ArticlePDF AvailableLiterature Review


Establishing and maintaining beneficial interactions between the host and its associated microbiota are key requirements for host health. Although the gut microbiota has previously been studied in the context of inflammatory diseases, it has recently become clear that this microbial community has a beneficial role during normal homeostasis, modulating the host's immune system as well as influencing host development and physiology, including organ development and morphogenesis, and host metabolism. The underlying molecular mechanisms of host-microorganism interactions remain largely unknown, but recent studies have begun to identify the key signalling pathways of the cross-species homeostatic regulation between the gut microbiota and its host.
All higher animals are associated with a diverse micro-
bial community that is composed mainly of bacteria
but also includes archea, viruses, fungi and protozoa.
Microorganisms cover essentially all host mucosal sur-
faces, but most reside within the gastrointestinal tract.
Studies had traditionally focused on examining the
role of the microbiota during human disease, for exam-
ple in inflammatory diseases such as colitis. However,
in the past decade, the field of microbiota research has
exploded, resulting in the publication of a plethora of
reports that describe both the individual members of our
intestinal microbiota and their wide-ranging impact on
host physiology. Thus, the traditional anthropocentric
view of the gut microbiota as pathogenic and solely
an immunological threat has been substituted with
an appreciation of its mainly beneficial influence on
The ‘normal’ gut microbiota is dominated by anaer-
obic bacteria, which outnumber aerobic and faculta-
tive anaerobic bacteria by 100- to 1,000-fold
. In total,
the intestinal microbiota consists of approximately
500–1,000 species that, interestingly, belong to only
a few of the known bacterial phyla
. By far the most
abundant phyla in the human gut are Firmicutes and
Bacteriodetes, but other species present are mem-
bers of the phyla Proteobacteria, Verrumicrobia,
Actinobacteria, Fusobacteria and Cyanobacteria
. Two
gradients of microbial distribution can be found in the
gastrointestinal tract. First, microbial density increases
both from the proximal to the distal gut (the stomach
contains 10
microbial cells per gram of content, the
duodenum 10
cells per gram, the jejunum 10
cells per
gram, the ileum 10
cells per gram and the colon up to
cells per gram) and along the tissue–lumen axis
(with few bacteria adhering to the tissue or mucus but
a large number being present in the lumen)
. Second,
bacterial diversity increases in the same axes and manner
as microbial density
. Many bacterial species are present
in the lumen, whereas fewer, but well-adapted species,
including several proteobacteria and Akkermansia
muciniphila, adhere and reside within the mucus layer
close to the tissue
. Colonization of the host begins dur-
ing birth, and the composition of the microbiota changes
throughout host development (BOX1).
In the adult intestine, a total of about 10
rial cells are present, which is ten times the number of
human cells in the body
. Their combined genomes
(known as the microbiome) contain more than 5 mil-
lion genes, thus outnumbering the hosts genetic poten-
tial by two orders of magnitude
. This large arsenal of
gene products provides a diverse range of biochemical
and metabolic activities to complement host physiol-
ogy. In fact, the metabolic capacity of the gut microbiota
equals that of the liver, and the intestinal microbiota can
therefore be considered as an additional organ
. These
bacteria are essential for several aspects of host biology.
For example, they facilitate the metabolism of otherwise
indigestible polysaccharides and produce essential vita-
mins; they are required for the development anddiffer-
entiation of the hosts intestinal epithelium and immune
system; they confer protection against invasion by
opportunistic pathogens
; and they have a key role in
maintaining tissue homeostasis. Recent studies have
also revealed that the human microbiota influences
Wallenberg Laboratory
for Cardiovascular and
Metabolic Research,
Sahlgrenska University
Hospital, Department of
Molecular and Clinical
Medicine, University
of Gothenburg.
Sahlgrenska Center for
Cardiovascular and Metabolic
Research, Department of
Molecular and Clinical
Medicine, University of
Gothenburg, SE‑413 45
Gothenburg, Sweden.
Novo Nordisk Foundation
Center for Basic Metabolic
Research, Section for
Metabolic Receptology and
Faculty of Health Sciences,
University of Copenhagen,
Copenhagen DK‑2200,
Correspondence to F.B.
Published online
25 February 2013
The sum of all microorganisms
(including bacteria, archaea,
eukaryotes and viruses) that
reside in and/or on a host or
a specified part of a host (such
as the gastrointestinal tract).
The gut microbiota — masters of host
development and physiology
Felix Sommer
and Fredrik Bäckhed
Abstract | Establishing and maintaining beneficial interactions between the host and its
associated microbiota are key requirements for host health. Although the gut microbiota has
previously been studied in the context of inflammatory diseases, it has recently become clear
that this microbial community has a beneficial role during normal homeostasis, modulating
the host’s immune system as well as influencing host development and physiology, including
organ development and morphogenesis, and host metabolism. The underlying molecular
mechanisms of host–microorganism interactions remain largely unknown, but recent studies
have begun to identify the key signalling pathways of the cross-species homeostatic
regulation between the gut microbiota and its host.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Pertaining to a relationship
between two organisms:
beneficial to both organisms.
The term originates from the
Latin word mutuus (lent,
borrowed or mutual).
A term that extends the
classical biological definition
of an organism (a living system
capable of autonomous
metabolism and reproduction)
by including the many
microorganisms that live in and
on that host organism, thus
yielding a superior degree of
complexity. The term originates
from the Latin supra (above)
and the Greek organon (organ,
instrument, tool).
Any close physical association
between two organisms,
usually from different species.
This includes mutualism,
commensalism and parasitism.
The term originates from the
Greek words syn (together) and
bio (life).
Normally harmless
microorganism that can
become pathogens under
certain environmental
the development and homeostasis of other host tissues,
including thebone
The microbiota also benefits from this mutualistic
association, as the mammalian intestine is a nutrient-rich
environment that is maintained at a constant tempera-
ture. However, it is also a dynamic habitat that undergoes
constant and rapid changes in its physiological para-
meters owing to variations in, for example, host diet,
lifestyle, hygiene or use of antibiotics, all of which affect
gut microbial composition (FIG.1). Thus, unlike the host
genome, the microbiome can change rapidly as a result of
modifications in either the composition of the microbial
community or individual microbial genomes, resulting
in modified transcriptomic, proteomic and metabolic
profiles. Accordingly, the establishment and preserva-
tion of beneficial interactions between the host and its
associated intestinal microbiota are key requirements
The dynamic fluctuations in the microbiota com-
bined with the vast numbers of bacterial cells and their
close proximity to the epithelial tissue represent a mas-
sive challenge to host immunity, as microbial growth
has to be restricted to ensure a beneficial homeostasis.
Furthermore, activation of the host immune system
has to be controlled to circumvent the detrimental
effects of chronic inflammation, so the interaction of
the gut microbiota with the host has to be tightly regu-
lated. In this Review, we discuss recent insights into the
impact of the normal microbiota on the development
and homeostasis of the immune system and other tis-
sues and organs, as well as on host physiology. We also
highlight recent advances in deciphering the under-
lying molecular mechanisms of host–microorganism
Tailoring immune development
Immunology was originally based on the concept of
self’ versus ‘non-self’ discrimination, with the assump-
tion that, because they are non-self, all micro organisms
are pathogens and thus the cause of infectious diseases.
The realization that we live in a microbially dominated
world and in fact benefit greatly from our microbiota
has led to a paradigm shift in immunology. Thus, the
definition of self in the superorganism theory has been
extended to incorporate the constituents of both our
own body and our microbiota
. It is also now widely
accepted that the hosts mucosal immune system is char-
acterized by tolerance to microorganisms rather than
. Furthermore, it has even been specu-
lated that the highly sophisticated adaptive immune
system of jawed vertebrates evolved to keep control of
the mutualistic or beneficial symbiosis with our complex
microbial ecosystem
The intestine, one essential organ in which the
mucosal immune system operates, has to accomplish
two apparently confounding tasks. First, it needs to
facilitate nutrient absorption; thus, the total surface area
of the gastrointestinal tract amounts to about 200 m
. Second, it needs to be resistant to infection
and inhibit microbial translocation across the tissue bar-
rier. Bacterial densities in the gut are the highest known
in any habitat to date and reach up to 10
cells per
gram in the lower intestine
. This highly dense micro-
bial community and the host intestinal epithelial cell
(IEC) lining are separated by only a few micro metres of
mucus in the small intestine and up to several hundred
micrometers in the colon, depending on the location
Because of this unique nature of the intestinal tract, its
mucosal immune system needs to fulfil several special
requirements. It has to be non-responsive to or tolerant
towards the huge number of mutualistic micro organisms
that reside in the intestinal lumen. At the same time, it is
thought that the mucosal immune system has to assure
a beneficial microbiota composition by keeping patho-
bionts in check, restricting microbial overgrowth and
reacting to penetrating microorganisms that breach the
intestinal chemical and physical barriers (such as secreted
soluble immunoglobulin A (IgA), antimicrobial peptides
(AMPs), the mucus layer and the tightly interconnected
IEC lining). In turn, the intestinal microbiota has a key
role in directing several aspects in the development and
regulation of the hosts immune tissues, immune cell
populations and immune mediators.
Mucus layer properties depend on intestinal bacteria.
The intestinal mucus layer covers the epithelial cell
lining and functions as a lubricant, facilitating gastro-
intestinal transport, and as a protective layer against
bacterial invasion, owing to its physical properties
The colonic mucus layer is in fact composed of two
. Both the inner and outer mucus layers are
secreted by goblet cells and are mainly made up of gel-
forming highly glyco sylated proteins termed mucins
Mucin2 (MUC2) is the main mucin in the small and
large intestines of both mice and humans
. The entire
mucus layer represents a selective microbial habitat
owing to microbial adhesion via lectins and glycosidases
that are expressed by only specific bacteria, and it also
serves as nutrient source
. However, bacteria are found
only in the outer layer
, probably owing to the specific
Box 1 | Colonization of the host
Human babies are colonized during passage through the birth canal by environmental
microorganisms (for example, from the mother’s vagina or skin) and during breast
feeding by microorganisms present in the milk
. Owing to the highly oxidative
environment in the gastrointestinal tract of the newborn, primary colonizers are
facultative anaerobic bacteria such as proteobacteria, which are thought to adjust the
environmental conditions by decreasing the oxygen concentration to allow successive
colonization by anaerobic microorganisms such as members of the genus Bacteroides
and members of the phyla Actinobacteria and Firmicutes. During the first year of life,
the intestinal microbiota composition is simple and fluctuates widely between
individuals and over time. Microbial signatures stabilize and start to resemble the ‘adult
state’ when the infant reaches 1–2years of age
Interestingly, conflicting evidence has been published concerning the driving force
for microbial transmission. In early studies of twins, the faecal microbial compositions in
the mother and her children were similar, indicating a mainly maternal transmission
However, in a more recent and extensive study, the same research group found that the
faecal microbiota of children was no more similar to that of their mothers than to that of
their biological fathers, and genetically unrelated but co‑habiting mothers and fathers
were significantly more microbially similar to one another than to members of different
. This indicates that, as well as genetics and kinship, environmental factors
have a considerable effect on the microbial composition of the infant.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Nature Reviews | Microbiology
Altered intestinal microbiota
Antibiotics Lifestyle Diet Hygiene
structure of the mucus layer as a whole, which is formed
of interconnected sheets that create pores smaller than a
bacterial cell and thus inhibit penetration
Comparisons of germ-free and conventionally raised
animals revealed that microorganisms have major effects
on mucus thickness and composition; compared with
conventionally raised animals, germ-free animals have
fewer goblet cells, a thinner mucus layer and also a
higher percentage of neutral mucins in the colon
Stimulation with bacterial products such as lipopolysac-
charide (LPS) and peptidoglycan is sufficient to estab-
lish conventional mucus properties in germ-free mice
but the underlying mechanisms for how the gut micro-
biota modulates goblet cells and mucus layer properties
remain largely elusive.
Notably, Muc2-deficient mice or those with aberrant
mucin glycosylation profiles (owing to a lack of specific
glycosyl transferases) show bacterial overgrowth and
either develop spontaneous colitis or are more suscep-
tible to chemical induction of colitis, an effect that can
be ameliorated by treatment with antibiotics
. This
demonstrates the importance of the mucus layer for
homeostasis in the gut and also highlights the recip-
rocal interaction between the mucus layer and the gut
microbiota. It remains to be clarified whether disease
onset in these mouse strains depends on a selectively
altered and thus more colitogenic microbiota, on
mislocalization of the same microbiota or merely on
increased bacterialload.
