Specialized metabolites from the microbiome in health and
disease
Gil Sharon
a,1
,
Neha Garg
b,1
,
Justine Debelius
c,1
,
Rob Knight
c,d
,
Pieter C. Dorrestein
b,e
, and
Sarkis K. Mazmanian
a
a
Division of Biology and Biological Engineering, California institute of Technology, Pasadena,
California, USA
b
Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego,
La Jolla, California, USA
c
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
d
Howard Hughes Medical Institute, Boulder, Colorado, USA
e
Department of Pharmacology, University of California at San Diego, La Jolla, California, USA
Abstract
The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-
microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of
gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with
various conditions, specific mechanisms of host-microbiota signaling remain largely elusive. We
discuss the synthesis of microbial metabolites, their absorption, and potential physiological effects
on the host. We propose that the effects of specialized metabolites may explain present knowledge
gaps linking the gut microbiota to biological host mechanisms during initial colonization, and in
health and disease.
Introduction
In the human body, microbial cells outnumber eukaryotic cells by as many as ten to one
(
Savage, 1977
), and contribute two orders of magnitude more genes to the hologenome (
Gill
et al., 2006
;
Turnbaugh et al., 2007
). Their significance to host health and disease is thus
unsurprising, although it was long overlooked. The bacterial metagenome contributes to
production of primary metabolites and conversion of small molecules into secondary
metabolites, also called “specialized metabolites”. Products of bacterial metabolism are
believed to modulate human health in many ways (
Hooper et al., 2012
,
Blumberg and
Powrie, 2012
). Crosstalk between microbial and human metabolites influences processes
such as nutrient and xenobiotic metabolism (
Maurice et al., 2013
), protection against
pathogens (
Clarke et al., 2010
), regulation of the enteric nervous system (
Soret et al., 2010
),
immune regulation (
Brestof and Artis, 2013
), resistance against colorectal cancer (
Hague et
al., 1995
;
Hinnebusch et al., 2002
;
Lan et al., 2007
;
Tang et al., 2011
;
Nicholson et al.,
1
Co-first Author
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Published in final edited form as:
Cell Metab
. 2014 November 4; 20(5): 719–730. doi:10.1016/j.cmet.2014.10.016.
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2012
), complex neurological behavior (
Hsiao et al., 2013
), and affect lipid and cholesterol
levels in serum (
Berggren et al., 1996
;
Delzenne et al., 2002
). Metabolic pathways operating
in the human body are thus the result of the combined activities of the human genome and
microbiome.
Diet is important to the microbiota and metabolome, as food is a major source of precursors
for metabolite production. Humanized mice fed a polysaccharide-deficient diet differed in
both the microbiome and metabolome from humanized mice on regular chow (
Marcobal et
al., 2013
). Conventionally raised mice fed the same diet were also significantly different
from conventional mice fed regular chow or the humanized mice (
Marcobal et al., 2013
). In
humans, both long term dietary patterns (
Ridaura et al., 2013
;
Wu et al., 2011
) and rapid,
extreme dietary changes (
Levy and Borenstein, 2014
) are reflected in the microbial
communities and metagenome. In particular, amino acid intake correlates with changes to
microbial communities. For example, increased amino acid intake increased the relative
abundance of Bacteroidetes, and changed the metabolome (
Ridaura et al., 2013
;
Wu et al.,
2011
). Individuals who ate a primarily animal-based diet with little to no fiber for two days
showed decreased levels of acetate and butyrate in the gut compared to those who consumed
a plant-based diet over the same period (
Levy and Borenstein, 2014
).
