Available online at www.sciencedirect.
com
Mechanisms controlling pathogen colonization of the gut
Bärbel Stecher1 and Wolf-Dietrich Hardt2
The intestinal microbiota can protect efficiently against
colonization by many enteric pathogens (‘colonization
resistance’, CR). This phenomenon has been known for
decades, but the mechanistic basis of CR is incompletely
defined. At least three mechanisms seem to contribute, that is
direct inhibition of pathogen growth by microbiota-derived
substances, nutrient depletion by microbiota growth and
microbiota-induced stimulation of innate and adaptive immune
responses. In spite of CR, intestinal infections are well known to
occur. In these cases, the multi-faceted interactions between the
microbiota, the host and the pathogen are shifted in favor of the
pathogen. We are discussing recent progress in deciphering the
underlying molecular mechanisms in health and disease.
Addresses
1
Max von Pettenkofer Institut, Pettenkoferstrasse 9a, 80336 München,
Germany
2
Institute of Microbiology, ETH Zürich, Switzerland
Corresponding authors: Stecher, Bärbel
(Stecher@mvp.uni-muenchen.de) and Hardt, Wolf-Dietrich
(hardt@micro.biol.ethz.ch)
Current Opinion in Microbiology 2011, 14:82–91
This review comes from a themed issue on
Host–microbe interactions: bacteria
Edited by Brett Finlay and Ulla Bonas
Available online 28th October 2010
1369-5274/$ – see front matter
# 2010 Elsevier Ltd. All rights reserved.
DOI 10.1016/j.mib.2010.10.003
To understand the whole it is necessary to understand the
parts. To understand the parts, it is necessary to under-
stand the whole. Such is the circle of understanding [1].
A word of caution
The mammalian gut is a highly complex ecosystem
shaped by the host, a complex microbial community
called microbiota and profoundly affected by interactions
with the outside environment, for example, the intake of
food or infection by pathogens [2]. This complexity has
been an immense obstacle for mechanistic studies. Sim-
plified model systems and recent advances in analytic
methodology have fuelled significant progress. However,
it should be kept in mind that no single study has so far
been able to monitor all relevant parameters (some of
which might still be unknown) of the complex mamma-
lian gut ecosystem in parallel. This may leave room for
alternative interpretations and explains the field’s keen
Current Opinion in Microbiology 2011, 14:82–91
interest in reproducible animal models and comprehen-
sive analytical tools.
The composition of the gastrointestinal
microbiota
The composition of the microbiota and its collective
genome, the microbiome, has been intensely studied.
Early cultivation based studies suggested that the human
intestinal microbiota harbors at least 400 different, mostly
obligate anaerobic bacterial species [3,4]. This was con-
firmed by modern, culture-independent approaches esti-
mating that an individual’s microbiota comprises not
more than 500 species [5]. Two predominant phyla were
observed, the Firmicutes and the Bacteroidetes. Other
phyla such as as Proteobacteria, Actinobacteria, Fusobac-
teria, Verrucomicrobia, and Cyanobacteria are minor con-
stituents. Of note, the murine and the human microbiota
are remarkably similar [6], suggesting that mouse models
can be used to study basic functional principles of
relevance for human health.
Nevertheless, data generated by novel culture-indepen-
dent approaches (i.e. 16S rRNA gene and metagenomic
sequence analyses) have to be interpreted with care as
certain species may be missed or underestimated in terms
of their abundance due to differential bacterial lysis
efficiency, primer bias and variable 16S rRNA gene copy
numbers [7,8]. Moreover, PCR on mixed templates can
give rise to significant ‘noise’ which leads to overestima-
tion of ecosystem complexity [5,9].
Deep microbiome sequencing analyses have revealed a
wide array of shared genes (‘core’ microbiome) but also
demonstrated a considerable degree of species diversity
among the microbiota, even between closely related hosts
[5]. Interestingly, despite this species diversity, different
microbiomes are functionally highly conserved as shown
by the abundance of COG categories [10]. Therefore,
besides all variability, some general ordering principles do
exist and lead to functionally widely conserved micro-
biota properties. This explains why key functional prop-
erties of the microbiome are consistently observed in
different laboratories worldwide, in spite of significant
lab-to-lab variations in the species composition of the
mouse colony microbiota. However, effects of the species
composition should be carefully addressed in each case.