Microorganisms induce the development of lymphoid
structures. The lymphatic system consists of a network
of lymphatic vessels connecting the primary and second-
ary lymphoid organs. The main functions of this sys-
tem are the recirculation of interstitial fluid and blood
as well as the transport of lymphocytes (such as Bcells
and Tcells) (BOX2) and antigen-presenting cells to lymph
nodes. Lymphoid tissue is classified as primary (thy-
mus and bone marrow) and secondary (lymph nodes,
Peyer’s patches, tonsils, spleen and lymphoid follicles).
Lymphocytes are generated in primary lymphoid tissues
and are then transported to secondary lymphoid tissues,
where the mature lymphocytes are exposed to antigens
by antigen-presenting cells and are thus activated to
initiate an adaptive immune response. The cellular
interactions that occur during lymphoid tissue develop-
ment and maturation are similar for both primary and
secondary lymphoid organs, although the molecular
frameworks differ a little (for details see REF.26).
In addition to host genetics, several environmen-
tal factors, including contact with microorganisms,
influence both the development and maturation of the
immune system. The development of secondary gut-
associated lymphoid tissue (GALT), such as Peyer’s
Figure 1 | Factors shaping intestinal microbial composition and effects of dysbiosis on host health. The composition
of the gut microbiota is influenced by various environmental factors, including the use of antibiotics, lifestyle, diet and
hygiene preferences. The host’s genetic disposition also has a role: hyperimmunity (owing to over-representation of
pro-inflammatory mediators such as interleukin-6 (IL-6), IL-12 or tumour necrosis factor (TNF)) or immunodeficiency
(owing to mutations in regulatory immune proteins such as NOD2 (nucleotide-binding oligomerization domain protein2)
or IL-10) can influence the gut microbiota composition. In turn, dysbiosis affects levels of immune mediators and induces
both chronic inflammation and metabolic dysfunction.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Somatic hypermutation
A programmed process of
mutation affecting the variable
regions of immunoglobulin
genes during affinity
maturation of Bcell receptors.
patches and mesenteric lymph nodes, is initiated pre-
natally in the sterile environment of the fetus through
induction by lymphoid tissue inducer (LTi) cells
Briefly, mesenchymal cells are induced by retinoic acid
to produce CXC-chemokine ligand13 (CXCL13), which
recruits LTi precursor cells and stimulates their cluster-
ing, leading to their maturation into LTi cells. These then
induce the differentiation of stromal organizer cells to
express several cytokines and adhesion molecules that
attract further immune cells, causing GALT forma-
. Maturation of these tissues, including an increase
in tissue size and the development of germinal centres
(sites of Bcell proliferation, differentiation and somatic
hypermutation in lymph nodes), depends on postnatal
microbial colonization
(FIG.2). Consequently, Peyer’s
patches, mesenteric lymph nodes and splenic white pulp
are underdeveloped in germ-free mice
Furthermore, in parallel with microbial coloniza-
tion, clusters of LTi-like cells termed cryptopatches
form at birth in the connective tissue between intestinal
crypts, known as the lamina propria
. Cryptopatches
recruit Bcells and develop into isolated lymphoid fol-
licles (ILFs), a type of lymphoid tissue that is structurally
similar to Peyer’s patches and serves as an inductive site
for intestinal immune reactions
. This process also
depends on the gut microbiota, as ILFs fail to develop
fully in germ-free mice
. ILF formation can be induced
by exposing germ-free mice to purified peptidoglycan
from Gram-negative bacteria, indicating that this pro-
cess is driven solely by a specific microbial pattern
Stromal and epithelial cells recognize the peptido-
glycan of resident microorganisms mainly via signalling
through the pattern recognition receptor (PRR) NOD1
(nucleotide-binding oligomerization domain contain-
ing 1) but also partially through another family of PRRs,
the Toll-like receptors (TLRs). Activation of NOD1
by the gut microbiota causes increased expression of
CC-chemokine ligand20 (CCL20) and presumably also
of β-defensin 3, both of which activate ILF formation
by binding to CC-chemokine receptor6 (CCR6) on LTi
The gut microbiota modulates immune cell differentia-
tion. In addition to regulating the development of lym-
phoid structures, the gut microbiota has been shown
to modulate the differentiation of immune cell subsets
(BOX2) and, therefore, maintain homeostatic interactions
between the host and the gut microbiota.
After birth, LTi-like cells that express nuclear RORγt
but lack NKp46 (in mice; also known as NCR1) or
NKp44 (in humans; also known as NCR2) markers accu-
mulate in both the mouse and human GALT and lamina
. Interestingly, theRORγt
cells can differentiate into RORγt
natural killer
(NK)-like cells, which differ from regular NK cells (BOX2)
in that they have intermediate expression of NK1.1 (also
known as KLRB1C) and do not produce interleukin-1β
(IL-1β) or kill tumour cells
. This differentiation
requires both IL-23, which is produced by activated
myeloid cells and epithelial or endothelial cells, and the
presence of the intestinal microbiota, as germ-free mice
have fewer RORγt
NK-like cells than conven-
tionally raised mice
. These cells produce IL-22, which in
mice promotes the integrity of the intestinal barrier and
reduces bacterial infiltration by inducing epithelial repair
via signal transducer and activator of transcription3
(STAT3) signalling and the production of antimicrobial
. Thus, the normal gut microbiota promotes
Box 2 | Lymphocyte subtypes
All lymphocytes differentiate and mature in primary lymphoid organs (the thymus and
bone marrow). Mature naive lymphocytes migrate to secondary lymphoid tissues,
where they become activated by antigen‑presenting cells such as dendritic cells.
Gut‑associated secondary lymphoid tissues include Peyer’s patches, mesenteric lymph
nodes and lymphoid follicles
. Here, we list and describe the lymphocytes that are
known to be modulated by the gut microbiota
Lymphoid tissue inducer cells
(LTi cells). A unique Tcell subpopulation that is characterized by the expression of
RORγt, CD4 and interleukin‑7 receptorα and the absence of CD3, B220 (an isoform
of CD45) and CD11c (also known as integrin αX). Their function is to recruit Bcells and
Tcells and thereby promote the formation of secondary lymphoid tissues.
Natural killer cells
(NK cells). Lymphocytes that recognize the abnormal antigen signatures of infected or
tumour cells, which NK cells kill by lysis or apoptosis. NK cells resemble cytotoxic Tcells
in function but belong to the innate immune system. They express various NK cell
receptors, including NKp46 (in mice; NKp44 in humans) and NKG2D. They can activate
Bcells and Tcells and thereby stimulate an adaptive immune response.
Natural killer T cells
(NKT cells). These cells have properties of both Tcells and NK cells, as they co-express
NK cell markers with a Tcell receptor. NKTcells mainly recognize lipids and glycolipids
presented by antigen-presenting cells via CD1d. Following activation, NKTcells
produce pro‑inflammatory cytokines such as tumour necrosis factor (TNF) and
interleukin‑17 (IL‑17). Invariant NKT (iNKT) cells are a specific subpopulation expressing
an invariant T cell receptor.
T helper 1 cells
1 cells). A subset of T
lymphocytes that is characterized by the expression of
interferon‑γ and transforming growth factorβ (TGFβ). T
1 cell differentiation is
induced by contact with activated macrophages or NK cells.
T helper 2 cells
2 cells). A subset of T
lymphocytes that is characterized by the expression of the
cytokines IL‑4, IL‑5 and IL‑13. T
2 cell differentiation is induced in response to, for
example, allergens and extracellular microorganisms.
T helper 17 cells
17 cells). A subset of T
cells that is characterized by the expression of IL‑17, which
stimulates stromal cells to express the pro‑inflammatory cytokines IL‑6 and IL‑8,
thereby attracting neutrophils and promoting inflammation to clear out invading
Regulatory T cells
cells). A Tcell subpopulation that is characterized by the expression of CD4, CD25
and FOXP3 and the production of the anti‑inflammatory cytokines TGFβ and IL‑10.
These cells can be subdivided into natural T
cells, which differentiate from CD4
Tcells in the thymus, and inducible T
cells, which arise from naive Tcells in secondary
lymphoid tissues. Both cell types function to suppress immune activation and prevent
self‑reactivity, thereby reducing the risk of autoimmune disease.
Type1 regulatory T cells
1 cells). These CD4
T cells are functionally equivalent to the
IL‑10‑producing T
cells. They respond to microorganisms and regulate intestinal
tolerance through the secretion of IL‑10.
Lymphocytes that are activated when the unique Bcell receptor binds its specific
antigen and that then mediate humoral immunity through the production of antibodies.
Bcells are also involved in lymphoid tissue organization.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Nature Reviews | Microbiology
Goblet cell
Peyer’s patch
Peyer’s patch
plasma cell
17 cell
B cell
T cell
Dendritic cell
B. fragilis
epithelial cell
AMP and
IgA production
Mucus thickness
Altered mucus properties
a Germ-free mice
b c
Conventionally raised mice
Figure 2 | Microbiota-induced maturation of the gastrointestinal tract. The microbiota promotes substantial
changes in gut morphology, including villus architecture, crypt depth, stem cell proliferation, blood vessel density, mucus
layer properties and maturation of mucosa-associated lymphoid tissues. a|In germ-free mice, the villi in the distal small
intestine are longer and thinner and have a less complex vascular network than the villi of conventionally raised animals. In
the absence of bacteria, intestinal crypts are less deep and contain fewer proliferating stem cells. Furthermore, germ-free
animals show reduced mucus thickness and altered mucus properties. b|Moreover, very few isolated lymphoid follicles,
immature Peyer’s patches and immature mesenteric lymph nodes (MLNs) are present under germ-free conditions, and
levels of both immunoglobulin A (IgA) and antimicrobial peptides (AMPs) are lower than in conventionally raised animals.
c|In conventionally raised mice, polysaccharideA (PSA) of Bacteroides fragilis is known to induce the expansion of
regulatory T (T
) cells, which have an anti-inflammatory effect and dampen immune responses. By
contrast, segmented filamentous bacteria (SFB) have been shown to induce the expansion of T helper 17 (T
17) cells,
which are pro-inflammatory.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Experimental autoimmune
An animal model of
Tcell-mediated autoimmune
disease in general and in
particular of demyelinating
diseases of the central nervous
system, such as multiple
T follicular helper cells
A Tcell subtype that resides in
the Bcell follicles of secondary
lymphoid organs and
expresses the Bcell homing
receptor CXC-chemokine
receptor5. These T cells
mediate Bcell activation and
trigger the formation of the
germinal centre.
intestinal barrier function by modulating mucosal
homeostasis, in part by promoting the differentiation of
NK-like cells.
The intestinal microbiota also modulates the abun-
dance of invariant NKTcells (iNKT cells), a unique
Tcell subset that expresses an invariant Tcell receptor
α-chain. These cells promote inflammation, as follow-
ing activation they secrete pro-inflammatory Thelper1
1)- and T
2-type chemokines and cytokines, including
interferon-γ, IL-2, IL-4, IL-13, IL-17A, IL-21 and tumour
necrosis factor (TNF)
. In contrast to the NK-like cells
described above, there are more iNKT cells in the colon
of germ-free mice than the colon of conventionally raised
, which suggests that the gut microbiota promotes
homeostasis by decreasing the number of these pro-
inflammatory cells. Importantly, a recent study elegantly
demonstrated an age dependency of the microbial effects
on the iNKT population and revealed that colonization of
neonatal but not adult germ-free mice with conventional
gut microbiota normalized iNKT cell numbers and pro-
tected against oxazolone-induced colitis as well as against
ovalbumin-induced allergic lung inflammation
It has become evident that the gut microbiota shapes
the Tcell landscape not only in the lamina propria but
also systemically and therefore modulates the homeo-
stasis of the superorganism
(FIG.2). Intestinal mucosal
Tcells are important ‘legislators’ of intestinal homeo-
stasis because they not only defend against intestinal
pathogens, but also promote wound healing, barrier
repair and regeneration as they rapidly accumulate at
sites of injury and infection
. Tcells can be assigned
to subpopulations that drive either a pro-inflammatory
immune response (T
1, T
2 and T
17 cells) or an anti-
inflammatory immune response (CD4
regulatoryT (T
) cells or CD4
regulatoryT (T
1) cells), depending on the cytokines
that they produce
(BOX2). The balance between both
pro- and anti-inflammatory Tcell subpopulations deter-
mines the overall immune equilibrium.
