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Box 1 | mutualistic relationships between hosts and their intestinal microbiota
The human intestine harbours an estimated 100 trillion bacteria, 7080% of which cannot yet be
cultured. Each individual is thought to host several hundred species of bacteria from only 7 to 9
phylotypes; these are mainly Gram-positive Firmicutes spp. (most notably Clostridium spp.,
Enterococcus spp. and Lactobacillus spp.) and Gram-negative Bacteroidetes spp. Recent
metagenomics studies predict a core of ~1,200 prevalent species and a total intestinal
microbiome that contains 150-fold more genes than the human genome4. The gut microbiome
encodes a core of redundant bacterial genes that are likely to be needed to resist stressful
conditions in the host intestine63 and to harvest nutrients that are necessary for bacterial
growth2,4. Competition between bacteria with distinct metabolic requirements might explain the
massive and rapid shifts in the structure of the intestinal microbial community that are provoked
by changes in host diet64. In addition to the genes that are necessary for microbial adaptation to
the host environment, the gut microbiome encodes multiple biosynthetic pathways that are
predicted to greatly increase the hosts capacity to metabolize glycans and xenobiotics and to
synthesize vitamins2,4. Moreover, studies in gnotobiotic mice have shown the broad influence of
the gut microbiota on host physiology. Intestinal colonizaton induces a spectrum of intestinal
and metabolic changes, which promote the digestion and absorption of nutrients and stimulate
fat storage65,66, accelerate gut epithelial renewal and alter epithelial locomotor activity67. The
signalling pathways that are involved remain largely elusive, but recent observations suggest
that overlapping mechanisms have been selected during hostmicrobiota co-evolution that
simultaneously control host metabolic and innate immune responses to the microbiota. In mice,
inactivation of Toll-like receptor 5 (TLR5), which is a receptor for bacterial flagellin that has an
established role in host innate immune responses, results in severe obesity and profound
alterations in the microbiota structure68. Furthermore, peroxisome proliferator-activated
receptor- (PPAR), which is a transcription factor that has a central role in glucidolipidic
metabolism, can control the production of microbicidal peptides by colonocytes and serves
as a feedback mechanism for the activation of nuclear factor-B (NF-B) in enterocytes69.
glossary
Ankylosing enthesopathy
IgE-associated allergies
Germinal centres
Highly specialized and dynamic microenvironments that
are located in secondary lymphoid tissues and give rise
to secondary B cell follicles during an immune response.
Germinal centres are the main sites of B cell proliferation
and differentiation, which leads to the generation of
memory B cells and plasma cells that produce high-affinity
antibodies.
Pathobionts
Microbial symbionts that can cause defined disease in
predisposed hosts following changes in the gastrointestinal
environment.
Proteobacteria
Gram-negative microorganisms that colonize very distinct
environments and are the second largest group of bacteria
on earth. Proteobacteria that colonize the intestine include
commensal, pathogenic and opportunistic species, such as
Salmonella, Shigella and Helicobacter spp. and Escherichia
coli strains. In healthy adults, proteobacteria represent less
than 1% of the enteric microbiota, but they are a major
cause of intestinal and extraintestinal diseases.
Peyers patches
Xenobiotics
Microbiome
Gnotobiotic mice
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PersPectives
by Helicobacter hepaticus15,17. Furthermore,
administration of PsA reduced the severity of disease in a model of trinitrobenzene
sulphonic acid (TnBs)-induced colitis17.
Therefore, B. fragilis may represent a prototype peace-keeper strain. Yet the outcome
of hostmicrobiota interactions cannot be
predicted from only the bacterium itself, and
a bacterium that is beneficial for an immunocompetent host can become a dangerous foe
when the immune system is weakened. This
is illustrated by the fact that B. fragilis causes
severe sepsis in immunocompromised hosts.
Likewise, normally harmless members of the
microbiota can initiate intestinal inflammation in individuals who cannot mount efficient intestinal humoral responses18,19 and in
individuals with impaired intestinal immunoregulation, most notably in those who lack a
functional IL-10 signalling pathway 20,21.
Promotion of effector immune responses.
