’ situation where a less simplistic microbiota is present that can potentially evade host immunity
to establish an infection. one method to more accurately
model the natural situation is the ‘infection’ of mice with
Helicobacter hepaticus. Helicobacter spp. are an example
of potential pathogens and are endozoonotic in wildtype mouse colonies. H. hepaticus causes an enteropathy
in ScID or Rag–/– mice and this disease can be attenuated by the transfer of cD4+ TReg cells67. H. hepaticus also
causes colitis in Il-10-deficient mice, protection from
which can be mediated by the transfer of cD4+ TReg cells
from H. hepaticus-infected (but not uninfected) wildtype mice68. Furthermore, treatment with a neutralizing
Il-10-specific antibody can initiate colitis in H. hepaticusinfected wild-type mice69. The colitogenic T cells in
these mice have TH1 and TH17 cell characteristics, and
disease is attenuated if recipient mice lack the p19 subunit of Il-23 or are infused with TReg cells69,70. Together,
these data suggest that mildly pathogenic constituents
of the intestinal microbiota may be actively tolerated in
the intestinal lumen, provided they do not reach a threshold of penetration into the intestinal mucosa, and that
Il-10 and TReg cells have an important role in maintaining
this homeostasis.
Three main points emerge from the discussion of
the balance between different subsets of cD4+ T cells
in the intestinal mucosa. First, regulatory responses
mediated by TReg cell subsets are necessary for homeostasis, especially in the presence of more potentially
pathogenic microbial constituents in the microbiota.
Second, the complexities of cellular and cytokinemediated regulatory mechanisms induced by constituents of the intestinal microbiota are compounded by
the interconversion of individual cD4+ T cell subsets,
which is now starting to be explored. It is also not clear
whether this regulation of cD4+ T cell subsets occurs
for all commensal microorganisms in immunocompetent animals or whether it is mainly important in the
presence of microorganisms that have a predisposition
to induce effector T cell subsets (such as segmented
filamentous bacteria). Finally, the downstream effects
of effector T cell subset activation are pleiotropic: TReg
cells can stimulate IgA induction in addition to their
regulatory functions, and T H17 cells also maintain
epithelial cell integrity in addition to their potentially
pro-inflammatory functions.
CD8αα+ γδ and αβ T cell subsets. Because the numbers of
innate immune leukocytes do not alter significantly when
germ-free mice are colonized with a commensal microbiota, evidence for their involvement in host–commensal
mutualism relies on functional data. Intraepithelial CD8αα+
T cells that express a γδ TcR produce keratinocyte growth
factor (KGF) and are required for intestinal epithelial cell
repair following enteropathy induced by dextran sodium
sulphate (DSS)71,72. These cells recognize the stressinduced atypical mHc class I molecules mHc class I
polypeptide-related sequence A (mIcA) in humans or
RAe1 in mice73 through natural killer group 2, member D
(nKG2D)74. In functional genomic studies of purified
γδ T cells, which consist mainly of cD8αα + and
double-negative (cD4 –cD8–) T cells, DSS-induced
damage was shown to trigger a complex transcriptional
programme, including the transcription of heat shock
proteins, cytoprotective factors and antibacterial factors
(including ReG3γ, although KGF was not detected)75.
experiments in germ-free mice showed that this transcriptional programme was largely dependent on the
presence of the intestinal microbiota. The functional consequence was that the translocation of commensal bacterial
to the mesenteric lymph nodes was enhanced in γδ T celldeficient DSS-treated mice (containing a simple microbiota)
compared with wild-type control mice75.