General functions of the microbiota
In most cases the beneficial functions of the microbiota
outweigh potentially harmful side effects. The micro-
biota provides digestive functions, modulates host metab-
olism and stimulates development of lymphatic tissue
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 Mechanisms controlling pathogen colonization Stecher and Hardt 83
Glossary
COG: cluster of orthologous groups of proteins used for phylogenetic
classification of proteins encoded in complete genomes
Colonization resistance (CR): characteristic of the intestinal
microbiota to block colonization of pathogens
Defensin: peptide with antimicrobial activity
Gnotobiotic: colonized with bacteria of known identity
IBD: inflammatory bowel disease (e.g. Crohn’s disease and
Ulcerative Colitis)
Microbiome: collective genome of all present bacteria
Metagenome: collective genome of all organisms present in a given
ecosystem
16S rRNA gene sequencing: The 16SrRNA gene is commonly used
for phylogenetic studies as it is highly conserved between different
species of bacteria and archaea
SPF: specified pathogen free
and the mucosal immune system. Moreover, it can effi-
ciently limit infection of the gut by pathogenic bacteria.
In fact, during pathogen infection, the microbiota may
have at least three cardinal functions: (i) it may block
growth of the pathogen and thus interfere with the in-
fection right from the beginning. This is termed as
colonization resistance (CR; Box 1) and will be the focus
of this review. (ii) The microbiota may prime the host’s
innate and adaptive immune defenses and prevent path-
ology which would otherwise be caused by the pathogen’s
virulence factors. This has been reviewed recently [11].
(iii) It can help to eliminate the pathogen from the gut
lumen at the end of an infection. This has recently been
demonstrated [12] and will be discussed elsewhere.
Even in the normal, healthy host, microbial products
released from the intestinal microbiota such as peptido-
glycan disseminate to the mesenteric lymph nodes and
even to systemic sites and stimulate immune cell matu-
ration [13]. In some cases, the presence of an intestinal
microbiota contributes to the etiology and progression of
diseases in humans, namely chronic inflammatory bowel
diseases (IBD) [14]. IBD is thought to result if barrier
functions, antimicrobial killing or dampening signaling
pathways of the innate and/or adaptive immune system
fail [15]. In addition, some bacterial species are associated
with the aggravation of autoimmune diseases and the
incidence of colorectal cancer [16]. Thus, microbiota
manipulation by the introduction or selective elimination
of relevant bacteria might represent future avenues for
cure or prevention. A ‘proof of principle’ study demon-
Box 1 Colonization resistance (CR) has been known for more than
50 years. Anecdotal observations in human patients and animal
studies had shown that disruption of the microbiota by antibiotics
dramatically increases the susceptibility towards enteric infections
[94,95]. This has been confirmed in numerous recent studies
[43,96,97]. Experiments in germ-free mice and ex-germfree mice
colonized with selected bacterial species lent further support to this
[29,45,98]. The mechanisms underlying this natural protection are
still unresolved and a matter of debate.
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Figure 1
Microbiota
composition -
10
8
Log10 cfu/g Salmonella
6
Bacteroidetes
Firmicutes
4
Deferribacteres
Verrucomicrobia
2 Proteobacteria
0
CON
Antibiotic-
Germfree
(Schaedler)
treated
LCM
Current Opinion in Microbiology
Colonization resistance against oral Salmonella infection in mice with
different types of microbiota. The figure summarizes published and
unpublished data from Salmonella-infected mice. Conventional mice
from different sources (n = 58), streptomycin-pretreated mice (n = 12)
and low-complexity microbiota (LCM) mice (n = 10; all from [29] and
Stecher and Hardt, unpublished) and germfree mice (n = 7; [45]) were
orally infected with Salmonella serovar Typhimurium or serovar
Enteritidis. Intestinal loads in cfu/g cecal content are depicted. Pie plots
illustrate microbiota composition in the respective groups
(Bacteroidetes: yellow; Firmicutes: green; Deferribacteres: purple;
Verrucomicrobia: blue; Proteobacteria: red; other phyla with abundance
<1%: not depicted).
strated recently that the microbiota can in fact be ‘trans-
planted’ between two hosts [17].