Interestingly, individual members of the gut micro-
biota have been found to drive specific Tcell responses
(FIG.2c). The Gram-negative bacterium Bacteroides fragilis
elicits an anti-inflammatory response by inducing the
differentiation of CD4
Tcells into T
cells locally in
the intestinal lamina propria but also in the circula-
. T
cells produce IL-10 and thereby suppress the
pro-inflammatory T
17 response
. This skewing event is
mediated by polysaccharide A (PSA) on the outer mem-
brane of the bacterium, which is recognized by TLR2 on
Tcells and activates a signalling cascade involving
myeloid differentiation88 (MYD88) to induce T
. Indeed, a mutant strain of B.fragilis
lacking PSA fails to initiate differentiation of T
whereas purified PSA has the same effect as the wild-type
Bacteria from the Gram-positive class Clostridia have
similar effects on the host immune system. A mixture of
46 Clostridia spp. belonging to clusters IV and XIVa was
isolated from mouse faeces, and colonization of germ-
free mice with this mixture induced the expansion of
cells in the mucosal lamina propria and thereby
increased levels of the immunosuppressive cytokine
IL-10 (REF.47). Notably, compared with non-colonized
germ-free mice, the Clostridiaspecies-colonized mice
were more resistant to chemically induced disruption
of the gut epithelium and displayed attenuated levels of
antigen-induced serum IgE. Furthermore, a similar T
cell response was observed when germ-free mice were
colonized with altered Schaedler flora, a cocktail of eight
defined bacteria including three Clostridia species
However, the specific species in this community that are
functionally responsible and the underlying molecular
mechanisms of this effect are so far unknown.
In contrast to the bacteria mentioned above,
segmented filamentous bacteria (SFB) elicit a pro-
inflammatory immune response by promoting the dif-
ferentiation of T
17 cells and, to a lesser extent, T
. SFB reside in the small intestine of mice and
are in direct contact with epithelial cells, which these
bacteria seem to readily invade. Invasion leads to local
actin polymerization in the epithelium at the interac-
tion site, and this presumably initiates a signalling event
that activates the differentiation of T
17 cells. Notably,
mono-association of germ-free mice with SFB is suffi-
cient to restore susceptibility to T
17 cell-mediated arthri-
tis and experimental autoimmune encephalomyelitis
. So
far, however, it is not known whether T
17 cell differ-
entiation is induced by IEC-produced mediators, by
direct interaction with antigen-presenting cells in the
lamina propria (dendritic cells or macrophages) or by
bacterially secreted signalling molecules (for example,
Gut microorganisms tweak the production of immune
mediators. It is clear that the gut microbiota regulates
the production of cytokines and chemokines to influ-
ence the Tcell repertoire of the intestine and surround-
ing tissue, but there is evidence that these bacteria also
modulate the production of other soluble immune
mediators (FIG.2). IgA is produced by plasma cells (dif-
ferentiated Bcells) in the lamina propria and is trans-
cytosed through the intestinal epithelium into the
lumen, where it binds microbial antigens and thereby
prevents bacterial translocation and infection
. The dif-
ferentiation of Bcells into IgA-producing plasma cells is
induced by sensing of gut microbiota-derived flagellin
via TLR5 on lamina propria dendritic cells
. IgA has a
key role in barrier homeostasis, as IgA-deficient mice
produce gut microbiota-specific serum IgG antibodies,
indicating that there is a breach in the mucosal barrier
of these mice and subsequent induction of the systemic
immune system
. Furthermore, a recent study showed
that microbial modulation of IgA homeostasis is in part
dependent on the host protein programmed cell death1
(PD1), which is expressed by T follicular helper cells in
the germinal centre
. PD1-deficient mice harbour an
altered IgA repertoire owing to changes in Bcell matura-
tion, leading to modified IgA specificity. This altered IgA
repertoire then shifts the normal gut microbiota com-
position by reducing the numbers of bacteria from the
genera Bifidobacterium and Bacteroides and increasing
the number from the family Enterobacteriaceae
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Crypts of Lieberkühn
Tubular invaginations of the
intestinal epithelium around
the villi. The crypt base
contains Paneth cells, which
secrete mainly antimicrobial
peptides as well as other
immune factors, and
continually dividing stem
cells that are the source of
all intestinal epithelial cells.
Xenobiotic metabolism
The metabolism of foreign
compounds that are neither
produced by nor naturally
found in the host, such as
Enterochromaffin cells
A subtype of enteroendocrine
cells in the intestinal or
respiratory epithelium.
Enterochromaffin cells are the
main source of serotonin in the
body and are thereby involved
in the regulation of intestinal
peristalsis and nausea.
A type of junctional complex
that is mainly found in epithelia
(specifically, in the lateral
plasma membrane of the
epithelial cell) and mediates
cell-to-cell adhesion to allow
cells to withstand shearing
Tight junctions
Junctional complexes that are
present only in vertebrates (the
invertebrate equivalents are
the septate junctions) and are
located at the transition of the
apical and lateral membrane,
closely connecting two
epithelial cells and thereby
making the epithelium
impermeable to water and
In addition to IgA, the gut microbiota regulates the
production of AMPs. These molecules are produced by
IECs as a consequence of their tight contact with a dense
and highly diverse microbial community and include
defensins, C-type lectins (such as REG3β and REG3γ),
ribonucleases (for example, angiopoietin4 (ANG4))
and S100 proteins (for example, psoriasin (also known
as S100A7)), which rapidly kill or inactivate microorgan-
isms (see REF.57 for detailed information). Some AMPs,
such as α-defensins and β-defensin1, are expressed
, whereas others, such as ANG4 and
REG3γ, are induced following a microbial encounter
either via PRR signalling (through TLRs and NOD-like
receptors (NLRs)) or in a PRR-independent manner
(for example, by microbially fermented butyrate)
Furthermore, intestinal lymphocyte-derived IL-17 and
IL-22, which are bacterially modulated (see above),
induce the production of AMPs by IECs and Paneth
. Induction of AMPs in epithelial cells is likely to
be one important mechanism for preventing breaches
of the mucosal barrier and, in particular, protecting the
stem cell niche in the crypts of Lieberkühn. Furthermore,
AMPs not only help to sustain host–microorganism
segregation, but also affect the microbiota composition.
Mice that are deficient in MYD88, NOD2 or matrilysin
(MMP7; a protease involved in the regulation of defen-
sin activity), as well as mice that are transgenic for
α-defensin 5, have an altered microbiota owing to shifted
AMP production
Regulation of host physiology
As mentioned above, the microbiome contains >5 million
genes, many of which encode biosynthetic enzymes, pro-
teases and glycosidases, thereby greatly expanding the
hosts own biochemical and metabolic capability
. The
effects of the gut microbiota on host metabolism — for
example, through the microbiota metabolizing other-
wise indigestible polysaccharides, producing essential
vitamins and carrying out xenobiotic metabolism — have
long been appreciated
. However, the effects on host
physiology exceed these purely biochemical properties.
In fact, the microbiota also influences a wide range of host
processes and characteristics that were thought to depend
solely on the genetic programme of the host, including
organ development and morphogenesis, cell proliferation,
bone mass, adiposity and even behaviour (FIG.3). Below,
we discuss recent advances in our understanding of the
microbial modulation of these physiological properties
of the superorganism.
Development and morphogenesis. Microorganisms
affect not only the development of immune tissues,
but also the development and morphogenesis of other
organs and body structures in a range of species. For
example, the symbiotic interaction between the fruit
fly Drosophila melanogaster and one of its gut bacteria,
Acetobacter pomorum, affects several host physiologi-
cal properties, including developmental rate, body size,
wing area, metabolism and stem cell activity
. Acetic
acid produced by the pyrroloquinoline quinone-depend-
ent alcohol dehydrogenase of A.pomorum triggers
D.melano gaster insulin signalling involving phospho-
inositide 3-kinase and the forkhead transcription factor
FOXO by an as-yet-unknown mechanism and thereby
tunes the homeostatic programmes in the fly. The squid
Euprymna scolopes has developed a close symbiosis with
the bacterium Vibrio fischeri, in which the bacterium
releases a tetrapeptide peptidoglycan monomer that,
together with the lipid A component of LPS, is sufficient
to drive the development of a light-emitting ‘organ’ in the
. Peptidoglycan signalling through a nuclear pep-
tidoglycan recogniton protein induces apoptosis, which
is an integral part of light organ morphogenesis
. This
organ camouflages the squid at night, as it resembles a
star to predators below; remarkably, the organ is reas-
sembled every night, as the bacteria are expelled every
In humans and other mammals, studies have shown
that the intestinal microbiota has a considerable effect
on the development of the gastrointestinal tract (FIG.3).
In newborns, the gastrointestinal tract is structurally
and functionally immature, and maturation is induced
by many factors, one them being the gut microbiota
(BOX1). Notably, the changes in microbiota composi-
tion during weaning in both mice and humans coincide
with gut maturation, indicating that specific bacteria in
the pre- and post-weaning microbiota have differen-
tial effects
. The most prominent feature of germ-free
animals is a greatly enlarged caecum
. Furthermore,
the overall intestinal surface area in germ-free mice is
reduced compared with that of conventional mice
Germ-free mice are impaired in brush border differ-
and have reduced villus thickness
owing to
reduced cell regeneration
and a longer cell cycle time
The number of serotonin-producing enterochromaffin
cells is also higher in the gut of germ-free compared
with conventional mice
, but interestingly, germ-free
mice have lower levels of serotonin
, and this is thought
to correlate with decreased intestinal peristaltic activ-
ity and a prolonged gastrointestinal transit time
Last, microorganisms modulate epithelial permeability
in the gastrointestinal tract. For example, in mice the
Gram-negative bacterium Bacteroides thetaiotaomicron
increases the resistance of the gut to injury by inducing
the expression of SPRR2A, which is involved in desmo-
some maintenance
. Moreover, several Lactobacillus
strains rigidify tight junctions between epithelial cells,
resulting in reduced epithelial permeability
. PRR sig-
nalling was found to be important in this process, as pep-
tidoglycan-induced TLR2 signalling in epithelial cells
improves tight junction function and reduces apoptosis
rates, thus enhancing barrier integrity and facilitating
wound repair after injury
Interestingly, recent work has shown that, in addition
to promoting gastrointestinal tract morphogenesis, the
gut microbiota influences the remodelling of the vascu-
lar system
(FIG.3). Colonization of the gut in germ-
free mice causes restructuring of intestinal villi, which
shorten and widen to prevent microbial infiltration. This
restructuring increases the demand for oxygen in the gut
epithelium and leads to increased amounts of sprout-
ing endothelial cells and, consequently, angiogenesis
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Nature Reviews | Microbiology
Intestinal function
GALT maturation
Tissue regeneration
Gut motility
Energy expenditure
Nutrient accessibility
Short-chain fatty acids
Intestinal vessel
TF glycosylation
Thrombin cleavage
PAR1 activation
TF phosphorylation
ANG1 expression
Bone homeostasis
17 cells
TNF in colon and bone
Bone mass
Synaptic connectivity
Pain perception
This process is associated with increased glycosylation
and surface translocation of tissue factor (TF), leading
to increased activation of thrombin. In turn, thrombin
activates proteinase-activated receptor 1 (PAR1), which
phosphorylates TF and promotes epithelial expression of
angiopoietin 1, a protein that is required for increased
Tissue and organ homeostasis. Tissue homeostasis
requires a balance between cell renewal and death, and
thus a tightly regulated cell cycle, which is also modified
by microorganisms. For example, in D.melanogaster,
infection with the pathogenic bacterium Erwinia caroto-
vora induces stem cell proliferation and epithelial cell
. Similarly, TLR signals derived from the gut
microbiota are required for regaining tissue homeostasis
following injury in the intestine in mice
. Importantly,
the gut microbiota also has direct effects on tissue
homeo stasis, as germ-free mice have reduced epithelial
cell turnover in the small intestine owing to reduced
IEC proliferation, reduced crypt-to-tip cellular migra-
tion and reduced apoptosis
(FIG.3). As the crypt
contains proliferative IECs and the villus contains differ-
entiated IECs that are in contact with the gut microbiota,
these observations suggest that epithelial cells along the
crypt–tip axis differ in their responses to microbial
Imbalanced cellular homeostasis can result in
the development of cancer, and inflammation has
a crucial role in cancer initiation and progression
Microorganisms modulate inflammation and thus could
influence carcinogenesis
. Indeed, an increased bacterial
load was detected in colonic biopsies from patients with
colorectal cancer or colonic adenomas
. In contrast to
the decreased microbial diversity that is associated with
obesity and inflammatory bowel disease
, microbial
diversity is increased in patients with colorectal adeno-
. In two mouse models of carcinogenesis, germ-
free animals were protected from or showed reduced
cancer development compared with conventionally
raised mice
. Notably, bacteria are also required for
the production of secondary bile acids, which have
carcinogenic effects
. Some microbial species, such as
B.fragilis, Streptococcus gallolyticus or Fusobacterium
nucleatum, have been associated with cancer develop-
. This suggests that certain groups of bacteria
promote, whereas others protect against, colon cancer.