Energy balance depends on the diet, but also on the microbiome. Kwashiorkor, a severe
form of malnutrition, can be transferred from affected people to mice by fecal
transplantation (
Smith et al., 2013
). Specifically, fecal samples from human twins, where
one co-twin was malnourished and the other was not, produced substantially different
phenotypes in recipient mice. Feeding the mice a traditional Malawi diet led to a loss of 30%
of body mass in just 3 weeks in the mice that received microbes from the malnourished co-
twin, while mice transplanted from the healthy co-twin maintained normal body weight on
this diet. These differences in the microbiome were coupled to differences in amino acid,
carbohydrate and fat metabolism, even on the same diet. Dietary responses also differed
depending on the microbiome: Ready-to-use Therapeutic Food, a nutrient rich and energy
dense dietary supplement, was able to rescue the mice receiving the kwashiorkor
microbiome from weight loss, but produced little change in the mice receiving the healthy
microbiome (
Smith et al., 2013
). This study reflects the importance of both microbiome
composition and diet in determining the metabolic profile, which, in turn, influences disease
outcomes.
At the other metabolic extreme, obesity can also be modulated by the gut microbiome,
metabolome, and diet. Ridaura et al transferred microbes from lean and obese co-twins into
germ-free mice (2013). The metagenomes of lean co-twins were enriched for genes
encoding proteins that ferment complex carbohydrates from plant sources. Co-housing lean
and obese mice mitigated the obese phenotype in a diet-dependent fashion. A low-fat, high
plant polysaccharide diet promoted weight loss in co-housed obese mice, while a diet high in
saturated fat and low in plant materials did not significantly alter the obese phenotype of co-
housed animals. Co-housed obese animals fed a low fat diet also differed in metabolite
profiles from controls.
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Commensal microbes, present at various mucosal surfaces of the mammalian host, play a
critical role in processing environmental signals (e.g., diet, xenobiotics) and relaying
“messages” to the epithelium and via the circulatory system. These messages are classically
thought of as microbial-associated molecular patterns (MAMPS), common to various
microorganisms, or as metabolites involved in paracrine or endocrine signaling to the host.
Often, these metabolites can be beneficial. For example, yet unknown secreted factors of
commensal skin bacteria can induce production of human antimicrobial peptides such as
defensins resulting in modulation of human innate immune response (
Maurice et al., 2013
).
An important function of the human microbiome is to supply essential water soluble
vitamins including vitamin K, vitamin B12, biotin, folate, thiamine, riboflavin and
pyridoxine which are then absorbed by the intestines (
Martens et al., 2002
;
Said, 2011
).
Several recent reports have now identified specific microbial metabolites beyond those
traditionally associated with gut bacteria, and may represent incipient advances in
understanding the inextricable chemical link between mammals and their microbiota.
Likely, the vast majority of interkingdom molecular communications remain unknown.
Here, we present pathways associated with the production of primary and specialized
metabolites, and examine their possible role in pathogenesis. We suggest a framework for
studying and understanding the role of specialized metabolites, focusing on their production
in the gut, followed by absorption, then circulation to their target sites (Figure 1).
Application of this framework would allow better understanding of many pathologies, and
potentially reveal new therapeutic targets.
Metagenome, metatranscriptome and metabolites
The microbial metagenome links taxonomic identification to metabolite production.
Metagenomic analysis catalogs genes within a microbial environment, and helps provide
mechanistic explanations for metabolic changes associated with disease. A systems-level
approach comparing the metagenomes of individuals with obesity or inflammatory bowel
disease (IBD) to healthy controls suggested that the disease states were associated with loss
or gain of enzymes which served to initiate or terminate metabolic pathways (
Greenblum et
al., 2011
). Furthermore, shifts in the microbial metagenome translate to changes in
metabolic profiles. Mice transplanted with microbes from obese humans had a reduction in
butyrate fermentation genes, along with decreased butyrate levels in the cecum (
Ridaura et
al., 2013
). Horizontal gene transfer between species, and poor species-level resolution in
16S rRNA gene sequencing, can limit the accuracy of direct metabolic predictions (Ploz et
al., 2013;
Wang et al., 2007
), although coarse-grained predictions of metabolism from the
metagenome has still been useful in both host-associated and environmental (
Larsen et al.,
2014
) contexts.