This review will summarize the recent literature pertain-
ing to the three-way interaction between the microbiota,
the host and enteric pathogens and discuss novel tech-
nologies which may aid analysis of CR in the future.
Mechanisms of CR
What do we know about the mechanisms underlying CR?
Innate immunity, adaptive immunity and bacterial inter-
actions are probably involved in modulating both the
composition of the microbiota and the outcome of infec-
tions. To establish successful infection, all pathogens
need to replicate in the gut lumen in order to reach a
sufficient population density for causing disease. In the
case of S. Typhimurium enterocolitis, this was demon-
strated by infecting mice with defined mixtures of the
wild-type pathogen and avirulent mutants [18]. At least
Current Opinion in Microbiology 2011, 14:82–91
84 Host–microbe interactions: bacteria
Figure 2
Three mechanisms of intestinal microbiota-mediated CR. There are at
least three mechanistic ways how the intestinal microbiota can confer
protection against enteric pathogens. (1) Direct inhibition of the pathogen
by antimicrobial effector molecules (bacteriocins, metabolic by-products).
(2) Efficient competition for nutrients establishes CR by shutting down all
potentially available nutrient niches for the pathogen. (3) Indirect inhibition
by stimulating the host’s antimicrobial defense system. The microbiota
releases microbial patterns (LPS, peptidoglycan) which are sensed by the
host’s epithelial cells thus triggering antibacterial defenses such as release
of epithelial-derived defensins, mucin secreted by goblet cells, and
secretory IgA produced by lamina propria plasma B-cells.
three possible mechanisms are conceivable how the
microbiota may convey CR (Figure 2):
(1) Direct inhibition: Bacterial species can inhibit the
growth of other bacteria, including pathogens, in differ-
ent ways, for example, by releasing inhibitory metab-
olites (i.e. acetate and butyrate) and bacteriocins.
Besides, oxygen depletion slows down the growth rates
of facultative anaerobic bacteria (such as most pathogens)
and competition for binding sites on epithelia or mucus-
derived receptor sites [19,20]. Direct inhibition in the
absence of the host has been demonstrated in vitro using
continuous colonic fermentation models [21]. Similarly,
the lag phase of pathogenic shiga-toxin producing Escher-
ichia coli (STEC) grown in fecal suspensions was corre-
lated to the CR of the donor, suggesting that the
inhibitory mechanisms are operational when uncoupled
from the intestine [22].
(2) Nutrient depletion: The microbiota is known to utilize
numerous nutrients not absorbed by the host’s intestine.
Current Opinion in Microbiology 2011, 14:82–91
The sheer complexity of the normal microbiota should
guarantee depletion of most nutrients which might other-
wise sustain growth of an incoming pathogen. The theory,
also known as ‘Freter’s nutrient-niche hypothesis’ claims
that intestinal colonization by a given bacterial species
requires that its growth rate is faster than its individual
washout rate and that it must consume one or a small
number of growth-limiting nutrients (i.e. mucus-derived
carbohydrates) better than all other competitors in the
ecosystem [23]. This theory was followed up experimen-
tally by P. Cohen and T. Conway using E. coli mutants in
defined metabolic pathways.
These studies beautifully demonstrate that E. coli strains
can grow on mucus and consume multiple mucin-derived
sugars in parallel. Conversely, a defect in consuming one
of these sugars (i.e. arabinose, fucose, and N-acetyl-glu-
cosamine) led to a competitive disadvantage against the
respective parental strain. Interestingly, different E. coli
strains showed distinct sugar utilization preferences [24].
A pathogenic E. coli was only excluded by strains with a
similar nutrient utilization spectrum (i.e. an isogen) or a
mixture of several commensal E. coli strains [25]. Along
this line, studies in mice and humans have shown that CR
correlates inversely with the number of different Enter-
obacteriaceae as well as different E. coli biotypes [26,27].
Accordingly, the density of commensal intestinal E. coli
was inversely correlated with the degree of CR against E.
coli and Salmonella spp. [28,29]. This might be explained
by the fact that the same global selective pressure (i.e.
presence/absence of a common inhibitor/nutrient) acts on
both species.
