ArticlePDF AvailableLiterature Review

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.
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
humanhealth.
The ‘normal’ gut microbiota is dominated by anaer-
obic bacteria, which outnumber aerobic and faculta-
tive anaerobic bacteria by 100- to 1,000-fold
1
. In total,
the intestinal microbiota consists of approximately
500–1,000 species that, interestingly, belong to only
a few of the known bacterial phyla
2,3
. 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
2,3
. 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
1
microbial cells per gram of content, the
duodenum 10
3
cells per gram, the jejunum 10
4
cells per
gram, the ileum 10
7
cells per gram and the colon up to
10
12
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)
4
. Second,
bacterial diversity increases in the same axes and manner
as microbial density
4
. 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
5,6
. 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
14
bacte-
rial cells are present, which is ten times the number of
human cells in the body
7
. 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
2,8
. 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
9
. 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
10
; and they have a key role in
maintaining tissue homeostasis. Recent studies have
also revealed that the human microbiota influences
1
Wallenberg Laboratory
for Cardiovascular and
Metabolic Research,
Sahlgrenska University
Hospital, Department of
Molecular and Clinical
Medicine, University
of Gothenburg.
2
Sahlgrenska Center for
Cardiovascular and Metabolic
Research, Department of
Molecular and Clinical
Medicine, University of
Gothenburg, SE‑413 45
Gothenburg, Sweden.
3
Novo Nordisk Foundation
Center for Basic Metabolic
Research, Section for
Metabolic Receptology and
Enteroendocrinology,
Faculty of Health Sciences,
University of Copenhagen,
Copenhagen DK‑2200,
Denmark.
Correspondence to F.B.
e‑mail:
Fredrik.Backhed@wlab.gu.se
doi:10.1038/nrmicro2974
Published online
25 February 2013
Microbiota
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
1,2
and Fredrik Bäckhed
1,2,3
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.
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Mutualistic
Pertaining to a relationship
between two organisms:
beneficial to both organisms.
The term originates from the
Latin word mutuus (lent,
borrowed or mutual).
Superorganism
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).
Symbiosis
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).
Pathobionts
Normally harmless
microorganism that can
become pathogens under
certain environmental
conditions.
the development and homeostasis of other host tissues,
including thebone
11
.
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
forhealth.
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
interactions.
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
12
. It is also now widely
accepted that the hosts mucosal immune system is char-
acterized by tolerance to microorganisms rather than
responsiveness
13
. 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
14
.
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
2
in
humans
15
. 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
12
cells per
gram in the lower intestine
16
. 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
17
.
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
18
.
The colonic mucus layer is in fact composed of two
layers
17
. 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
18
.
Mucin2 (MUC2) is the main mucin in the small and
large intestines of both mice and humans
18
. 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
19,20
. However, bacteria are found
only in the outer layer
17
, 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
137
. 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
4
.
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
108,111
.
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
families
138
. This indicates that, as well as genetics and kinship, environmental factors
have a considerable effect on the microbial composition of the infant.
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Altered intestinal microbiota
Immunodeficiency
NOD2
IL-10
Hyperimmunity
IL-6
IL-12
TNF
Antibiotics Lifestyle Diet Hygiene
Chronic
inflammation
Metabolic
dysfunction
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
21
.
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
22
.
Stimulation with bacterial products such as lipopolysac-
charide (LPS) and peptidoglycan is sufficient to estab-
lish conventional mucus properties in germ-free mice
23
,
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
23–25
. 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.
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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
27
.
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-
tion
26
. 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
28
(FIG.2). Consequently, Peyer’s
patches, mesenteric lymph nodes and splenic white pulp
are underdeveloped in germ-free mice
29
.
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
30
. 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
31,32
. This process also
depends on the gut microbiota, as ILFs fail to develop
fully in germ-free mice
33
. 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
34
.
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
cells
34
.
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
propria
35–37
. Interestingly, theRORγt
+
NKp46
LTi-like
cells can differentiate into RORγt
+
NKp46
+
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
36,37
. 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
+
NKp46
+
NK-like cells than conven-
tionally raised mice
37
. 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
proteins
38
. 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
139
. Here, we list and describe the lymphocytes that are
known to be modulated by the gut microbiota
43,140,141
.
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
(T
H
1 cells). A subset of T
H
lymphocytes that is characterized by the expression of
interferon‑γ and transforming growth factorβ (TGFβ). T
H
1 cell differentiation is
induced by contact with activated macrophages or NK cells.
T helper 2 cells
(T
H
2 cells). A subset of T
H
lymphocytes that is characterized by the expression of the
cytokines IL‑4, IL‑5 and IL‑13. T
H
2 cell differentiation is induced in response to, for
example, allergens and extracellular microorganisms.
T helper 17 cells
(T
H
17 cells). A subset of T
H
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
microorganisms.