Metagenome sequencing also shows how pathogenic organisms adapt to polymicrobial
infections in the host. Sequencing
Rothia mucilaginosa
genomes from cystic fibrosis (CF)
patients and healthy controls revealed adaption by encoding multiple genes for lactate
dehydrogenase, enabling utilization of lactate produced by the host and co-inhabiting
pathogens (
Lim et al., 2013
). Other means of adaption included acquisition of genes for
phage lysins, modification of genes responsible for horizontal gene transfer, and genes
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speculated to play roles in modulation of biofilm formation, namely CRISPR elements (
Lim
et al., 2013
). Metagenomic prediction could, potentially, be refined through
metatranscriptomic and metaproteomic analyses. These methods may provide mechanistic
insight into the regulation of enzymes of interest, as the presence of a gene does not
guarantee expression of the corresponding protein product. Bacterial protein expression is
regulated at the transcriptional and the translational level by many mechanisms (reviewed in
Berthoumieux et al., 2013;
Quax et al., 2013
). Thus expression-level techniques may be
especially useful in examining rapid changes in bacterial function (
Poretsky et al., 2009
;
McCarren et al., 2010
;
Kolmeder et al., 2012
). Integrating multi-meta-omic techniques may
provide many more direct links between bacteria and their metabolites than are currently
known.
Microbial metabolite synthesis acts in concert with host metabolism
The best-studied microbial pathways influencing human health involve production of short
chain fatty acids (SCFAs) including propionate, butyrate, and acetate. The end product of
microbial fermentation of complex non-digestible polysaccharide in the colon (
Cummings,
1983
;
Brestof and Artis, 2013
), SCFAs, and their role in metabolism and immunity, have
been appreciated for years (see review by
Brestof and Artis, 2013
). They contribute to
protection from infection and inflammation (
Fukuda, et al., 2011
,
Maslowski, et al., 2009
,
Kim, et al., 2013
), recruitment and maturation of various subsets of immune cells (Arapaia,
et al., 2013,
Smith et al., 2013
,
Sina, et al., 2009
), and metabolism (
Bellahcene et al. 2013
),
and mediate host-microbe interactions. SCFAs interact with the host in several ways: via
specific G-coupled protein receptors (GPR) -41 and -43 (FFAR3 and 2, respectively)
(
Brown, et al., 2003
;
Le Poul, et al., 2003
), inhibiting histone-deacetylases (HDAC) and
thereby altering host gene expression (
Waldecker, et al., 2008
), and inducing autophagy
(
Brestof and Artis, 2013
).
Propionate production is especially important in human health, promoting satiety,
preventing liver lipogenesis, lowering cholesterol, and providing anti-carcinogenic activities
(
Havenaar, 2011
). Pathways leading to bacterial propionate formation in the human gut have
been extensively investigated using multiple approaches (PCR amplification by degenerate
primers, 16S rRNA gene analysis, tblastn analysis, and microbial physiology), highlighting
dominant microbes and microbially-influenced propionate pathways in the human gut
(
Reichardt, et al., 2014
). The succinate pathway may be the most abundant pathway leading
to propionate formation in the human gut, as it is present both in Bacteroidetes, the most
abundant phylum in the gut, and the less-abundant phylum Negativicutes. The biosynthetic
route via the propanediol pathway is found mostly in Lachnospiraceae, and may be the most
important pathway utilizing deoxy-sugars such as rhamnose and fucose from host glycans.
The acrylate pathway is the least widespread, and
Coprococcus catus
was the first human
gut bacteria in which this pathway was identified. Propionate and butyrate pathways mainly
operate in phylogenetically distinct groups of anaerobic bacteria (
Reichardt, et al., 2014
). In
general, caution should be used in predicting pathways using
in silico
methods, because the
presence of pathways may simply use butyrate or propionate as energy sources rather than
produce them (
Ridaura et al., 2013
;
Vital et al., 2014
). Further, the importance of assessing
the directionality of pathways along with gene abundance was found to be critical in
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differentiating between herbivores and carnivores (
Muegge et al., 2011
). Thus, identifying
the directionality may also be crucial for understanding the link between microbes and
metabolites. These findings highlight that future studies deciphering roles of specific
microbial species in human health via biosynthetic pathways from metagenomes should be
performed via multiple approaches (
Muegge et al., 2011
;
Reichardt, et al., 2014
).