Therefore, different combinations of microbiota species
could confer CR against a given pathogen, as long as key
nutrients are depleted. This would be in line with the
high level of host-to-host COG-conservation discussed,
above. Formation of an ecological ‘food-web’ consisting
of several primary and secondary fermenters may be
required for the efficient degradation of all potential
nutrient sources available to pathogens. Recently, func-
tional principles of such food-webs have been studied
more in detail. Association experiments with Bacteroides
thetaiotaomicron (B. t.) in gnotobiotic mice demonstrated
that co-colonization with different probiotic strains can
affect the efficiency of B. t. metabolism [30,31]. Con-
versely, B. t. opens up new nutrient sources for the co-
colonizing strains, as they themselves do not produce a
wide spectrum of secreted polysaccharide lyases and
glycoside hydrolases. Co-association also increases the
total microbiota density and boosts the yield of fermenta-
tion products, such as short chain fatty acids (i.e. butyrate)
which in turn serve as nutrient source for colonic epi-
thelial cells and modulate host gene expression [32].
(3) Stimulation of immune defenses: This mechanism is quite
complex and difficult to analyze: On the one hand,
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 Mechanisms controlling pathogen colonization Stecher and Hardt 85
microbiota-derived stimuli are not easily provided in the
absence of life bacterial colonization. On the other hand,
the presence of a complex bacterial community in the gut
does not allow disentangling inhibitory effects mediated
by a particular bacterial product or a certain bacterial
species.
Defensins produced by the host’s specialized epithelium
are secreted into the gut lumen in order to increase mucosal
barrier function against luminal bacteria. Mice lacking
matrix metalloproteinase 7 (MMP7), and hence devoid
of mature paneth-cell a-defensins, show an altered micro-
biota composition [33]. Conversely, transgenic mice over-
expressing a human beta-defensin were protected against
lethal S. Typhimurium challenge [34]. So far, it is unclear if
defensins merely protect by killing pathogens approaching
the mucosal surface or indirectly, by inducing microbiota
shifts and modulating CR. Besides antimicrobial peptides,
IgA is also secreted in the gut lumen in high quantities and
can protect against insult from pathogens, steady state
penetration of bacterial products and accidental entry of
microbiota [12,35,36].
On the other hand, the capsule polysaccharide (PSA) of
Bacteroides fragilis was found to stimulate T-cell and
lymphoid organ development and protects mice from
experimental Helicobacter hepaticus colitis, presumably
by stimulating Foxp-3(+) IL10 producing T-cells and
inhibiting pro-inflammatory TH17 responses [37,38].
Conversely, antibiotic-mediated microbiota depletion
reduced the secretion of the antimicrobial lectin RegIIIg
and resulted in increased susceptibility to oral Enterococ-
cus infection [39]. Also, several studies linked particular
members of the microbiota (i.e. segmented filamentous
bacteria, SFB) to intestinal TH17 responses [40–42].
Confirmation and detailed mechanistic analysis of these
observations would require culturing of the SFB and
studies in defined model systems. Anyhow, these data
suggest that antibiotics and facility-specific microbiota
differences may modify susceptibility to enteric infec-
tions and autoimmune diseases [29,43,44].
Of note, the degree of CR can vary dramatically between
individual mice ranging from no detectable colonization
(below 103 cfu/g) to levels reached in GF mice (>109 cfu/
g) [29,45] (Figure 1). Substantial differences, for example,
the presence/absence of SFB, can be observed between
mice from different sources and the microbiota compo-
sition can have significant effects on the immune
responses of the host (e.g. TH17 responses [44]). These
differences can be minimized by breeding littermate
controls or by swapping litters (Stecher and Hardt,
unpublished observation). In conclusion, extreme care
should be taken with respect to the appropriate design of
such animal experiments. Not only the genetic back-
ground of the mice must be matched (i.e. wild type
and knock-out) but also the respective microbiota [46].
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Studies on the long-term effects of the microbiota on the
host are still at the beginning and we urgently need to
investigate the effects in more detail to avoid misinter-
pretation of experimental data. Most likely, one needs to
revisit the current SPF concept: animal breeders should
change from a definition ‘free of pathogens’ to rather
declare a ‘positive list’ of microorganisms that are present
in a certain mouse flora [47].