Although certain members of the microbiota
have adopted peace-keeper activities to colonize the intestine, others are, undoubtedly,
endowed with pro-inflammatory properties.
one such group, which has recently attracted
much attention, is segmented filamentous
bacteria (sFB). These unculturable species
settle in the rodent intestine at the time of
weaning and stimulate the postnatal maturation of immune responses in the mouse
gut. Mice that are colonized by a microbiota
that lacks sFB have weaker IgA antibody
responses22 and much poorer intestinal
T cell responses compared with mice that
are colonized with sFB. notably, mice that are
colonized by an sFB-deficient microbiota
lack mucosal TH17 cells10,23. Furthermore,
these animals cannot control colonization by
the invasive pathogen Citrobacter rodentium,
which suggests that microbiota-induced
immune responses participate in the barrier function of the flora23. This hypothesis
is also supported by recent work that shows
that the destruction of the microbiota following treatment with antibiotics can jeopardize innate immune responses in the gut
and promote colonization by pathogens24.
A striking feature of sFB is their strong
adherence to the surface epithelium of the
ileum and the Peyers patches shortly after
weaning 25. This is in contrast with most other
members of the microbiota, which remain
entrapped within the mucus and have little
or no physical contact with host epithelium25.
This attachment, which is perhaps necessary
to initiate the replication of sFB, is likely to
facilitate the sampling and presentation of
sFB antigens to T cells by DCs in the Peyers
patches and to stimulate pro-inflammatory
PAMP
Bacterium
TLR
Intestinal lumen
Intestinal
epithelial cell
MYD88
Expression of IRAK1
decreased by LPS
from microbiota
IRAK1
ROS induced by
microbiota inhibit
ubiquitin ligases
IB ubiquitylated and
targeted to the proteasome
for degradation
IB
p50 p65
NF-B
Nuclear translocation
of NF-B
p50 p65
p65 PPAR
PPAR
NF-B transcribes
pro-inflammatory
cytokines and
chemokines and
defensins
PPAR induced in
response to microbiota
LPS diverts NF-B
from nucleus
PPAR upregulates
colonic -defensins
to sustain gut barrier
Pathway impaired
in patients with
Crohns disease
PersPectives
a
M cell
Intestinal lumen
Bacterium
MHC
Peptide
Intestinal epithelium
TCR
Naive T cell
CX3CR1expressing
phagocyte
Direct sampling of
bacteria in lumen?
Antigen transfer?
Lamina propria
CD103+
Peyers patch
DC
c
IgA molecules are
transcytosed by polymeric
IgA receptors and retain
bacteria in the mucus
B. fragilis
TLR
Mucus layer
Dimeric
secretory
IgA
SFB
Microbiotaderived products
activate TLRs
BAFF,
APRIL
TSLP,
TGF,
retinoic
acid
ATP
SAA
TReg cell
induction
Epithelial
cell
B. fragilis capsular
polysaccharide A
Tolerogenic DC
Inflammatory
DCs
FOXP3
TReg cell
+
IL-12
IL-1, IL-6,
IL-23
TH17 cell
SFB induce
IL-12-producing
DCs by unknown
mechansims
TH1 cell
secretory igA molecules form immune complexes with bacteria, which are
then retained in the mucus. c | cD103+ Dcs are conditioned by epithelial
cell-derived factors, such as thymic stromal lymphopoietin (TsLP), transforming growth factor- (TGF) and retinoic acid, to acquire a tolerogenic phenotype; these Dcs can promote the induction of forkhead box P3 (FOXP3)+
regulatory T (Treg) cells77. Bacteria-derived products, such as the capsular
polysaccharide A from Bacteroides fragilis, can further
induction
Naturepromote
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| Immunology
of interleukin-10 (iL-10)-producing Treg cells through a TLr2-dependent
mechanism15,17. However, some commensal bacteria can stimulate the differentiation of inflammatory mucosal T cells. T helper 17 (TH17) cell differentiation can be promoted by bacteria-derived ATP, which activates a subset of
Dcs that produce iL-1, iL-6 and iL-23 (rEF. 78), or by serum amyloid A protein (sAA), which is an acute phase protein that is produced in response to
segmented filamentous bacteria (sFB)23. sFB can also drive the expansion of
mucosal TH1 cell populations11, presumably by inducing iL-12 production by
Dcs. in addition, inflammatory Dcs might stimulate the conversion of
Treg cells into TH17 and/or TH1 cells in the lamina propria (not shown)79. TH1
and TH17 cells maintain the intestinal barrier by recruiting and activating
macrophages and neutrophils that eliminate penetrating bacteria. iL-22 that
is produced by a subset of TH17 cells can also promote the production of
antibacterial defensins by epithelial cells. M cell, microfold cell.