There is also some evidence that the other main
innate cD8αα+ T cell population, which expresses an
αβ TcR, in the intraepithelial compartment may have
similar protective effects for host microbial mutualism,
although the evidence is indirect. When transferred into
lymphopenic recipients, these cD8αα+ αβ T cells protect
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REVIEWS
Mucin and
antimicrobial peptides
NK cell
IL-22
TGFβ
IL-17
IL-22
Phagocytosed
microorganisms
Epithelium
Microbial molecules
and phagocytosed
microorganisms
Microbial molecules
and phagocytosed
microorganisms
CD103+
IL-12
IL-6
IL-6
IL-23
DC
Retinoic
acid
IL-6
Subepithelial
macrophage
TGFβ
IL-10
TNF
Retinoic
acid
IL-12
TGFβ
IL-10
IL-12
IFNγ
TGFβ
TH17 cell
FOXP3– TR1 cell
FOXP3+ TReg cell
IL-17A
IL-17F
Neutrophil
chemotaxis
IL-10
Negative
regulation
TGFβ
Negative
regulation
TH1 cell
IL-10
Figure 5 | Regulatory networks for intestinal CD4+ T cells. T helper 17 (TH17) cells are induced
by transforming
growth
Nature
Reviews | Immunology
factor-β (TGFβ) and interleukin-6 (IL-6) and matured by IL-23 following the activation of intestinal dendritic cells (DCs) by
phagocytosed microorganisms or stimulatory microbial molecules that have crossed the surface epithelial cell barrier
and/or activated epithelial cells. The signature cytokines of TH17 cells, IL-17A and IL-17F, have pro-inflammatory effects
and mediate neutrophil chemotaxis. TH17 cells also express IL-22, which contributes to epithelial homeostasis and
stimulates the secretion of antimicrobial molecules. Acute inflammation is normally avoided through the induction of two
classes of CD4+ regulatory T (TReg) cells that can be differentiated on the basis of their expression of the transcription factor
forkhead box P3 (FOXP3). FOXP3+ TReg cells are induced by retinoic acid produced by CD103+ DCs in the presence of TGFβ.
Conversely FOXP3– TR1 cells are induced by IL-6 but inhibited by retinoic acid. TReg cells secrete IL-10 and/or TGFβ, which
have negative regulatory effects on effector T cells. Commensal bacteria and their associated molecules also stimulate
DCs to secrete IL-12, which activates interferon-γ (IFNγ) secretion by TH1 cells, which in turn activates phagocytic activity
of subepithelial macrophages. NK, natural killer; TNF, tumour necrosis factor.
against colitis in the naive colitogenic cD45RBhicD4+
T cell transfer model of chronic intestinal inflammation
in an Il-10-dependent manner 76. As described earlier,
these colitogenic T cells require the presence of an intestinal microbiota to induce enteropathy, so cD8αα+ αβ
T cells seem to be another regulatory subset relevant for
mucosal immune homeostasis.
Lymphoid-tissue inducer cell
(LTi cell). A cell that is present
in developing lymph nodes,
Peyer’s patches and nasopharynx-associated lymphoid
tissue. LTi cells are required
for the development of these
lymphoid organs and are
characterized by expression of
the transcription factor retinoic
acid receptor-related orphan
receptor-γt (RORγt),
interleukin-7 receptor-α and
lymphotoxin-α1β2.
Intestinal NK cells. Intestinal nK cells have received little attention relative to other lymphocytes, but a population of intestinal nK cells has recently been described
that express nKp46 (also known as ncR1), the Il-15R
β-chain (also known as cD122) and the nK cell receptors
nKG2D and nKG2A77. They have variable levels of nK1.1
(also known as KlRB1c) expression, and they have a phenotype that resembles immature bone marrow nK cells
in that they lack expression of cD3, cD11b (also known
as αm integrin), cD27, lY49c (also known as KlRA3),
lY49D (also known as KlRA4), lY49H (also known as
KlRA8) and lY49G2 (also known as KlRA7). The development of these intestinal nK cells was shown to depend
on the transcription factor retinoic acid receptor-related
orphan receptor-γt (RoRγt), suggesting that they may be
derived from lymphoid-tissue inducer cells. Although they
had only weak conventional nK cell effector functions,
these intestinal nK cells produced Il-22, a cytokine that
is known to promote epithelial cell homeostasis and the
secretion of antimicrobial factors78.
The picture that emerges from the role of these different immune cells and factors in the intestinal mucosa is
one of tightly regulated layers of immunity that can condition epithelial cells to avoid penetration by commensal
microorganisms and/or eliminate the low numbers of
bacteria that penetrate without an acute inflammatory
response. Presumably there is a numerical threshold
beyond which regulatory mechanisms are no longer (or
less) sufficient and inflammatory responses are needed
for the neutralization and clearance of pathogens.
Mucosal immune firewalls
The mucosal immune system has the difficult task of
confining commensal microorganisms to the lumen
of the gut without excessive inflammation while maintaining the ability to clear intestinal infections with an
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REVIEWS
Specific pathogen-free (SPF)
mice
Mice kept in specific vivarium
conditions whereby a number
of pathogens are excluded or
eradicated from the colony.