Therefore, selective manipulation of the gut microbiota
might provide new avenues to prevent carcinogenesis
In addition to its effect on immune system and gut
homeostasis, the gut microbiota affects homeostasis in
other tissues, for example by altering bone mineral den-
sity in mice (FIG.3). Bone remodelling occurs through
the antagonistic activity of bone-forming osteoblasts
and bone-resorbing osteoclasts
. Bone cells express
receptors for serotonin, which, as mentioned above, is
reduced in germ-free mice, and serotonin signalling
inhibits bone formation
. Furthermore, bone loss is
associated with inflammation, and Tcells are responsible
for bone resorption in autoinflammatory diseases
17 cells and the pro-inflammatory cytokines TNF and
IL-1β all promote bone resorption by inducing osteo-
. Consistent with this, germ-free mice
have been shown to have a higher bone mineral den-
sity than conventional mice, highlighting the fact that
microbial modulation of Tcell function (see above),
serotonin levels and cytokine profiles might contribute
to microbial modulation of bone homeostasis
. Taken
together, these findings suggest that the gut microbiota
can be considered an environmental factor that might
contribute to osteoporosis.
Metabolism and adiposity. The microbiome encodes
a more versatile metabolome than the host
. Although
gut microbial composition differs significantly between
individuals, a core microbiome can be identified,
Figure 3 | Microbial impact on host physiology. The gut microbiota has been shown
to affect several aspects of host physiology; arrows represent either stimulatory or
inhibitory effects of the gut microbiota on host physiological processes. The microbiota
has been shown to influence intestinal function in the host, promoting gut-associated
lymphoid tissue (GALT) maturation, tissue regeneration (in particular of the villi) and gut
motility, and reducing the permeability of epithelial cells lining the gut, thus promoting
barrier integrity. Similarly, the gut microbiota influences the morphogenesis of the
vascular system surrounding the gut. This is associated with increased glycosylation of
tissue factor (TF), which leads to cleavage of thrombin, in turn activating proteinase-
activated receptor1 (PAR1). This then phosphorylates TF to promote epithelial
expression of angiopoietin 1 (ANG1), which promotes increased vascularization.
Changes in the microbiota composition or a complete lack of a gut microbiota has been
shown to affect metabolism, behaviour and tissue homeostasis, suggesting that the
microbiota also regulates these processes. Specifically, the gut microbiota can influence
the host’s nervous system, decreasing synaptic connectivity and promoting anxiety-like
behaviour and pain perception. In the case of host metabolism, the gut microbiota has
been shown to facilitate energy harvest from the diet, to modulate host metabolism (for
example, by decreasing energy expenditure) and to promote host adiposity. Finally, the
gut microbiota can influence tissue homeostasis, for example decreasing bone mass by
promoting the function of osteoclasts (which cause bone resorption) and increasing
the numbers of pro-inflammatory T helper17 (T
17) cells.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
An imbalance in the structural
and/or functional configuration
of the microbiota, leading to a
disruption of host–
microorganism homeostasis.
indicating the requirement for stable functional meta-
bolic interactions with the host
. Studies have sug-
gested that there are differences in the gut microbiota
composition between obese and non-obese individuals,
although results about the gut microbiota composition
in obese individuals have been conflicting
. Compared
with the gut microbiome of non-obese mice, that of
obese mice is enriched in genes encoding carbohydrate
metabolism enzymes and was demonstrated to have
a greater capacity to extract energy from the diet and
to generate short-chain fatty acids
(FIG.3). Moreover,
obese humans harbour an altered microbiota with
reduced diversity
, but the functional impact of
this reduced diversity on the development of obesity is
not yet clear. A recent report demonstrated that the gut
microbiome is altered in Chinese individuals with type2
. Strikingly, the composition of the gut micro-
biota was able to predict type2 diabetes in a second,
A link between the gut microbiota and metabolism
has also been demonstrated in studies using germ-free
mice. These mice have reduced adiposity and require
a higher caloric intake to achieve the same weight as
conventionally raised mice
. This has in part been attrib-
uted to reduced energy extraction from a carbohydrate-
rich diet in germ-free mice
. However, these mice are
also resistant to diet-induced obesity when fed a fat- and
sucrose-rich ‘Western’ diet containing almost no com-
plex carbohydrates
. Thus, the gut microbiota is likely to
directly modulate host metabolism (FIG.3). For example,
compared with in conventionally raised mice, the small
intestine of germ-free mice has a higher expression of
angiopoietin-like protein 4 (ANGPTL4; also known as
fasting-induced adipose factor), which promotes fatty
acid oxidation in skeletal muscle
. Furthermore, the
gut microbiota might also contribute to increased adi-
posity and impaired glucose metabolism by stimulating
inflammation and macrophage accumulation in adipose
. Indeed, LPS from Gram-negative bacteria
promotes hepatic insulin resistance
In addition to obesity, an altered gut microbiome
was recently associated with symptomatic atheroscle-
. The microbiomes of patients who have had a
stroke were shown to have lower levels of carotene-
and lycopene-producing enzymes and higher levels of
peptidoglycan-producing enzymes than the microbiomes
of individuals who have not had a stroke, suggesting
that patients who have had a stroke have a more inflam-
matory gut milieu. Furthermore, cardiovascular disease
in humans is associated with altered microbial metabo-
lism of dietary choline
. For further details about how
host–microorganism interactions can programme host
metabolism, readers are referred to a recent review
Effects on the brain and behaviour. Animal behaviour and
social context have been shown to shape the microbiota
composition in several species, including bumble bees
the squid E.scolopes
and chimpanzees
. In turn, the
impact of the microbiota reaches far outside thegastro-
intestinal tract, also affecting behaviour (FIG.3). For
example, the gut bacterium Lactobacillus plantarum
modulates mate choice in D.melanogaster
; larval
settle ment of the marine tubeworm Hydroides elegans is
regulated by the biofilm bacterium Pseudoalteromonas
; and the composition of the human
skin microbiota influences attraction for mosquitoes
with potential consequences for disease spread. In mice,
the gut microbiota modulates the levels of several
signalling molecules, such as brain-derived neuro-
trophic factor and noradrenaline, in different areas of
the brain
. Germ-free mice display an altered stress
response, dysregulation of the hypothalamus–pituitary–
adrenal gland axis and decreased inflammatory pain
To date, the best studied microbial effects are the
effects on anxiety-like behaviour. Dysbiosis, as a result
of either pathogenic infection or antibiotic treatment,
increases anxiety-like behaviour in conventionally
raised mice
, whereas germ-free mice show little
anxiety-like behaviour
. The neurological defects in
germ-free mice can be resolved only by colonization of
neonates, indicating that there is a critical time window
in which microbially induced maturation of the nervous
system occurs
. Notably, compared with the striatum
of conventionally raised mice, the striatum of germ-free
mice has higher levels of the synaptic proteins synap-
tophysin and PSD95 (also known as DLG4), which are
both involved in synaptogenesis, indicating that the gut
microbiota might affect synaptic connectivity
For further discussion of microbial effects on the
development of the nervous system and behaviour,
readers are referred to a recent review
Research over the past decade has accumulated a large
body of evidence linking alterations in the gut microbial
composition to several diseases, such as inflammatory
bowel disease, asthma, arthritis, obesity and cardiovascu-
lar disease. Furthermore, it is now clear that the normal
intestinal microbiota also influences numerous physio-
logical aspects in the healthy host, including organ mor-
phogenesis, immune system and gastrointestinal tract
development and maturation, intestinal vascularization,
tissue regeneration, carcinogenesis, bone homeostasis,
metabolism and behaviour.
An important insight that has come from these stud-
ies it that the timing of colonization of germ-free mice
seems to be crucial if these mice are to recapitulate the
phenotypes of conventionally raised mice. Whereas col-
onization of adult germ-free mice restores adiposity to
normal levels
, colonization before weaning is required
to normalize behaviour and protect against the iNKTcell
accumulation that is associated with asthma and inflam-
matory bowel disease
. Such early microbial coloniza-
tion might have an epigenetic effect on the host through
early-life imprinting, but it remains to be demonstrated
how the gut microbiota achieves this. It is possible that
in Tlr2-deficient mice, the altered microbiota contrib-
utes to altered DNA methylation patterns in cells of the
colonic mucosa
. The impact of the gut microbiota as
a modulator of methylation in other organs remains to
be identified.
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
Pertaining to an organism:
associated with a defined
microbiota. For example,
laboratory mice can be reared
under sterile (germ-free)
conditions or colonized with a
specific collection of
microorganisms. From the
Greek gnosis (known or
knowledge) and bios (life),
Analyses of biopsy samples obtained from gnoto-
biotic mouse models or from mice treated with antibiot-
ics have been extensively used to elucidate how the gut
microbiota modulates metabolic interactions and gene
expression in different tissues. However, further studies
are required to expand our currently limited knowledge
and to establish how the gut microbiota regulates the
functions of distinct cell populations in thegut.
It is important to stress that findings obtained from
the study of animal models remain to be translated to
diagnostic, prophylactic or therapeutic treatments for
humans. One potential caveat is that microbiota mem-
bers differ not only among host species but also between
individual host organisms
. For example, the potent
immune system-modulating SFB are found only in mice
and have not yet been detected in humans. Diet is also
one important factor modulating the composition of the
gut microbial ecosystem
. Thus, variation in dietary
habits among humans might contribute to the large
inter-individual differences in the relative abundances
of given microorganisms. This might constitute a major
challenge when developing diagnostic markers based
on the gut microbiota. Although comparisons of gnoto-
biotic and conventionally raised animals are useful for
identifying important physiological functions that are
modulated by the gut microbiota, such comparisons
cannot be automatically extrapolated to humans, and it
remains unclear whether an altered microbiota associ-
ated with a disease in humans is causing, contributing
to or merely a consequence of the diseasestate.
Immense progress has been made not only in identi-
fying, isolating and culturing members of the gut micro-
biota, but also in the development of genetic tools, such
as whole-genome sequencing, and in the availability of
novel genetic models to dissect the interplay between
the microbiome, host genetics and host physiology.
Combining these tools for further studies in the upcom-
ing years will greatly deepen our understanding of the
molecular targets in the homeostatic interaction between
the gut microbiota and the host, and thereby promises to
reveal new ways to treat chronic inflammatory diseases
and maintainhealth.
1. Clemente,J.C., Ursell,L.K., Parfrey,L.W. &
Knight,R. The impact of the gut microbiota on human
health: an integrative view. Cell 148, 1258–1270
2. Human Microbiome Project Consortium. Structure,
function and diversity of the healthy human
microbiome. Nature 486, 207–214 (2012).
A detailed catalogue of the human gut microbiome.
3. Qin,J. etal. A human gut microbial gene catalogue
established by metagenomic sequencing. Nature 464,
59–65 (2010).
The first catalogue of the human microbiome.
4. Sekirov,I., Russell,S.L., Antunes,L.C. & Finlay,B.B.
Gut microbiota in health and disease. Physiol. Rev. 90,
859–904 (2010).