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PersPectives
unusual symbiont has a particularly important role in shaping the gut immune system
across evolution. However, again, the outcome of sFBhost interactions depends on
the immune status of the host; sFB has been
associated with the development of intestinal
inflammation29 or arthritis30 in mice with
impaired immunoregulation and can also
aggravate experimental autoimmune encephalomyelitis31 (FIG. 3). Interestingly, sFB alone
were not able to induce intestinal inflammation in immunodeficient mice and instead
synergized with a pathogen-free flora. This
finding highlights how interactions in the
microbiota community can influence host
immune responses, thereby adding an
additional level of complexity.
The case of pathobionts. A particular subset of bacteria further exemplifies how the
behaviour of the microbiota is dependent on
the immune status of the host. Although these
bacteria, which are known as pathobionts,
colonize the gastrointestinal tract of many
individuals asymptomatically, they also have
the potential to cause disease. A recent study
showed that Helicobacter hepaticus, which
is a member of the epsilon subgroup of
proteobacteria, uses its type VI secretion system
(T6ss) to regulate bacterial colonization and
inhibit host innate and adaptive immune
responses, thereby actively maintaining
symbiotic relationships with immunocompetent hosts32. However, this bacterium can
cause severe typhocolitis in Il10/ mice or
in the severe combined immunodeficient
(sCID) transfer model of colitis. These
findings highlight the central role of host
adaptive regulatory responses in maintaining symbiotic relationships with the
microbiota32.
In humans, the most classical example
of a pathobiont is Helicobacter pylori, which
uses various mechanisms to dampen host
immune responses and persist in the stomach. Gastric colonization by this bacterium
remains asymptomatic in most individuals and has even been suggested to protect
against the development of oesophageal
carcinomas owing to downmodulation of
gastric acid secretion. Yet this bacterium
is the major cause of gastritis and gastric
cancers. The circumstances that lead to this
bacterium becoming a serious health concern are not completely understood but are
thought to include the selection of specifically aggressive strains and/or host predisposing factors, notably polymorphisms in
gene promoters that increase the production
of tumour necrosis factor (TnF) or IL-1,
which is a pro-inflammatory cytokine
Physiological inflammation
strengthens gut barrier in
immunocompetent hosts
Intestinal inflammation
in SCID mice transferred
with effector T cells
Arthritis in
K/BxN mice
Enhanced
sensitization
following
challenge with
MOG peptide
Increased
severity of EAE
Figure 3 | Effects of SFB colonization on the immune system. segmented filamentous bacteria
(sFB) are spore-forming bacteria that are related to the genus Clostridium28. inherited from the
Nature Reviews | Immunology
mother microbiota, sFB develop strong interactions with the ileal mucosa and in immunocompetent mice, the bacteria can largely recapitulate the inducing effects of the whole microbiota on
the postnatal maturation of the gut immune system. sFB induce the production of reg iii/ microbicidal peptides10,23,80, which protect against colonizing pathogens24. Additionally, sFB simultaneously activate strong secretory igA responses22, induce the recruitment and activation of cytotoxic
intraepithelial lymphocytes (ieLs)81 and drive various T cell responses, including a robust T helper 17
(TH17) cell response11,23. in immunocompetent mice, sFB-induced pro-inflammatory and regulatory
responses balance each other, which results in physiological inflammation that strengthens the
gut barrier. By contrast, colonization by sFB promotes the development of colitis in severe combined immunodeficient (sciD) mice that have been reconstituted with effector T cells29. intestinal
colonization by sFB can also promote the development of inflammatory diseases outside of the
gut. sFB promote arthritis in autoimmune non-obese diabetic (NOD) mice that express a transgenic T cell receptor (Tcr) that is specific for a self peptide (known as K/BxN mice), an effect
ascribed to the induction of TH17 cells 30. sFB also enhance the severity of myelin oligodendrocyte
glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (eAe). These aggravating
effects may reflect the strong adjuvant properties of sFB. Treg cells, regulatory T cells.