Environmental factors affecting the
microbiota
The determinants influencing stability and composition
of the microbiota are not completely understood. Besides
antibiotics other factors are known that lead to alterations
of intestinal bacterial communities and may, as a con-
sequence, affect CR. The diet has a profound effect on
the microbiota composition [48] as shown by next-gener-
ation deep sequencing analysis of the human microbiota
[49,50]. Both studies found that the microbiota can
respond rapidly to changes in diet in as little as one
day. Thus, one day it might become feasible to design
diets or nutrient additives which foster ‘favorable’ or
‘unfavorable’ microbiota compositions thus enhancing
CR. However, today we are clearly far away from such
‘rational microbiota management’.
CR and intestinal inflammation
Mucosal inflammation has a profound effect on the host’s
mucosa, on the nutrient availability in the gut and on the
microbiota composition. For practical reasons, we dis-
tinguish between chronic gut inflammation caused by
effects of the commensal microbiota (IBD) and acute
inflammation caused by enteric pathogens. Nevertheless,
some functional principles might be common to both
types of disease.
Work on acute Salmonella and Citrobacter infection models
has revealed that enteropathogenic bacteria can subvert
the inflammation in order to out-compete the microbiota
[51–54]. Similarly, inflammation seems to enhance gut
colonization by other pathogens like Vibrio cholerae or
Clostridium difficile [55,56]. This growth advantage
might be attributable in part to the high levels of anti-
microbial peptides/defensins secreted by the inflamed
mucosa [57–61] and the relatively high resistance which
pathogens like S. Typhimurium have against these com-
pounds [57,62,63]. On the other hand, inflammation alters
the mix of electron donors and acceptors available in the
gut (Figure 3). The inflamed mucosa secretes large
amounts of high energy glycosylated proteins in the
gut lumen, which are utilized by S. Typhimurium [64].
Furthermore, it secretes lipocalin which interferes with
iron uptake by commensal bacteria, but not by S. Typhi-
murium [65]. Finally, it was found recently that the
inflamed mucosa can convert H2S, a typical metabolic
product released by commensals, into tetrathionate and
that the latter can serve as a primary electron acceptor for
Current Opinion in Microbiology 2011, 14:82–91
86 Host–microbe interactions: bacteria
Figure 3
Inflammation-induced Salmonella overgrowth in the gut. Salmonella may
exploit intestinal inflammation to out-compete the microbiota using
different strategies: (1) Salmonella uses mucin-derived carbohydrates
which are released in the gut in the course of inflammation [64]. (2)
Salmonella can use tetrathionate as an electron acceptor which is more
abundant in the inflamed gut [66]. (3) Salmonella is resistant to a variety
of host-derived defensins and antimicrobial peptides and avoids
inhibition of the host-derived antimicrobial peptide lipocalin-2 that
sequesters the siderophore enterochelin by the production of
salmochelin [65]. Inflamed mucosa depicted in red. PMN: transmigrated
polymorphonuclear leucocyte.
S. Typhimurium [66]. Respiration would allow S.
Typhimurium to grow faster than the microbiota, most
of which are not able to respire. It will be interesting to
see whether the tetrathionate-mediated growth
advantage might be affected by facility-specific differ-
ences in microbiota composition.
Microbial community imbalances are also observed in
human inflammatory bowel disease (IBD) patients as well
as experimental mouse colitis models [51,67]. However,
the events initiating CR are still controversial. Reduction
of antimicrobial peptide and mucin production [68], epi-
thelial cell dysfunction (ER stress), [69] and lack of
microbial pattern recognition receptors [70] are prime
candidates that may lead to a generally weakened mucosal
barrier. Secondary to this, a pathologically altered micro-
biota may trigger or aggravate chronic gut inflammation. It
was demonstrated that the microbiota derived from
animals suffering from colitis was a potent inducer of colitis
after transfer and members of the Enterobacteriaceae
family contributed to this effect [71]. Conversely, an acute
and chronically inflamed intestine presents a considerably
altered environment for the intestinal microbiota and
fosters growth of pathogens and facultative anaerobic
commensals [52]. E. coli overgrowth is commonly observed
in human IBD patients. Here, the so-called adherent and
Current Opinion in Microbiology 2011, 14:82–91
invasive E. coli (AIEC) are thought to lead to aggravation of
disease symptoms. In patients affected by Crohn’s disease,
AIEC were found in close contact with the inflamed ileal
mucosa and even invaded intestinal epithelial cells [72,73].