Regulatory T cells
(T
Reg
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
Reg
cells, which differentiate from CD4
+
Tcells in the thymus, and inducible T
Reg
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
(T
R
1 cells). These CD4
+
CD25
+
FOXP3
T cells are functionally equivalent to the
IL‑10‑producing T
Reg
cells. They respond to microorganisms and regulate intestinal
tolerance through the secretion of IL‑10.
Bcells
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.
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Mucus
Goblet cell
PSA
SFB
Peyer’s patch
Immature
Peyer’s patch
Immature
MLN
MLN
IgA-producing
plasma cell
T
H
17 cell
B cell
T cell
Dendritic cell
T
Reg
cell
B. fragilis
Intestinal
crypt
Intestinal
epithelial cell
AMP and
IgA production
Vessel
density
Villus
Mucus thickness
Altered mucus properties
a Germ-free mice
b c
Blood
vessel
AMP
IgA
Microbiota
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
CD4
+
CD25
+
FOXP3
+
regulatory T (T
Reg
) 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
H
17) cells,
which are pro-inflammatory.
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Experimental autoimmune
encephalomyelitis
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
sclerosis.
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
RORγt
+
NKp46
+
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
(T
H
1)- and T
H
2-type chemokines and cytokines, including
interferon-γ, IL-2, IL-4, IL-13, IL-17A, IL-21 and tumour
necrosis factor (TNF)
39,40
. 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
mice
41
, 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
41
.
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
42
(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
43
. Tcells can be assigned
to subpopulations that drive either a pro-inflammatory
immune response (T
H
1, T
H
2 and T
H
17 cells) or an anti-
inflammatory immune response (CD4
+
CD25
+
FOXP3
+
regulatoryT (T
Reg
) cells or CD4
+
CD25
+
FOXP3
type1
regulatoryT (T
R
1) cells), depending on the cytokines
that they produce
44
(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
Reg
cells locally in
the intestinal lamina propria but also in the circula-
tion
45
. T
Reg
cells produce IL-10 and thereby suppress the
pro-inflammatory T
H
17 response
46
. This skewing event is
mediated by polysaccharide A (PSA) on the outer mem-
brane of the bacterium, which is recognized by TLR2 on
CD4
+
Tcells and activates a signalling cascade involving
myeloid differentiation88 (MYD88) to induce T
Reg
cell
differentiation
45
. Indeed, a mutant strain of B.fragilis
lacking PSA fails to initiate differentiation of T
Reg
cells,
whereas purified PSA has the same effect as the wild-type
bacterium
29
.
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
T
Reg
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
Reg
cell response was observed when germ-free mice were
colonized with altered Schaedler flora, a cocktail of eight
defined bacteria including three Clostridia species
48
.
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
H
17 cells and, to a lesser extent, T
H
1
cells
49,50
. 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
H
17 cells. Notably,
mono-association of germ-free mice with SFB is suffi-
cient to restore susceptibility to T
H
17 cell-mediated arthri-
tis and experimental autoimmune encephalomyelitis
51,52
. So
far, however, it is not known whether T
H
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,
metabolites)
15
.
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
53
. 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
54
. 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
55
. 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
56
. 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
56
.
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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
drugs.
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.
Desmosome
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
forces.
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
solutes.
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
constitutively
58
, whereas others, such as ANG4 and
REG3γ, are induced following a microbial encounter
59,60
,
either via PRR signalling (through TLRs and NOD-like
receptors (NLRs)) or in a PRR-independent manner
(for example, by microbially fermented butyrate)
61,62
.
Furthermore, intestinal lymphocyte-derived IL-17 and
IL-22, which are bacterially modulated (see above),
induce the production of AMPs by IECs and Paneth
cells
59,63
. 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
64–66
.
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
2,3
. 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
10
. 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
67
. 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
squid
68
. Peptidoglycan signalling through a nuclear pep-
tidoglycan recogniton protein induces apoptosis, which
is an integral part of light organ morphogenesis
69
. 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
morning
70
.
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
71
(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
72
. The most prominent feature of germ-free
animals is a greatly enlarged caecum
73
. Furthermore,
the overall intestinal surface area in germ-free mice is
reduced compared with that of conventional mice
74
.
Germ-free mice are impaired in brush border differ-
entiation
75
and have reduced villus thickness
76
owing to
reduced cell regeneration
77
and a longer cell cycle time
78
.
The number of serotonin-producing enterochromaffin
cells is also higher in the gut of germ-free compared
with conventional mice
16
, but interestingly, germ-free
mice have lower levels of serotonin
79
, and this is thought
to correlate with decreased intestinal peristaltic activ-
ity and a prolonged gastrointestinal transit time
80,81
.
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
82
. Moreover, several Lactobacillus
strains rigidify tight junctions between epithelial cells,
resulting in reduced epithelial permeability
83
. 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
84,85
.