5. Sina,C. etal. Extracellular cathepsin K exerts
antimicrobial activity and is protective against chronic
intestinal inflammation in mice. Gut 22Mar 2012
6. Swidsinski,A., Loening-Baucke,V., Lochs,H. &
Hale,L.P. Spatial organization of bacterial flora in
normal and inflamed intestine: a fluorescence in situ
hybridization study in mice. World J.Gastroenterol.
11, 1131–1140 (2005).
7. Xu,J. & Gordon,J.I. Honor thy symbionts. Proc. Natl
Acad. Sci. USA 100, 10452–10459 (2003).
8. Human Microbiome Project Consortium. A framework
for human microbiome research. Nature 486,
215–221 (2012).
9. Gill,S.R. etal. Metagenomic analysis of the human
distal gut microbiome. Science 312, 1355–1359
10. Smith,K., McCoy,K.D. & Macpherson,A.J. Use of
axenic animals in studying the adaptation of mammals
to their commensal intestinal microbiota. Semin.
Immunol. 19, 59–69 (2007).
11. Sjogren,K. etal. The gut microbiota regulates bone
mass in mice. J.Bone Miner. Res. 27, 1357–1367
A study demonstrating that the gut microbiota
affects bone mass, possibly by inhibiting
osteoclastogenesis through modulation of the Tcell
12. Lederberg,J. Infectious history. Science 288, 287–293
13. Arrieta,M.C. & Finlay,B.B. The commensal microbiota
drives immune homeostasis. Front. Immunol. 3, 33
14. McFall-Ngai,M. Adaptive immunity: care for the
community. Nature 445, 153 (2007).
15. Hooper,L.V., Littman,D.R. & Macpherson,A.J.
Interactions between the microbiota and the immune
system. Science 336, 1268–1273 (2012).
16. O’Hara,A.M. & Shanahan,F. The gut flora as a
forgotten organ. EMBO Rep. 7, 688–693 (2006).
17. Johansson,M.E. etal. The inner of the two Muc2
mucin-dependent mucus layers in colon is devoid of
bacteria. Proc. Natl Acad. Sci. USA 105,
15064–15069 (2008).
An article showing that the inner mucus layer
shields the intestinal epithelium from bacterial
18. Johansson,M.E., Larsson,J.M. & Hansson,G.C.
The two mucus layers of colon are organized by the
MUC2 mucin, whereas the outer layer is a legislator of
host–microbial interactions. Proc. Natl Acad. Sci. USA
108 (Suppl. 1), 4659–4665 (2011).
19. Juge,N. Microbial adhesins to gastrointestinal mucus.
Trends Microbiol. 20, 30–39 (2012).
20. Derrien,M. etal. Mucin-bacterial interactions in the
human oral cavity and digestive tract. Gut Microbes 1,
254–268 (2010).
21. Ambort,D. etal. Calcium and pH-dependent packing
and release of the gel-forming MUC2 mucin. Proc.
Natl Acad. Sci. USA 109, 5645–5650 (2012).
22. Sharma,R., Schumacher,U., Ronaasen,V. & Coates,M.
Rat intestinal mucosal responses to a microbial flora
and different diets. Gut 36, 209–214 (1995).
23. Petersson,J. etal. Importance and regulation of the
colonic mucus barrier in a mouse model of colitis.
Am. J.Physiol. Gastrointest. Liver Physiol. 300,
G327–G333 (2011).
24. An,G. etal. Increased susceptibility to colitis and
colorectal tumors in mice lacking core 3-derived
O-glycans. J.Exp. Med. 204, 1417–1429 (2007).
25. Fu,J. etal. Loss of intestinal core 1-derived O-glycans
causes spontaneous colitis in mice. J.Clin. Invest. 121,
1657–1666 (2011).
26. van de Pavert,S.A. & Mebius,R.E. New insights into
the development of lymphoid tissues. Nature Rev.
Immunol. 10, 664–674 (2010).
27. Mebius,R.E. Organogenesis of lymphoid tissues.
Nature Rev. Immunol. 3, 292–303 (2003).
28. Renz,H., Brandtzaeg,P. & Hornef,M. The impact
of perinatal immune development on mucosal
homeostasis and chronic inflammation. Nature Rev.
Immunol. 12, 9–23 (2012).
29. Round,J.L. & Mazmanian,S.K. The gut microbiota
shapes intestinal immune responses during health and
disease. Nature Rev. Immunol. 9, 313–323 (2009).
30. Kanamori,Y. etal. Identification of novel lymphoid
tissues in murine intestinal mucosa where clusters of
lympho-hemopoietic progenitors
develop. J.Exp. Med. 184, 1449–1459 (1996).
31. Eberl,G. Inducible lymphoid tissues in the adult gut:
recapitulation of a fetal developmental pathway?
Nature Rev. Immunol. 5, 413–420 (2005).
32. Eberl,G. & Littman,D.R. Thymic origin of intestinal
αβ T cells revealed by fate mapping of RORγt
Science 305, 248–251 (2004).
33. Hamada,H. etal. Identification of multiple isolated
lymphoid follicles on the antimesenteric wall of the
mouse small intestine. J.Immunol. 168, 57–64
34. Bouskra,D. etal. Lymphoid tissue genesis induced by
commensals through NOD1 regulates intestinal
homeostasis. Nature 456, 507–510 (2008).
A study which reveals that microbial induction
of ileal lymphoid follicles is mediated via
peptidoglycans that are recognized mainly by
the intracellular NOD1 receptor.
35. Cupedo,T. etal. Human fetal lymphoid tissue-inducer
cells are interleukin 17-producing precursors to
natural killer-like cells. Nature
Immunol. 10, 66–74 (2009).
36. Luci,C. etal. Influence of the transcription factor RORγt
on the development of NKp46
cell populations in gut
and skin. Nature Immunol. 10, 75–82 (2009).
37. Sanos,S.L. etal. RORγt and commensal microflora
are required for the differentiation of mucosal
interleukin 22-producing NKp46
cells. Nature
Immunol. 10, 83–91 (2009).
38. Zheng,Y. etal. Interleukin-22 mediates early host
defense against attaching and effacing bacterial
pathogens. Nature Med. 14, 282–289 (2008).
39. Cohen,N.R., Garg,S. & Brenner,M.B. Antigen
presentation by CD1 lipids, T cells, and NKT cells in
microbial immunity. Adv. Immunol. 102, 1–94 (2009).
40. Van Kaer,L., Parekh,V.V. & Wu,L. Invariant natural
killer T cells: bridging innate and adaptive immunity.
Cell Tissue Res. 343, 43–55 (2011).
41. Olszak,T. etal. Microbial exposure during early life
has persistent effects on natural killer T cell function.
Science 336, 489–493 (2012).
An elegant study demonstrating that the gut
microbiota is required for normal development of
iNKTcells in neonates and thereby protects from
inflammatory diseases, thus confirming the hygiene
42. Kieper,W.C. etal. Recent immune status determines
the source of antigens that drive homeostatic T cell
expansion. J.Immunol. 174, 3158–3163 (2005).
43. Smith,P.M. & Garrett,W.S. The gut microbiota and
mucosal T cells. Front. Microbiol. 2, 111 (2011).
44. Hooper,L.V. & Macpherson,A.J. Immune
adaptations that maintain homeostasis with the
intestinal microbiota. Nature Rev. Immunol. 10,
159–169 (2010).
45. Round,J.L. etal. The Toll-like receptor 2 pathway
establishes colonization by a commensal of the human
microbiota. Science 332, 974–977 (2011).
46. Maynard,C.L. etal. Regulatory T cells expressing
interleukin 10 develop from Foxp3
and Foxp
precursor cells in the absence of interleukin 10.
Nature Immunol. 8, 931–941 (2007).
47. Atarashi,K. etal. Induction of colonic regulatory
Tcells by indigenous Clostridium species. Science
331, 337–341 (2011).
48. Geuking,M.B. etal. Intestinal bacterial colonization
induces mutualistic regulatory T cell responses.
Immunity 34, 794–806 (2011).
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
49. Gaboriau-Routhiau,V. etal. The key role of segmented
filamentous bacteria in the coordinated maturation of
gut helper T cell responses. Immunity 31, 677–689
50. Ivanov,I.I. etal. Induction of intestinal Th17 cells by
segmented filamentous bacteria. Cell 139, 485–498
51. Lee,Y.K., Menezes,J.S., Umesaki,Y. &
Mazmanian,S.K. Proinflammatory T-cell responses to
gut microbiota promote experimental autoimmune
encephalomyelitis. Proc. Natl Acad. Sci. USA 108
(Suppl. 1), 4615–4622 (2011).
52. Wu,H.J. etal. Gut-residing segmented filamentous
bacteria drive autoimmune arthritis via T helper 17
cells. Immunity 32, 815–827 (2010).
53. Macpherson,A.J. & Uhr,T. Induction of protective
IgA by intestinal dendritic cells carrying commensal
bacteria. Science 303, 1662–1665 (2004).
54. Uematsu,S. etal. Regulation of humoral and cellular
gut immunity by lamina propria dendritic cells
expressing Toll-like receptor 5. Nature Immunol. 9,
769–776 (2008).
55. Macpherson,A.J. etal. A primitive T cell-independent
mechanism of intestinal mucosal IgA responses to
commensal bacteria. Science 288, 2222–2226
56. Kawamoto,S. etal. The inhibitory receptor PD-1
regulates IgA selection and bacterial composition in
the gut. Science 336, 485–489 (2012).
An article which shows that the gut microbiota is
required for the development of completely
functional IgA-producing cells and thereby
maintains microbial homeostasis in the intestine.
57. Gallo,R.L. & Hooper,L.V. Epithelial antimicrobial
defence of the skin and intestine. Nature Rev.
Immunol. 12, 503–516 (2012).
58. Putsep,K. etal. Germ-free and colonized mice
generate the same products from enteric
prodefensins. J.Biol. Chem. 275, 40478–40482
59. Cash,H.L., Whitham,C.V., Behrendt,C.L. &
Hooper,L.V. Symbiotic bacteria direct expression of
an intestinal bactericidal lectin. Science 313,
1126–1130 (2006).
60. Hooper,L.V., Stappenbeck,T.S., Hong,C.V. &
Gordon,J.I. Angiogenins: a new class of microbicidal
proteins involved in innate immunity. Nature Immunol.
4, 269–273 (2003).
61. Franchi,L. etal. NLRC4-driven production of IL-1β
discriminates between pathogenic and commensal
bacteria and promotes host intestinal defense. Nature
Immunol. 13, 449–456 (2012).
Work revealing that intestinal phagocytes
discriminate commensals from pathogens using
the intracellular NLRC4 (NOD-, LRR- and CARD-
containing 4) inflammasome and by being
hyporesponsive to commensal-derived TLR stimuli.
62. Schauber,J. etal. Expression of the cathelicidin LL-37
is modulated by short chain fatty acids in colonocytes:
relevance of signalling pathways. Gut 52, 735–741
63. Liang,S.C. etal. Interleukin (IL)-22 and IL-17 are
coexpressed by Th17 cells and cooperatively enhance
expression of antimicrobial peptides. J.Exp. Med.
203, 2271–2279 (2006).
64. Petnicki-Ocwieja,T. etal. Nod2 is required for the
regulation of commensal microbiota in the intestine.
Proc. Natl Acad. Sci. USA 106, 15813–15818
65. Salzman,N.H. etal. Enteric defensins are essential
regulators of intestinal microbial ecology. Nature
Immunol. 11, 76–83 (2010).
66. Vaishnava,S. etal. The antibacterial lectin RegIIIγ
promotes the spatial segregation of microbiota and
host in the intestine. Science 334, 255–258 (2011).
67. Shin,S.C. etal. Drosophila microbiome modulates
host developmental and metabolic homeostasis via
insulin signaling. Science 334, 670–674 (2011).
A detailed analysis revealing the molecular
pathway of a symbiotic interaction between the
fruit fly and one of its gut bacteria; this interaction
is required for a normal developmental rate, body
size, wing area and metabolism, as well as for
normal stem cell activity.
68. Koropatnick,T.A. etal. Microbial factor-mediated
development in a host-bacterial mutualism. Science
306, 1186–1188 (2004).