These data suggest that there might be a link between
AIEC overgrowth in the inflamed intestine and aggravation
of disease symptoms in IBD.
In conclusion, chronic and acute inflammation profoundly
affects CR, but the underlying mechanisms are still not
entirely understood. Elucidating how different commen-
sal bacteria adapt to growth in the inflamed and non-
inflamed gut and how this affects their interaction with
the host will be of high relevance.
Future directions
In the future, two developments will have a great impact
on analyzing CR, simplified model systems and improved
systems biology techniques (Box 2).
Gnotobiology has already contributed significantly to our
current understanding of the microbiota–host cross-talk
Box 2 Mouse models for studying CR. Conventionally raised (CON)
mice harbor a complex gut flora consisting of >500 different
species conferring CR against enteropathogens including
Salmonella enterica serovar Typhimurium (S. Typhimurium; Figure
1). Upon disruption of the gut microbiota, for example, by antibiotic
treatment or in germfree mice (GF), susceptibility to enteric
infections is greatly increased [45,96,97]. Re-association of
microbiota-depleted mice with a CON gut flora re-establishes CR
[99–101]. This enabled pioneering studies of the bacterial species
conferring CR, that is the ground-breaking work by Rolf Freter and
colleagues in the 1960s. GF mice have an enlarged cecum (>5% of
total body weight versus 1% in conventional mice; attributed to
non-digested complex carbohydrates). Association of GF mice with
species of a CON microbiota can ‘normalize’ the cecal size and
physiology [102,103]. E. coli served as an indicator strain for CR and
relative cecal size or the degree of normalization is directly linked to
intestinal E. coli titers [104]. Thus, CR can be quantified by orally
contaminating animals with E. coli and measuring fecal colonization
levels [27,95,105,106]. Analyzing CR upon re-introducing
combinations of microbiota strains R. Freter demonstrated that CR
requires obligate anaerobes [107], for example, a combination of
Clostridium spp. and three Lactobacillus strains established CR
against E. coli in GF mice [79,80]. Recent work assigned these
species to the Clostridium clusters XIVa and IV [81]. The
mechanisms how these bacteria induce cecal normalization and CR
are yet to be elucidated. In order to investigate microbiota functions
including CR, efforts towards a controlled colonization of mice with
a defined microflora have been made and served as model in
biological research since the 1960 s [108,109]. Interestingly, mice
associated with a low-complexity type of microbiota (LCM) derived
from the altered Schaedler flora (ASF) [110] are highly susceptible to
enteric Salmonellosis in a similar way as GF mice [29]. Again,
transfer of a complex flora derived from CON mice induces
protection against S. Typhimurium colonization and gut
inflammation [12,29,89]. The colonization status of ASF mice can be
stably maintained in individually ventilated cages [111] making this
mouse model an attractive tool in combination with a deep
16SrRNA gene pyrosequencing strategy and phylogenetic
sequence analysis to identify bacteria contributing to CR.
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 Mechanisms controlling pathogen colonization Stecher and Hardt 87

Table 1

Overview on host–microbiota interaction studies in gnotobiotic mice and mice colonized with undefined microbial consortia

Bacteria used in gnotobiotic model Phenotype observed Effect on CR versus Citation

germfree/conventional
situation
Segmented filamentous SFB induces IgA-producing cells, ND [78]
bacteria (SFB), MHCII expression on epithelial cells
Candidatus arthromitus Induction of TH17 responses [40,44]
Induction of EAE in mouse model [41,42]
(immunization with MOG in CFA)
Induction of rheumatoid arthritis
16 Bacteroides strains or Significantly reduced induction of IL-17 ND [44]
46 Clostridia strains production in CD4-T-cells compared to
mice associated with SFB; Increase in
IFNg producing CD4-T-cells.