PersPectives
of proteobacteria3840. strikingly, comparable
changes in the microbiota have been seen
in mice in which intestinal inflammation
was induced by either an invasive pathogen
or by the injection of transgenic T cells
that attacked the gut epithelium27. In these
two distinct models, host inflammation
suppressed the growth of Firmicutes and
Bacteroides spp., allowing proteobacteria,
which are apparently more resistant to hostderived microbicidal factors, to outcompete
these normally dominant resident bacteria27.
notably, outgrowth of proteobacteria was
Gut
lumen
Physiological microbiota
Peace-keeping
bacterium
Pathobiont
Mucus
Healthy
epithelial
barrier
Damaged epithelial
barrier, increased
bacterial adherence
and penetration
TH1 cell
Lamina
propria
TH17 cell
IgA+
plasma cell TReg cell
Physiological inflammation
Pathological inflammation
Immune
gene variants
NOD2, ATG16L1,
IL-23R, IRGM
Environment
Stress, diet, infections, vaccine?
PersPectives
Effects on the peripheral immune system.
The exact impact of the gut microbiota on
the hosts peripheral immune system is controversial. Two groups have convincingly
shown that specific immune responses to
the intestinal microbiota are largely confined
to the intestinal lymphoid compartment in
immunocompetent mice with an efficient
gut barrier 13,44,45. However, studies comparing mice that were raised in conventional
or germ-free conditions highlight the
importance of the intestinal microbiota for
the development of the peripheral immune
system in immunocompetent hosts. notably,
the spleens of germ-free mice contain fewer
and smaller germinal centres46 and decreased
numbers of memory CD4+ T cells, and
cytokine production by these T cells shows a
TH2-type profile47.
The mechanisms that underlie the
stimulatory effects of the microbiota on the
peripheral immune system of immunocompetent hosts are not well understood.
Recent work suggests that soluble factors
that are produced by the microbiota can
translocate from the gut to the bloodstream
and activate innate immune cells. For
example, the opsonophagocytic activity of
neutrophils is primed by microbiota-derived
peptidoglycan, which results in enhanced
protection against pneumococcal sepsis48.
Moreover, monocolonization with B. fragilis
corrects systemic T cell deficiencies and
the TH1/TH2 imbalance of germ-free mice
due to the stimulation of DC IL-12 production by the bacteriums unusual capsular
polysaccharide47.
Allergy and dysbiosis. The hygiene
hypothesis, which has been revised
several times since its initial formulation by strachan in 1989, stipulates that
decreased exposure to infectious agents,
as well as changes in the intestinal microbiota during infancy, might alter immune
regulatory networks and account for the
dramatic increase in the incidence of
allergic diseases that has been observed in
developed countries49. several studies have
reported differences in the composition
of the faecal microbiota of infants who
develop an allergic disease and those who
do not. notably, a decreased frequency
of Lactobacillus and Bifidobacterium spp.
has been suggested to precede the onset
of allergy 50, and prophylactic approaches,
which are based on the administration of
probiotics to mothers and newborns at
high risk for IgE-associated allergies, have
been initiated. A recent study reports
that 1 month of prenatal and 6 months of
postnatal pre- and probiotic supplementation can reduce the incidence of eczema
and food-specific IgE in a subset of highrisk children who are born by caesarean
section51. This protective effect was not
seen in vaginally delivered children and
was transient, as it was significant at
2 years of age but not by 5 years of age.
The results of such interventions remain
conflicting and a causative link between dysbiosis, which is induced by changes in lifestyle or recent medical practices, and allergy
remains difficult to establish51,52. Moreover,
experimental studies that support the role
of the microbiota in the development of
allergic diseases are still scarce (TABLE 1). one
study has reported increased development
of allergic airway disease in mice that were
treated with a short course of oral antibiotics53. Another interesting study showed that
TLR4 activation by microbiota-derived
LPs was necessary to prevent anaphylaxis
after oral immunization with the peanutderived allergen Arah 1. TLR4-deficient or
antibiotic-treated mice showed an increased
TH2-type skewing of cytokine responses
compared with control mice. Conversely,
activation of TLR9 by oral administration of
CpG oligodeoxynucleotides could abrogate
allergic symptoms and correct the TH1/TH2
imbalance54. However, additional work is
needed to delineate whether and how the
composition of the microbiota might
influence the onset of allergy.
Autoimmunity and the microbiota. The
possibility that the intestinal microbiota is
involved in the development of systemic
autoimmunity has recently attracted growing attention. Changes in the composition of
the gut flora have been reported in patients
in the early phases of rheumatoid arthritis55
when compared with a control group with
fibromyalgia. However, such studies cannot
establish a link between dysbiosis and the
development of disease. Therefore, the role
of the microbiota has been more directly
addressed by comparing the onset and/or
severity of experimental autoimmune diseases in germ-free mice with disease onset
and/or severity in mice that have been
colonized by a diverse microbiota.