69. Troll,J.V. etal. Peptidoglycan induces loss of a nuclear
peptidoglycan recognition protein during host tissue
development in a beneficial animal–bacterial
symbiosis. Cell. Microbiol. 11, 1114–1127 (2009).
70. McFall-Ngai,M. Host-microbe symbiosis: the squid-
Vibrio association—a naturally occurring,
experimental model of animal/bacterial partnerships.
Adv. Exp. Med. Biol. 635, 102–112 (2008).
71. Wagner,C.L., Taylor,S.N. & Johnson,D. Host factors
in amniotic fluid and breast milk that contribute to gut
maturation. Clin. Rev. Allergy Immunol. 34, 191–204
72. Reinhardt,C., Reigstad,C.S. & Bäckhed,F. Intestinal
microbiota during infancy and its implications for
obesity. J.Pediatr. Gastroenterol. Nutr. 48, 249–256
73. Wostmann,B.S. The germfree animal in nutritional
studies. Annu. Rev. Nutr. 1, 257–279 (1981).
74. Gordon,H.A. & Bruckner-Kardoss,E. Effect of normal
microbial flora on intestinal surface area. Am.
J.Physiol. 201, 175–178 (1961).
75. Abrams,G.D., Bauer,H. & Sprinz,H. Influence of the
normal flora on mucosal morphology and cellular
renewal in the ileum. A comparison of germ-free and
conventional mice. Lab. Invest. 12, 355–364 (1963).
76. Reinhardt,C. etal. Tissue factor and PAR1 promote
microbiota-induced intestinal vascular remodelling.
Nature 483, 627–631 (2012).
An investigation which demonstrates that bacteria
promote vessel formation in the intestinal
epithelium by modulating tissue factor signalling.
77. Banasaz,M., Norin,E., Holma,R. & Midtvedt,T.
Increased enterocyte production in gnotobiotic rats
mono-associated with Lactobacillus rhamnosus GG.
Appl. Environ. Microbiol. 68, 3031–3034 (2002).
78. Alam,M., Midtvedt,T. & Uribe,A. Differential cell
kinetics in the ileum and colon of germfree rats.
Scand. J.Gastroenterol. 29, 445–451 (1994).
79. Wikoff,W.R. etal. Metabolomics analysis reveals
large effects of gut microflora on mammalian blood
metabolites. Proc. Natl Acad. Sci. USA 106,
3698–3703 (2009).
80. Husebye,E., Hellstrom,P.M. & Midtvedt,T. Intestinal
microflora stimulates myoelectric activity of rat small
intestine by promoting cyclic initiation and aboral
propagation of migrating myoelectric complex. Dig.
Dis. Sci. 39, 946–956 (1994).
81. Samuel,B.S. etal. Effects of the gut microbiota on
host adiposity are modulated by the short-chain
fatty-acid binding G protein-coupled receptor, Gpr41.
Proc. Natl Acad. Sci. USA 105, 16767–16772
82. Hooper,L.V. etal. Molecular analysis of commensal
host-microbial relationships in the intestine. Science
291, 881–884 (2001).
83. Lutgendorff,F., Akkermans,L.M. & Soderholm,J.D.
The role of microbiota and probiotics in stress-induced
gastro-intestinal damage. Curr. Mol. Med. 8, 282–298
84. Cario,E., Gerken,G. & Podolsky,D.K. Toll-like
receptor2 controls mucosal inflammation by regulating
epithelial barrier function. Gastroenterology 132,
1359–1374 (2007).
85. Rakoff-Nahoum,S., Paglino,J., Eslami-Varzaneh,F.,
Edberg,S. & Medzhitov,R. Recognition of commensal
microflora by Toll-like receptors is required for
intestinal homeostasis. Cell 118, 229–241 (2004).
86. Stappenbeck,T.S., Hooper,L.V. & Gordon,J.I.
Developmental regulation of intestinal angiogenesis
by indigenous microbes via Paneth cells. Proc. Natl
Acad. Sci. USA 99, 15451–15455 (2002).
87. Buchon,N., Broderick,N.A., Chakrabarti,S. &
Lemaitre,B. Invasive and indigenous microbiota
impact intestinal stem cell activity through multiple
pathways in Drosophila. Genes Dev. 23, 2333–2344
88. Crawford,P.A. & Gordon,J.I. Microbial regulation of
intestinal radiosensitivity. Proc. Natl Acad. Sci. USA
102, 13254–13259 (2005).
89. Savage,D.C., Siegel,J.E., Snellen,J.E. & Whitt,D.D.
Transit time of epithelial cells in the small intestines of
germfree mice and ex-germfree mice associated with
indigenous microorganisms. Appl. Environ. Microbiol.
42, 996–1001 (1981).
90. Blumberg,R. & Powrie,F. Microbiota, disease, and
back to health: a metastable journey. Sci. Transl. Med.
4, 137rv7 (2012).
91. Hope,M.E., Hold,G.L., Kain,R. & El-Omar,E.M.
Sporadic colorectal cancer – role of the commensal
microbiota. FEMS Microbiol. Lett. 244, 1–7 (2005).
92. Swidsinski,A. etal. Association between intraepithelial
Escherichia coli and colorectal cancer. Gastroenterology
115, 281–286 (1998).
93. Ley,R.E. etal. Obesity alters gut microbial ecology.
Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005).
94. Sanapareddy,N. etal. Increased rectal microbial
richness is associated with the presence of colorectal
adenomas in humans. ISME J. 6, 1858–1868
95. Uronis,J.M. & Jobin,C. Microbes and colorectal
cancer: is there a relationship? Curr. Oncol. 16,
22–24 (2009).
96. Dove,W.F. etal. Intestinal neoplasia in the Apc
mouse: independence from the microbial and natural
killer (beige locus) status. Cancer Res. 57, 812–814
97. Breuer,N. & Goebell,H. The role of bile acids in
colonic carcinogenesis. Klin. Wochenschr. 63, 97–105
98. Toprak,N.U. etal. A possible role of Bacteroides
fragilis enterotoxin in the aetiology of colorectal
cancer. Clin. Microbiol. Infect. 12, 782–786 (2006).
99. Abdulamir,A.S., Hafidh,R.R. & Abu Bakar,F. The
association of Streptococcus bovis/gallolyticus with
colorectal tumors: the nature and the underlying
mechanisms of its etiological role. J.Exp. Clin. Cancer
Res. 30, 11 (2011).
100. Kostic,A.D. etal. Genomic analysis identifies
association of Fusobacterium with colorectal
carcinoma. Genome Res. 22, 292–298 (2012).
101. Del Fattore,A., Teti,A. & Rucci,N. Bone cells and the
mechanisms of bone remodelling. Front. Biosci. (Elite
Ed.) 4, 2302–2321 (2012).
102. Bliziotes,M. etal. Serotonin transporter and receptor
expression in osteocytic MLO-Y4 cells. Bone 39,
1313–1321 (2006).
103. Yadav,V.K. etal. Lrp5 controls bone formation by
inhibiting serotonin synthesis in the duodenum. Cell
135, 825–837 (2008).
104. Kong,Y.Y. etal. Activated T cells regulate bone loss
and joint destruction in adjuvant arthritis through
osteoprotegerin ligand. Nature 402, 304–309
105. Sato,K. etal. Th17 functions as an osteoclastogenic
helper T cell subset that links T cell activation and
bone destruction. J.Exp. Med. 203, 2673–2682
106. Wei,S., Kitaura,H., Zhou,P., Ross,F.P. &
Teitelbaum,S.L. IL-1 mediates TNF-induced
osteoclastogenesis. J.Clin. Invest. 115, 282–290
107. Zwerina,J. etal. TNF-induced structural joint damage
is mediated by IL-1. Proc. Natl Acad. Sci. USA 104,
11742–11747 (2007).
108. Turnbaugh,P.J. etal. A core gut microbiome in obese
and lean twins. Nature 457, 480–484 (2009).
109. Ley,R.E. Obesity and the human microbiome. Curr.
Opin. Gastroenterol. 26, 5–11 (2010).
110. Turnbaugh,P.J. etal. An obesity-associated gut
microbiome with increased capacity for energy
harvest. Nature 444, 1027–1031 (2006).
111. Ley,R.E., Turnbaugh,P.J., Klein,S. & Gordon,J.I.
Microbial ecology: human gut microbes associated
with obesity. Nature 444, 1022–1023 (2006).
112. Qin,J. etal. A metagenome-wide association study of
gut microbiota in type 2 diabetes. Nature 490,
55–60 (2012).
A report which reveals that there are alterations in
the gut microbiome in Chinese patients with type2
diabetes, and that these alterations can predict the
occurrence of diabetes.
113. Bäckhed,F. etal. The gut microbiota as an
environmental factor that regulates fat storage. Proc.
Natl Acad. Sci. USA 101, 15718–15723 (2004).
The first demonstration that the gut microbiota
modulates adiposity.
114. Bäckhed,F., Manchester,J.K., Semenkovich,C.F. &
Gordon,J.I. Mechanisms underlying the resistance to
diet-induced obesity in germ-free mice. Proc. Natl
Acad. Sci. USA 104, 979–984 (2007).
115. Caesar,R. etal. Gut-derived lipopolysaccharide
augments adipose macrophage accumulation but is
not essential for impaired glucose or insulin tolerance
in mice. Gut 61, 1701–1707 (2012).
116. Cani,P.D. etal. Metabolic endotoxemia initiates
obesity and insulin resistance. Diabetes 56,
1761–1772 (2007).
117. Karlsson,F.H. etal. Symptomatic atherosclerosis is
associated with an altered gut metagenome. Nature
Commun. 3, 1245 (2012).
118. Wang,Z. etal. Gut flora metabolism of
phosphatidylcholine promotes cardiovascular disease.
Nature 472, 57–63 (2011).
119. Tremaroli,V. & Bäckhed,F. Functional interactions
between the gut microbiota and host metabolism.
Nature 489, 242–249 (2012).
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
120. Koch,H. & Schmid-Hempel,P. Socially transmitted gut
microbiota protect bumble bees against an intestinal
parasite. Proc. Natl Acad. Sci. USA 108,
19288–19292 (2011).
121. Boettcher,K.J., Ruby,E.G. & McFall-Ngai,M.J.
Bioluminescence in the symbiotic squid Euprymna
scolopes is controlled by a daily biological rhythm.
J.Comp. Physiol. A Neuroethol. Sens. Neural Behav.
Physiol. 179, 65–73 (1996).
122. Degnan,P.H. etal. Factors associated with the
diversification of the gut microbial communities within
chimpanzees from Gombe National Park. Proc. Natl
Acad. Sci. USA 109, 13034–13039 (2012).
123. Sharon,G. etal. Commensal bacteria play a role in
mating preference of Drosophila melanogaster. Proc.
Natl Acad. Sci. USA 107, 20051–20056 (2010).
124. Huang,Y., Callahan,S. & Hadfield,M.G. Recruitment
in the sea: bacterial genes required for inducing larval
settlement in a polychaete worm. Sci. Rep. 2, 228
125. Verhulst,N.O. etal. Composition of human skin
microbiota affects attractiveness to malaria
mosquitoes. PLoS ONE 6, e28991 (2011).
126. Forsythe,P. & Kunze,W.A. Voices from within: gut
microbes and the CNS. Cell. Mol. Life Sci. 70, 55–69
127. Amaral,F.A. etal. Commensal microbiota is
fundamental for the development of inflammatory
pain. Proc. Natl Acad. Sci. USA 105, 2193–2197
128. Sudo,N. etal. Postnatal microbial colonization
programs the hypothalamic-pituitary-adrenal system
for stress response in mice. J.Physiol. 558, 263–275
129. Bercik,P. etal. The intestinal microbiota affect central
levels of brain-derived neurotropic factor and behavior
in mice. Gastroenterology 141, 599–609 (2011).
130. Lyte,M., Li,W., Opitz,N., Gaykema,R.P. &
Goehler,L.E. Induction of anxiety-like behavior in
mice during the initial stages of infection with the
agent of murine colonic hyperplasia Citrobacter
rodentium. Physiol. Behav. 89, 350–357 (2006).
131. Heijtz,R.D. etal. Normal gut microbiota modulates
brain development and behavior. Proc. Natl Acad. Sci.
USA 108, 3047–3052 (2011).