Interestingly, recent work has shown that, in addition
to promoting gastrointestinal tract morphogenesis, the
gut microbiota influences the remodelling of the vascu-
lar system
76,86
(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
76
.
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Nature Reviews | Microbiology
Intestinal function
GALT maturation
Tissue regeneration
Gut motility
Permeability
Metabolism
Energy expenditure
Nutrient accessibility
Short-chain fatty acids
Adiposity
Intestinal vessel
formation
TF glycosylation
Thrombin cleavage
PAR1 activation
TF phosphorylation
ANG1 expression
Vascularization
Bone homeostasis
T
H
17 cells
TNF in colon and bone
Osteoclastogenesis
Bone mass
Behaviour
Synaptic connectivity
Anxiety
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
vascularization
76
.
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
renewal
87
. Similarly, TLR signals derived from the gut
microbiota are required for regaining tissue homeostasis
following injury in the intestine in mice
85
. 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
75,88,89
(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
contact.
Imbalanced cellular homeostasis can result in
the development of cancer, and inflammation has
a crucial role in cancer initiation and progression
90
.
Microorganisms modulate inflammation and thus could
influence carcinogenesis
91
. Indeed, an increased bacterial
load was detected in colonic biopsies from patients with
colorectal cancer or colonic adenomas
92
. In contrast to
the decreased microbial diversity that is associated with
obesity and inflammatory bowel disease
3,93
, microbial
diversity is increased in patients with colorectal adeno-
mas
94
. In two mouse models of carcinogenesis, germ-
free animals were protected from or showed reduced
cancer development compared with conventionally
raised mice
95,96
. Notably, bacteria are also required for
the production of secondary bile acids, which have
carcinogenic effects
97
. Some microbial species, such as
B.fragilis, Streptococcus gallolyticus or Fusobacterium
nucleatum, have been associated with cancer develop-
ment
98100
. 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
90
.
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
101
. Bone cells express
receptors for serotonin, which, as mentioned above, is
reduced in germ-free mice, and serotonin signalling
inhibits bone formation
102,103
. Furthermore, bone loss is
associated with inflammation, and Tcells are responsible
for bone resorption in autoinflammatory diseases
104,105
.
T
H
17 cells and the pro-inflammatory cytokines TNF and
IL-1β all promote bone resorption by inducing osteo-
clastogenesis
105107
. 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
11
. 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
9
. 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
H
17) cells.
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Dysbiosis
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
108
. 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
109
. 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
110
(FIG.3). Moreover,
obese humans harbour an altered microbiota with
reduced diversity
93,108,111
, 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
diabetes
112
. Strikingly, the composition of the gut micro-
biota was able to predict type2 diabetes in a second,
smallercohort.
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
113
. This has in part been attrib-
uted to reduced energy extraction from a carbohydrate-
rich diet in germ-free mice
113
. 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
114
. 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
114
. Furthermore, the
gut microbiota might also contribute to increased adi-
posity and impaired glucose metabolism by stimulating
inflammation and macrophage accumulation in adipose
tissue
115
. Indeed, LPS from Gram-negative bacteria
promotes hepatic insulin resistance
116
.
In addition to obesity, an altered gut microbiome
was recently associated with symptomatic atheroscle-
rosis
117
. 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
118
. For further details about how
host–microorganism interactions can programme host
metabolism, readers are referred to a recent review
119
.
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
120
,
the squid E.scolopes
121
and chimpanzees
122
. 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
123
; larval
settle ment of the marine tubeworm Hydroides elegans is
regulated by the biofilm bacterium Pseudoalteromonas
luteoviolacea
124
; and the composition of the human
skin microbiota influences attraction for mosquitoes
125
,
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
126
. Germ-free mice display an altered stress
response, dysregulation of the hypothalamus–pituitary–
adrenal gland axis and decreased inflammatory pain
perception
127,128
.
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
129,130
, whereas germ-free mice show little
anxiety-like behaviour
131,132
. 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
128,131
. 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
131,133
.
For further discussion of microbial effects on the
development of the nervous system and behaviour,
readers are referred to a recent review
134
.
Conclusion
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
113
, 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
41,131
. 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
135
. The impact of the gut microbiota as
a modulator of methylation in other organs remains to
be identified.
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Gnotobiotic
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
136
. 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
136
. 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.
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Acknowledgements
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.
FURTHER INFORMATION
Fredrik Bäckhed’s homepage: http://www.wlab.gu.se/backhed
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VOLUME 11 www.nature.com/reviews/micro
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... 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). ...
Article
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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 ( www.swisstargetprediction.ch/ ) and the TargetNet website ( http://targetnet.scbdd.com/ ). With the aid of Genecards ( https://www.genecards.org/ ), OMIM ( https://omim.org/ ), TTD ( http://db.idrblab.net/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. ...
Article
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. ...
Thesis
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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. ...
Article
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.
Article
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.
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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.
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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.
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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.