Bacteroides fragilis Induction of Foxp3(+) Treg cells ND [38]
Spore-forming bacteria Induction of TH17 responses similar to ND [40]
colonization with SFB. This was not as
pronounced in mice associated with the
culturable fraction of
conventional microbiota
Human baby flora derived Protection against E. coli infection Increased CR against [22]
bacterial mixture E. coli
Human fecal flora ND [49]
Mouse flora
(1) E. coli Positive effect on cecal ‘normalization’ Increased CR from (1) to [79–81]
(2) E. coli + Lactobacillus and colonization resistance (7) against E. coli
(3) (2) + Lb + Candida
(4) (3) + 3 anaerobic fusiform
bacteria
(5) (4) + 30 anaerobes
(6) 50 strict anaerobes + 80
facultative anaerobes
(7) Chloroform-resistant
spore-forming Bacteria
(Clostridia)
Escherichia coli K-12, Exclusion of B. longum but not L. paracasei Increased CR against [82]
Lactobacillus johnsonii NCC533, from the gut; E. coli Nissle led to displacement B. longum
and Bifidobacterium of Escherichia coli K-12, Lactobacillus johnsonii
longum NCC2705 NCC533;
Altered Schaedler flora No protection against S. Typhimurium infection Decreased CR against S. [12,29]
and induction of intestinal inflammation Tm compared to CON mice
Bifidobacterium animalis Reduced fecal S. Typhimurium excretion Increased CR against S. Tm [83]
Lactobacillus delbrueckii Protection against systemic L. monocytogenes ND [84]
UFV-H2b20 infection
Bacteroides thetaiotaomicron Induction of mucin fucosylation by fucose ND [85–87]
consumption
Induction of angiogenins and RegIIIg [30,88,89]
Flexible foraging behavior (host-derived mucus
and food particles)
+Eubacterium rectale ND [90]
Ruminococcus gnavus E1, Elimination of C. perfringens from the intestine Increased CR against [91]
Bacteroides thetaiotaomicron C. perfringens
LEMF4, Clostridium hathewayi
LEMC7, and Clostridium
orbiscindens LEMH9
+Methanobrevibacter smithii Increased energy harvest from diet; higher ND [92]
yields of acetate and formate produced by
B. t.; Expansion of B. t. sugar substrate range
+Desulfovibrio piger No effect ND [92]
+Lactobacillus casei Expansion of B. t. sugar substrate range ND [89]
+Bifidobacterium longum
Acetogenic bacteria Expansion of B. t. sugar substrate range ND [31]
Lactobacillus plantarum Expansion of B. t. sugar substrate range ND [93]

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88 Host–microbe interactions: bacteria
(Table 1). We will need to invest into improved GF and
gnotobiotic animal models for analyzing particular strains
(or combinations thereof). An increasing catalogue of
sequenced microbial genomes and development of
genetic tools for molecular manipulation of the
sequenced strains will allow deciphering molecular mech-
anisms of CR [74,75]. Also, GF mice allow re-association
with ‘human’ microbiota [49]. And the generation of GF
KO and transgenic mice will be important for analyzing
the host’s contributions to CR [76]. It should be men-
tioned that the methods for generating and breeding GF
mice have been significantly improved since their inven-
tion and that key gnotobiotic techniques (embryo transfer
and isolators) have become available in most animal
facilities worldwide.
On the other hand, high throughput methods for systems
wide analysis will have a great impact. Technological
quantum leaps like extremely deep sequencing and
RNAseq will enable a second generation of system-wide
microbiome, system-transcriptome analysis [31]. These
kinds of data will allow the discovery of novel bacterial
functions as recently exemplified by an algae degrading
enzyme that was potentially transferred from a marine
bacterium, Zobellia galactanivorans into the genome of
Bacteroides plebeius, a commensal isolated from Japanese
individuals [77]. A combination of genomic approaches,
functional screens, directed mutagenesis and gnotobiotic
models systems will enable us to disentangle the complex
microbiota–host–pathogen interaction-network explain-
ing CR and enteric disease.
Acknowledgements
We are grateful to numerous colleagues for stimulating discussions and to
Yvonne Lötscher for assisting with figure design. Work was supported by
the Swiss National Science Foundation (310030-113623, 310030-132997 to
WDH), the UBS foundation (1004/A, to WDH) and the BMBF
Infektionsgenomik (to BS).
References and recommended reading
Papers of particular interest, published within the period of review,
have been highlighted as:
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Slightly Mad (1997).
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