The finding that the gut microbiota affects the
development of the brain and anxiety-like
132. Neufeld,K.M., Kang,N., Bienenstock,J. & Foster,
J.A. Reduced anxiety-like behavior and central
neurochemical change in germ-free mice.
Neurogastroenterol. Motil. 23, 255–e119 (2011).
133. Diamond,B., Huerta,P.T., Tracey,K. & Volpe,B.T.
It takes guts to grow a brain: increasing evidence of
the important role of the intestinal microflora in
neuro- and immune-modulatory functions during
development and adulthood. Bioessays 33, 588–591
134. Collins,S.M., Surette,M. & Bercik,P. The interplay
between the intestinal microbiota and the brain.
Nature Rev. Microbiol. 10, 735–742 (2012).
135. Kellermayer,R. etal. Colonic mucosal DNA
methylation, immune response, and microbiome
patterns in Toll-like receptor 2-knockout mice.
FASEBJ. 25, 1449–1460 (2011).
136. Ley,R.E. etal. Evolution of mammals and their gut
microbes. Science 320, 1647–1651 (2008).
137. Dominguez-Bello,M.G. etal. Delivery mode shapes
the acquisition and structure of the initial microbiota
across multiple body habitats in newborns. Proc. Natl
Acad. Sci. USA 107, 11971–11975 (2010).
138. Yatsunenko,T. etal. Human gut microbiome viewed
across age and geography. Nature 486, 222–227
An extensive analysis of the gut microbiome of
healthy children and adults from three different
geographical regions.
139. Koboziev,I., Karlsson,F. & Grisham,M.B. Gut-
associated lymphoid tissue, T cell trafficking, and
chronic intestinal inflammation. Ann. NYAcad. Sci.
1207 (Suppl. 1), e86–e93 (2010).
140. Veenbergen,S. & Samsom,J.N. Maintenance of small
intestinal and colonic tolerance by IL-10-producing
regulatory T cell subsets. Curr. Opin. Immunol. 24,
269–276 (2012).
141. Walker,J.A., Barlow,J.L. & McKenzie,A.N. Innate
lymphoid cells - how did we miss them? Nature Rev.
Immunol. 13, 75–87 (2013).
The authors thank R.Perkins for editing the manuscript and
A.Hallén for contributions to the figures. Work in the Bäckhed
laboratory is supported by the Swedish Research Council, the
Swedish Foundation for Strategic Research, the Knut and Alice
Wallenberg Foundation, the Swedish Heart Lung foundation,
the Swedish Diabetes Foundation, the European Union-funded
project TORNADO (grant FP7-KBBE-222720), Ragnar
Söderberg’s Foundation, Torsten Söderberg’s Foundation, the
NovoNordisk Foundation, AFA Insurance, IngaBritt and Arne
Lundberg’s Foundation and a LUA-ALF grant from the Swedish
Västra Götalandsregionen.
Competing interests statement
The authors declare competing financial interests: see Web
version for details.
Fredrik Bäckhed’s homepage:
APRIL 2013
© 2013 Macmillan Publishers Limited. All rights reserved
... The phylum Bacteroidetes is absolutely dominant in the intestinal and have many functions such as enzymatic carbohydrates, participation in polysaccharide metabolism, bile acid and steroids, and maintenance of normal intestinal physiology, etc., which have an important impact on human health (50). Ritchie, L.E. et al. found that the intestinal damage profile of the DSS-induced UC rat model was negatively correlated with Firmicutes, Actinobacteria and Acidobacteria (51). ...
Full-text available
Objective To investigate the therapeutic effect and possible mechanism of artemisinin on ulcerative colitis (UC) induced by sodium glucan sulfate (DSS) in rats based on network pharmacology. Methods First, according to the 3D structure of artemisinin, the effective targets of the active compounds were obtained through the Swissstarge website ( ) and the TargetNet website ( ). With the aid of Genecards ( ), OMIM ( ), TTD ( ) to obtain effective targets of disease. The disease gene-drug target network was constructed by extracting the intersection targets of the two, and the visualization operation and analysis were performed by using Cytoscape 3.7.2. Gene function enrichment analysis and pathway analysis were performed on the intersection targets with the help of R language software. Autidock Vina was used for molecular docking of artemisinin to key targets. Then, 40 male Wistar rats were randomly divided into normal group, model group, mesalazine group (0.315 g/kg·d) and artemisinin group (0.1 g/kg·d), with 10 rats in each group. Except for the normal group, the rats in the other groups were given 3.5% DSS solution freely for 10 days to replicate the UC model. After the successful modeling, the rats were given intragastric administration. The normal group and the model group were given the same amount of 0.9% normal saline, once a day, for 14 days. The general condition of the rats was recorded every day and the disease activity index (DAI) score was performed. After the administration, the colonic mucosal damage index (CMDI) was scored, the histopathological changes of the colon were observed by HE staining, and the levels or activities of serum CRP, TNF-α, MDA, SOD, HIF-1α and T-AOC were detected by ELISA, and fecal and intestinal microbiota of rats were detected by 16S rDNA sequencing. Results Network pharmacology shows that, there were 98 key targets of artemisinin screening, 4853 effective targets of UC, and 43 intersection targets for artemisinin and UC, involving 48 signaling pathways. The molecular docking results showed that the binding energies of the key proteins to artemisinin were less than -5.0 kJ·mol ⁻¹ , and the binding energy of PTGS2 NOS3 to artemisinin was the best. Animal experiments have shown that, Compared with the model group, the DAI and CMDI scores of the artemisinin group and the mesalazine group decreased, the levels and activities of serum CRP, TNF-α, MDA and HIF-1α decreased, the levels and activities of SOD and T-AOC increased, the abundance and diversity of inteatinal microbiota increased, and the abundance of p-Acidobacteria, p-Chloroflexi, p-Gemmatimonadetes, p-Nitrospirae in artemisinin group increased ( P< 0.05), and there was no significant change in others. Conclusion Artemisinin intervenes with UC through key target proteins such as PTGS2 and ESR1, and involves various biological processes such as inflammation and intestinal microbiota, revealing that molecular basis of artemisinin in the treatment of UC. Artemisinin is effective in improving the symptoms of UC rats, and its mechanism may be to relieve oxidative stress response by inhibiting inflammation, thus promoting intestinal mucosal repair. The regulatory effect on intestinal microbiota needs to be further studied.
... This involves nutrition extraction from indigestible fibres, tissue homeostasis preservation, and pathogen prevention. This link is reciprocal; nutrition, lifestyle, age, antibiotics, and disease progression may all influence the microbiota [43]. The liver influences the makeup of the gut microbiome by synthesizing and transporting bile acids (which have antimicrobial characteristics) into the intestine, where IgA antibodies are produced. ...
Full-text available
Background: The human gastrointestinal tract (GIT) population of almost 200 common bacteria, viruses, and fungi supplies the host with distinct metabolic activities and is critical in health and illness state.
... In addition to human cells, the gut also hosts large microbial populations, up to 10 7 for the ileum alone 293 , which colonize us after birth and follows us for the rest of our lives. ...
Full-text available
Modern day ethics and laws call for more safety and use of fewer animals in biomedical research. It became crucial to develop novel in vitro devices of higher relevance. Since the end of the twentieth century, several systems have been proposed by researchers in attempts to palliate the shortcomings of current systems. Notably, organs-on-chip systems are specifically tailored to recapitulate tissue functions in a manner that remains easily accessible for the experimenter. Despite the significant improvements that were brought during the last century to in vitro cell and tissue culture systems, the field of bioengineering is still young and much progress remains to be done. The work presented here details the development of an organ-on-chip that includes a biocompatible and actuatable hydrogel membrane, with controlled physico-chemical properties. Such chip is relevant when hosting barrier tissues, which are composed of several cell types, disposed on each side of a barrier, as well as within its bulk, and are often submitted to mechanical stimuli. During this PhD, several objectives have been attained. Notably, we: - Designed and produced an organ-on-chip including a biocompatible and actuatable hydrogel layer, as well as a microfluidic system allowing the independent control of both flow and actuation. - Characterized the deformation of the hydrogel layer. - Cultured intestinal cells within the chip, which formed a three dimensionally structure epithelium, and characterized its apparent permeability to molecules of varying sizes
... That finding is consistent with our results of significantly lower expression levels of Claudin6 and ZO1 in grass carp exposed to florfenicol ( Figure 7A). Intestinal microbiota play important roles in the safeguarding the integrity and functioning of the mucosal barrier and they should be targeted when evaluating intestinal health (55). Our correlation analysis of key genera with mucosal barrier proteins showed that Cetobacterium had a positive correlation with ZO1 and Claudin6, while ZOR0006 had a positive correlation with ZO3 and Claudin6, thus indicating that these key genera contribute to the intestine mucosal barrier function of grass carp fish. ...
Full-text available
Gut microbiota play a vital role in fish health homeostasis. Antibiotics are known to alter microbial community composition and diversity; however, the substantial effects of antibiotics upon the gut microbiome with respect to immune-related pathways in healthy fish remain unclear. Accordingly, here we explored the impact of two antibiotics on the intestinal health, immune response, microbiome dynamics, and transcriptome profiles of grass carp. A two-week feeding trial was carried out in which the basal diet was complemented with enrofloxacin (10 mg/kg) or florfenicol (10 mg/kg). The results showed that: (1) Enrofloxacin and florfenicol both induced intestinal oxidative stress and reduced the digestive enzyme activity of grass carp. (2) High-throughput sequencing of 16S rDNA revealed that enrofloxacin but not the florfenicol treatment influenced gut microbiota diversity in grass carp by shifting α/β-diversity with more abundant pathogens detected. (3) Transcriptome profiling demonstrated that florfenicol down-regulated the immune-related pathways of grass carp, and the network analysis revealed that IgA was negatively correlated with certain pathogens, such as Shewanella and Aeromonas . (4) Antibiotic-induced alternations of gut core microbes were revealed via immune-related transcripts, as were lower mRNA expression levels of mucosal-related genes. (5) Apoptosis and histopathological changes were detected in the enrofloxacin- and florfenicol-treated groups compared with the control group. Overall, administering antibiotics will promote oxidative stress, cause intestinal flora dysbiosis, inhibit the mucosal immune system, and induce apoptosis in grass carp.
Background Efficient identification of microbe-drug associations is critical for drug development and solving problem of antimicrobial resistance. Traditional wet-lab method requires a lot of money and labor in identifying potential microbe-drug associations. With development of machine learning and publication of large amounts of biological data, computational methods become feasible. Methods In this article, we proposed a computational model of neighborhood-based inference (NI) and restricted Boltzmann machine (RBM) to predict potential microbe-drug association (NIRBMMDA) by using integrated microbe similarity, integrated drug similarity and known microbe-drug associations. First, NI was used to obtain a score matrix of potential microbe-drug associations by using different thresholds to find similar neighbors for drug or microbe. Second, RBM was employed to obtain another score matrix of potential microbe-drug associations based on contrastive divergence algorithm and sigmoid function. Because generalization ability of individual method is poor, we used an ensemble learning to integrate two score matrices for predicting potential microbe-drug associations more accurately. In particular, NI can fully utilize similar (neighbor) information of drug or microbe and RBM can learn potential probability distribution hid in known microbe-drug associations. Moreover, ensemble learning was used to integrate individual predictor for obtaining a stronger predictor. Results In global leave-one-out cross validation (LOOCV), NIRBMMDA gained the area under the receiver operating characteristics curve (AUC) of 0.8666, 0.9413 and 0.9557 for datasets of DrugVirus, MDAD and aBiofilm, respectively. In local LOOCV, AUCs of 0.8512, 0.9204 and 0.9414 were obtained for NIRBMMDA based on datasets of DrugVirus, MDAD and aBiofilm, respectively. For five-fold cross validation, NIRBMMDA acquired AUC and standard deviation of 0.8569 ± −0.0027, 0.9248 ± −0.0014 and 0.9369 ± −0.0020 on the basis of datasets of DrugVirus, MDAD and aBiofilm, respectively. Moreover, case study for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed that 13 out of the top 20 predicted drugs were verified by searching literature. The other two case studies indicated that 17 and 17 out of the top 20 predicted microbes for the drug of ciprofloxacin and minocycline were confirmed by identifying published literature, respectively.