These animals are maintained
in the absence of most of the
known chronic and latent
persistent pathogens. Although
this enables better control of
experimental conditions
related to immunity and
infection, it also sets apart
such animal models from
pathogen-exposed humans or
non-human primates, whose
immune systems are in
constant contact with potential
pathogens.
appropriate degree of inflammation. It is clear that there
are extensive immune adaptations to intestinal commensal microorganisms and mucosal immune responses are
tightly regulated. The induction of mucosal immunity
depends on some sampling of live commensal microorganisms, particularly by intestinal Dcs that sample the
lumen by passing dendritic processes between the tight
junctions of the epithelial cell layer 34,35 or sample in the
dome of intestinal lymphoid follicles or Peyer’s patches33.
Such leakiness could potentially enhance the risk of
mucosal infection, but both B and T cells can be activated
by low numbers of penetrant bacteria, and commensal
microorganisms are susceptible to phagocyte biocidal
activity 33,79. nevertheless, even for microorganisms that
do not contain pathogenicity islands, expressing proteins
to subvert immune microbicidal mechanisms80, a system
of containment, or ‘firewall’, beneath the epithelial cell
layer is needed.
Where is the boundary of this immune firewall?
The geography of the mucosal immune system is helpful to understand this. Bacteria that enter the blood are
mainly cleared by macrophages in the marginal zones of
the spleen, and those that enter the mesenteric vascular
system are delivered through the portal vein to the liver
and cleared by Kupffer cells. By contrast, bacteria that
are taken up by intestinal Dcs are contained within the
mucosal tissue and can be carried by Dcs to the draining mesenteric lymph nodes, but the bacteria do not
penetrate further to reach systemic secondary lymphoid
structures33. As intestinal Dcs loaded with commensal
bacteria can induce protective secretory IgA33, this system
has the advantage that induction of mucosal immunity
is confined to the mucosal tissue, but the effects of this
induction can be distributed throughout the intestinal
mucosa and other mucosal surfaces through the recirculation of activated B and T cells via the mucosal lymphatics and vasculature before they home back to the mucosal
tissue81–83. The limited biocidal activity of Dcs84 and
their limited lifespan are probably crucial for the system
to function: Dcs can sample intestinal microorganisms
and induce appropriate mucosal immune responses but
the survival of the Dcs containing live microorganisms is
limited (and, hence, so is the potential for infection).
These data indicate that the mesenteric lymph nodes
have a role as a firewall against bacteria that have penetrated epithelial defences or microorganisms that have
been deliberately sampled by intestinal Dcs to induce
mucosal immunity. In wild-type specific pathogen-free
(sPF) mice, the mucosal immune system is primed by
intestinal microorganisms, but the adaptive systemic
immune system remains unprimed (or ignorant)32,85. It is
thought that lymphoid structures are heavily influenced
by the milieu of commensal bacterial molecules that penetrate host tissues, although penetration of live commensal
bacteria and the induction of adaptive immune responses
are absent or limited in immunocompetent hosts47,60. This
adaptive systemic ignorance is lost in SPF mice in which
mesenteric lymph nodes (which are a crucial part of the
firewall) have been surgically removed33. under conditions in which commensal microorganisms can penetrate
and persist in the systemic immune system, for example
in ‘clean’ mice with severe innate immune deficiencies
that affect biocidal activity, or in ‘dirty’ humans with a
diverse microbiota containing some mild pathogens, systemic immune priming is consistent with eliminating the
microorganisms and avoiding sepsis. The compartmentalization of mucosal and systemic priming thus requires
functionality of the intestinal barriers and the innate
immune system. For example, in mice deficient in IgA
expression, serum IgG responses, which are indicative of
a systemic immune response, are spontaneously primed
against commensal bacteria32. Similarly, innate immune
defects, such as a deficiency in the TlR signalling adaptor molecules myeloid differentiation primary-response
protein 88 (mYD88) or TIR-domain-containing adaptor
protein inducing IFnβ (TRIF; also known as TIcAm1),
or the absence of the reactive oxygen burst in phagocytes
also results in serum IgG priming against intestinal commensal bacteria86. The conclusion is that small numbers
of commensal bacteria are probably continuously penetrating the intestinal epithelial cell layer, but they usually
never reach the threshold of priming a systemic adaptive
immune response because of effective phagocytosis and
biocidal activity by phagocytic cells. This is supported by
the occurrence of commensal microorganism-induced
sepsis in mice with defects in phagocyte biocidal activity
and in neutropenic and severely immunocompromised
humans79.