In several models of autoimmunity,
the progression of disease was comparable between both sets of mice5658. In
other models, contradictory roles for the
microbiota have been reported (TABLE 1).
The microbiota was shown to trigger
disease in several mouse models of autoimmune arthritis. For example, in a mouse
strain that is prone to the spontaneous
PersPectives
Table 1 | Effect of the microbiota on systemic immune-mediated diseases
model
Animal strain
observed effects
Refs
induction of anaphylactic
symptoms, increased production of
ige and iL-13
54
49,53
Allergy
ige-mediated food allergy Weanling c3H mice or
to peanut allergen
c57BL/6 mice
Tlr4 mutant or Tlr4/ mice
None
systemic lupus
erythematosus
MrL/lpr mice
Germ-free mice
No change in autoimmunity
58
APeceD
Aire/ mice*
Germ-free mice
No change in autoimmunity
56
spontaneous gastritis
Aid/ mice
Germ-free mice
No change in autoimmunity
57
collagenous arthritis
Germ-free rats
61
Germ-free rats
increased severity
Germ-free mice
No disease
Germ-free mice
No disease
No disease
Disease restored
Germ-free mice
No disease
ige-mediated allergic
airway disease induced
by Aspergillus fumigatus
spores or ovalbumin
Autoimmunity
Type 1 diabetes
spontaneous ankylosing
enthesopathy
spontaneous arthritis
Autoimmune arthritis
experimental
autoimmune
encephalomyelitis
Disease restored
None
None
increased severity
Germ-free mice
No disease
Disease restored
Germ-free mice
Weak severity
Maximal severity
intermediate severity
c57BL/6J mice
62
59
60
30
31
Aid, activation-induced cytidine deaminase; Aire, autoimmune regulator; APeceD, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy; iL,
interleukin; Il1Ra, iL-1 receptor antagonist; Myd88, myeloid differentiation primary-response protein 88; NOD, non-obese diabetic; Tlr, Toll-like receptor. *Aire
regulates the transcription of peripheral autoantigens in medullary thymic epithelial cells and is necessary for thymic negative selection; AiD is central for
class-switch recombination and somatic hypermutation in B cells; NOD mice provide a polygenic model of type 1 diabetes; ||Mice with a transgenic T cell receptor
against a self peptide that is derived from glucose-6-phosphate isomerase.
system and the microbiota, and the difficulties in attempting to delineate the
respective roles of host predisposing
factors and specific bacterial species. To
determine the therapeutic implications
of these observations, further research is
needed to elucidate how the microbiota
is able to influence peripheral immune
responses and how such microbiotadriven responses can interfere with the
immunological mechanisms that underlie
a given autoimmune disease.
Conclusion
An increasing number of studies are progressively unravelling the fascinating interactions that occur between eukaryotes and
their bacterial symbionts. It is now clear
that the intestinal microbiota profoundly
influences host metabolic and immune
pathways and participates in human health
and disease. Compelling evidence shows a
pivotal role for the microbiota in the development of many gastrointestinal diseases,
from inflammation to cancer. Recent work
PersPectives
adaptation to new ecological conditions. An
in-depth understanding of the principles
and mechanisms that underlie microbial
community structures and hostsymbiont
relationships will be pivotal for the development of therapeutic approaches that manipulate the intestinal microbiota to maintain
human health.
Nadine Cerf-Bensussan and Valrie Gaboriau-Routhiau
are at the Institut National de la Sant et de la
Recherche Mdicale (INSERM) U989, Universit Paris
Descartes, 156 rue de Vaugirard, 75730 Paris
Cedex 15, France; and the Institut National de la
Recherche Agronomique (INRA) UM1319, Domaine de
Vilvert, 78350 Jouy-en-Josas, France.
Correspondence to N.C.-B.
e-mail: nadine.cerf-bensussan@inserm.fr
doi:10.1038/nri2850
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Acknowledgements
FURTHER INFORMATION
Nadine cerf-Bensussans homepage: http://www.
fondationimagine.org/Nadine-cerf-Bensussan_uk.php
All lInkS ARE ActIvE In thE onlInE PdF
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