The development of probiotics for chickens is a rapidly expanding field. The main approach to probiotics is to administer the probiotic strain throughout the bird's life, usually through incorporation in the feed. However, probiotics which would utilize bacterial strains capable of permanently colonizing the gut after a single exposure are likely to have a greater impact on the developing gut community as well as on the host, would simplify probiotic use and also reduce costs in an industrial setting. Finally, very limited and conflicting information about the colonization ability of different bacterial strains has been reported. Here we report two colonization experiments using 14 different bacterial strains from diverse phylogenetic groups. In both experiments, groups of chicks were orally inoculated on the day of hatch with different bacterial strains that had been previously isolated from adult heavy breeders. In the first experiment, colonization of the bacterial strains in broiler chicks was determined 7 days after treatment. In the second experiment, colonization was followed in layer chicks until day 17. Ten of the bacterial strains, including Lactobacillales and Bacteroidales strains, were able to colonize chicks after a single exposure for the duration of the experiment. For a few of these strains, exposure had little effect compared to non-treated chicks due to natural background colonization. Only 4 strains failed to colonize the chicks. Moreover, it is shown that fecal samples are useful to identify and provide a dynamic view of colonization. We further analyzed the effects of artificial colonization on microbiota composition. Some of the strains used in this research were found to reduce Enterobacteriaceae family abundance, implying that they might be useful in reducing relevant pathogen levels. To conclude, our results show that the development of single exposure based probiotics is possible.
Recent data suggest that short-chain fatty acids (SCFAs), the major fermentation product from gut microbial degradation of dietary fiber, have protective effects against renal ischemia–reperfusion (IR) injury, colitis, and allergic asthma. However, the effect of SCFAs on acute lung injury (ALI) caused by IR is still unclear. In this study, we examine whether SCFAs have protective effects against IR-induced ALI and explore possible protective mechanisms. IR-induced ALI was established by 40 min ischemia followed by 60 min reperfusion in isolated perfused rat lungs. Rats were randomly assigned to one of six groups: control, control + acetate (400 mg/kg), IR, and IR + acetate at one of three dosages (100, 200, 400 mg/kg). Bronchoalveolar lavage fluids (BALF) and lung tissues were obtained and analyzed at the end of the experiment. In vitro, mouse lung epithelial cells (MLE-12) subjected to hypoxia-reoxygenation (HR) were pretreated with acetate (25 mmol/L) and GPR41 or GPR43 siRNA. Acetate decreased lung weight gain, lung weight/body weight ratios, wet/dry weight ratios, pulmonary artery pressure, and protein concentration of the BALF in a dose-dependent manner for IR-induced ALI. Acetate also significantly inhibited the production of TNF-α, IL-6 and CINC-1 in the BALF. Moreover, acetate treatment restored suppressed IκB-α levels and reduced nuclear NF-κB p65 levels in lung tissues. In addition, acetate mitigated IR-induced apoptosis and tight junction disruption in injured lung tissue. In vitro analyses showed that acetate attenuated NF-κB activation and KC/CXCL-1 levels in MLE-12 cells exposed to HR. The protective effects of acetate in vitro were significantly abrogated by GPR41 or GPR43 siRNA. Acetate ameliorates IR-induced acute lung inflammation and its protective mechanism appears to be via the GPR41/43 signaling pathway. Based on our findings, acetate may provide a novel adjuvant therapeutic approach for IR-induced lung injury.
Early bacterial colonization and succession within the gastrointestinal tract have been suggested to be crucial in the development of host immunity. In this study, we have investigated the changes in live weight and concentrations of selected serum parameters in relation to their fecal bacterial communities as determined by high throughput sequencing of the 16S rRNA gene over the same period in lambs. The results showed that lambs’ growth performance, the serum parameters, fecal bacterial community and fecal bacterial functions were all affected (P<0.05) by age of the lambs. Similarity within age groups of fecal microbiota was lower in the preweaning period and increased sharply (P<0.05) after weaning at 60 days. The similarity between the samples collected from birth to 90 days of age and those collected at 120 days of age, increased (P<0.05) sharply after 30 days of age. Some age-associated changes in microbial genera were correlated with the changes in concentrations of immune indicators, including negative (P<0.05) correlations between the relative abundance of Lachnospiraceae UCG-010, Eubacterium coprostanoligenes group, Ruminococcaceae UCG-005, Ruminococcaceae UCG-009, Ruminococcaceae UCG-013, Ruminiclostridium 6, Ruminococcaceae UCG-008, and Oscillibacter with serum concentrations of lipopolysaccharide (LPS), D-lactate dehydrogenase (DLA), immunoglobulin (IgA, IgM, and IgG), and cytokines (interleukin-1β (IL-1β), IL-6, IL-12, IL-17), tumor necrosis factor-α (TNF-α), and the relative abundance of these genera increased from 45 days of age. In conclusion, these results suggested that the age-related abundances of particular genera were correlated with serum markers of immunity in lambs, and there might be a critical window in the period from birth to 45 days of age which provide an opportunity for potential manipulation of the fecal microbial ecosystems to enhance immune function.
Turtle populations around the world are continually confronted with changing environments that affect their ecology and conservation status. Among freshwater turtles, population dynamics are thought to be mediated by complex yet often cryptic causes. One recent direction of focus in addressing these causes is the turtle-associated microbiota. In turtles, the gut-associated microbiota is of exceptional interest due to its continual association with host species under changing conditions. Diet-based fluctuations and changes in microbial diversity may correspond to varying external environments at both the individual and population level. Environmental responses are of particular interest due to the anthropogenic changes that may underlie them. Pollutants, disruption of climatic patterns, and habitat fragmentation all have the potential to affect turtle-associated microbiota and subsequent population and species conservation. To better understand potential human-induced changes, the diversity of turtle-associated microbiota over local spatial gradients must be better understood. We examined microbial community α- and β-diversity among 30 adult False Map Turtles (Graptemys pseudogeographica) at three sites within the lower Missouri River, United States. Our results indicate significant microbial community centroid differences among sites (β-diversity), which are likely mediated by various local environmental factors. Such factors will have to be carefully considered in any future attribution of anthropogenic determinants on turtle-associated microbiota as it relates to turtle population dynamics.
Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are terpene compounds, as methanogen membranes are composed of isoprenoid lipids resulting in a higher flux through isoprenoid biosynthetic pathways compared to Eukarya and Bacteria. To assess the metabolic plasticity of methanogens, our laboratory has engineered the methanogen Methanosarcina acetivorans to produce the hemiterpene isoprene. We hypothesized that isoprene producing strains would result in a decreased growth phenotype corresponding to a depletion of metabolic precursors needed for isoprenoid membrane production. We found that the engineered methanogens responded well to the modification, directing up to 4% of total towards isoprene production and increasing overall biomass despite the additional metabolic burden. Using flux balance analysis and RNA sequencing we investigated how the engineered strains respond to isoprene production and how production can be enhanced. Advisor: Nicole R. Buan
Full-text available
Diabetes and obesity are two metabolic diseases characterized by insulin resistance and a low-grade inflammation. Seeking an inflammatory factor causative of the onset of insulin resistance, obesity, and diabetes, we have identified bacterial lipopolysaccharide (LPS) as a triggering factor. We found that normal endotoxemia increased or decreased during the fed or fasted state, respectively, on a nutritional basis and that a 4-week high-fat diet chronically increased plasma LPS concentration two to three times, a threshold that we have defined as metabolic endotoxemia. Importantly , a high-fat diet increased the proportion of an LPS-containing microbiota in the gut. When metabolic endotoxemia was induced for 4 weeks in mice through continuous subcutaneous infusion of LPS, fasted glycemia and insulinemia and whole-body, liver, and adipose tissue weight gain were increased to a similar extent as in high-fat–fed mice. In addition, adipose tissue F4/80-positive cells and markers of inflammation, and liver triglyceride content, were increased. Furthermore, liver, but not whole-body, insulin resistance was detected in LPS-infused mice. CD14 mutant mice resisted most of the LPS and high-fat diet–induced features of metabolic diseases. This new finding demonstrates that metabolic endotoxemia dysregulates the inflammatory tone and triggers body weight gain and diabetes. We conclude that the LPS/CD14 system sets the tone of insulin sensitivity and the onset of diabetes and obesity. Lowering plasma LPS concentration could be a potent strategy for the control of metabolic diseases.
Full-text available
Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-stage MGWAS based on deep shotgun sequencing of the gut microbial DNA from 345 Chinese individuals. We identified and validated approximately 60,000 type-2-diabetes-associated markers and established the concept of a metagenomic linkage group, enabling taxonomic species-level analyses. MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance. An analysis of 23 additional individuals demonstrated that these gut microbial markers might be useful for classifying type 2 diabetes.
Aim: To study the role of intestinal flora in inflammatory bowel disease (IBD). Methods: The spatial organization of intestinal flora was investigated in normal mice and in two models of murine colitis using fluorescence in situ hybridization. Results: The murine small intestine was nearly bacteria-free. The normal colonic flora was organized in three distinct compartments (crypt, interlaced, and fecal), each with different bacterial compositions. Crypt bacteria were present in the cecum and proximal colon. The fecal compartment was composed of homogeneously mixed bacterial groups that directly contacted the colonic wall in the cecum but were separated from the proximal colonic wall by a dense interlaced layer. Beginning in the middle colon, a mucus gap of growing thickness physically separated all intestinal bacteria from contact with the epithelium. Colonic inflammation was accompanied with a depletion of bacteria within the fecal compartment, a reduced surface area in which feces had direct contact with the colonic wall, increased thickness and spread of the mucus gap, and massive increases of bacterial concentrations in the crypt and interlaced compartments. Adhesive and infiltrative bacteria were observed in inflamed colon only, with dominant Bacteroides species. Conclusion: The proximal and distal colons are functionally different organs with respect to the intestinal flora, representing a bioreactor and a segregation device. The highly organized structure of the colonic flora, its specific arrangement in different colonic segments, and its specialized response to inflammatory stimuli indicate that the intestinal flora is an innate part of host immunity that is under complex control.
Diabetes and obesity are two metabolic diseases characterized by insulin resistance and a low-grade inflammation. Seeking an inflammatory factor causative of the onset of insulin resistance, obesity, and diabetes, we have identified bacterial lipopolysaccharide (LPS) as a triggering factor. We found that normal endotoxemia increased or decreased during the fed or fasted state, respectively, on a nutritional basis and that a 4-week high-fat diet chronically increased plasma LPS concentration two to three times, a threshold that we have defined as metabolic endotoxemia. Importantly , a high-fat diet increased the proportion of an LPS-containing microbiota in the gut. When metabolic endotoxemia was induced for 4 weeks in mice through continuous subcutaneous infusion of LPS, fasted glycemia and insulinemia and whole-body, liver, and adipose tissue weight gain were increased to a similar extent as in high-fat–fed mice. In addition, adipose tissue F4/80-positive cells and markers of inflammation, and liver triglyceride content, were increased. Furthermore, liver, but not whole-body, insulin resistance was detected in LPS-infused mice. CD14 mutant mice resisted most of the LPS and high-fat diet–induced features of metabolic diseases. This new finding demonstrates that metabolic endotoxemia dysregulates the inflammatory tone and triggers body weight gain and diabetes. We conclude that the LPS/CD14 system sets the tone of insulin sensitivity and the onset of diabetes and obesity. Lowering plasma LPS concentration could be a potent strategy for the control of metabolic diseases.
Bone is a peculiar connective tissue which functionally interacts with many other organs and tissues, including bone marrow, lymphoid tissue, kidney, adipose tissue, endocrine pancreas, brain and gonads. Bone functions are accomplished by three principal cell types: the osteoblasts, cells of mesenchymal origin having osteogenic functions, the osteoclasts, giant multinucleated cells arising from the monocyte-macrophage line and devoted to resorb bone, and the osteocytes, the latter arising from mature osteoblasts that, once deposited the bone matrix, remain trapped in it, becoming quiescent cells. Osteocytes are known for their role as mechanosensors, however, old and new evidence showed their active contribution to mineral homeostasis. Moreover, the cross-talk between bone cells is crucial, since a correct bone homeostasis relies on a right coupling between osteoblast and osteoclast functions. Any deregulation of this coupling is responsible for bone disease condition, which reflects on other organs with which bone interacts.