The result of the mesenteric lymph node firewall is
that there is a way for the luminal microbial contents to
be immunologically sampled and for relevant protective
adaptive immune responses to be induced in the intestinal mucosa. The induction is confined to the mucosal
immune system, but the recirculation of B and T cells
through the lymph and blood to home back to mucosal
tissues ensures that the local response is disseminated
and averaged over the mucosal surfaces as a whole.
Immunodeficiency and homeostasis
Inflammatory bowel disease (IBD) comprises a broad
group of disorders that are characterized by severe
inflammation of the intestine. IBD can be defined as
ulcerative colitis or crohn’s disease based on clinical
phenotype criteria obtained from structural and histopathological analysis. Despite the prevalence of the
disease in europe and north America, the exact causes
of IBD remain unclear. However, increasing evidence
suggests that the disease arises from dysregulated control of host–microorganism interactions. For example,
patients with IBD have increased numbers of epithelial
cell surface-associated bacteria87, suggesting a failure of
mechanisms that normally limit direct contact between
the microbiota and the epithelium.
Supporting this hypothesis, several IBD risk alleles
alter epithelial cell innate immune function. one of the
first IBD risk alleles identified was the cytoplasmic pathogen recognition receptor noD2. Polymorphisms in the
NOD2 gene are associated with ileal crohn’s disease88,89.
Patients with NOD2 defects have lower α-defensin expression by Paneth cells, which coincides with severe intestinal inflammation90. one possible model is that decreased
α-defensin production promotes increased association of
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© 2010 Macmillan Publishers Limited. All rights reserved
REVIEWS
bacteria with the epithelial cell surface. This could contribute to uncontrolled inflammation, perhaps in conjunction
with other genetic defects. Similarly, autophagy 16 relatedlike 1 (ATG16l1), encoded by a crohn’s disease risk
allele, contributes to intestinal inflammation by impairing exocytosis of Paneth cell secretory granules, thereby
inhibiting antimicrobial protein release91. The mechanism
by which ATG16L1 contributes to abnormal Paneth cell
exocytosis remains unclear. However, as in the case of
NOD2 risk alleles, defects in ATG16L1 could impair the
ability of Paneth cells to limit bacterial association with
the mucosal surface, thereby increasing the likelihood of
bacterial penetration and mucosal inflammation. Finally,
loss of the transcription factor X-box-binding protein 1
(XBP1), which is required for normal development of
Paneth and goblet cells, triggers spontaneous intestinal
inflammation in mice. Hypomorphic variants of XBP1
are also linked to IBD in humans92 indicating a requirement for normal Paneth and goblet cell development in
intestinal homeostasis.
Together, these studies suggest that defects leading
to reduced antimicrobial protein and/or mucus production may increase the likelihood of bacterial invasion
of the epithelial cell barrier with consequent inflammation. However, it is important to note that epithelial cell
defects, such as genetic Paneth cell ablation, are insufficient to produce inflammation in mice25,93. This suggests that the manifestation of inflammatory disease
in humans may require additional genetic defects that
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Acknowledgements
L.V.H. thanks the students and colleagues from her laboratory for the many discussions that contributed to the ideas in
this manuscript. Work in L.V.H.’s laboratory is supported by
the Howard Hughes Medical Institute, the US National
Institutes of Health (DK070855), the Burroughs Wellcome
Foundation and the Crohn’s and Colitis Foundation. A.M.
acknowledges K. McCoy, E. Slack, S. Hapfelmeier, M. Stoehl
and M. Geuking.
Competing interests statement
The authors declare no competing financial interests.
DATABASES
UniProtKB: www.uniprot.org
ATG16L1 | IL-22 | KGF | lipocalin 1 | lipocalin 2 | MICA | MUC2 |
NOD2 | REG3γ | XBP1
FURTHER INFORMATION
Lora V. Hooper’s homepage : http://www.hhmi.org/
research/investigators/hooper_bio.html
Andrew J. Macpherson’s homepage: http://www-fhs.
mcmaster.ca/medicine/gastro/faculty-member_
macpherson.htm
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