Bacterial and host enzymes are linked into complex metabolic pathways. For example, the
neurotransmitter serotonin (5-hydroxytryptamine) is a specialized metabolite synthesized
through the interaction between the host and its microbiome. Approximately 90% of the
serotonin in a human is synthesized in the gastrointestinal tract (
Berger et al., 2009
), and
serotonin acts locally to regulate gastrointestinal, cardiac, respiratory, and endocrine
functions, as well as crossing the blood-brain barrier (
Berger et al., 2009
;
Nakatani et al.,
2008
). At the most basic level, serotonin is derived from tryptophan by tryptophan
hydroxylases -1 or -2 in a tetrahydrobiopterin-coupled reaction, followed by a
decarboxylation by amino acid decarboxylase (
Walther et al., 2003
;
Sainio et al., 1996
).
Tryptophan is an essential amino acid; it must be obtained from dietary or microbial sources
(
Young, 1994
). Germ-free (GF) mice have lower levels of tryptophan, serotonin, and indoles
than conventionally raised or humanized (i.e., colonized with human microbiota) animals
(
Marcobal et al., 2013
). Tryptophan is synthesized from chorismate by members of several
bacterial phyla including Proteobacteria, Actinobacteria, and Firmicutes through enzymes
whose genes are encoded in complex operons (
Yanofsky, 2004
).
Escherichia coli
can
synthesize chorismate, a tryptophan precursor, which acts as a branch-point for many
microbial metabolic pathways (
LeBlanc et al., 2013
;
Dosselaere and Vanderleyden, 2001
).
Bifidobacteria are also predicted to have the capacity to synthesize chorismate (
LeBlanc et
al., 2013
). Consistent with this key role for bacteria, antibiotic treatment altered tryptophan
and indole metabolism in rats (Zheng et al, 2011).
Short chain fatty acid and indole production are among the better-characterized microbial
metabolic pathways. They also highlight different strategies in metabolic synthesis. SCFAs
are fermented from a variety of different sugars via distinct pathways that do not intersect
(
Reichardt, et al., 2014
). Serotonin and tryptophan biosynthesis are evolutionarily conserved
(
Radwanski and Last, 1995
), and reflect the interaction of host and microbial symbionts in
the production of specialized metabolites. These examples may provide a framework for the
characterization of novel metabolic pathways: confirming metagenomic prediction using
integrated approaches including microbial genomics, microbial community analyses, and
microbial physiology (
Reichardt, et al., 2014
).
Bioavailability of microbial metabolites
The mucosal epithelium regulates passage of essential nutrients into circulation. The
epithelium is composed of a single layer of cells, dominated by enterocytes, that separate the
gut lumen from the underlying lamina propria. Tight-junction proteins securely bind
neighboring epithelial cells at the apical side and regulate molecular transport (see reviews
by
Marchiando et al., 2010
,
Peterson et al., 2014
). Two modes of transport through the
epithelium are possible: transcellular (through cells) and paracellular (between cells). The
different nature of different specialized microbial metabolites, from small polar molecules to
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larger peptides, affects their ability to withstand the intestinal environment, as well as their
capacity to cross the intestinal epithelium into the circulation (Figure 2).
Pharmacokinetic concepts help describe the bioavailability of microbial metabolites
produced in the intestines. In the healthy gut, a metabolite (or a drug) may be absorbed into
circulation by passive or active mechanisms. Based on their lipophilicity, size, and degree of
ionization (intestinal pH varies from 6.6 in the proximal small intestine to 7.5 in the terminal
ileum, and 6.4 in the cecum to an average of 7 in the colon (
Evans et al., 1988
)), metabolites
may be absorbed by passive diffusion down a concentration gradient. However, more
hydrophilic metabolites cannot penetrate membranes easily. Some hydrophilic molecules
reversibly bind carriers that travel down concentration gradients, then cross the epithelium
via facilitated passive diffusion. Metabolites (or drugs) that structurally resemble substrates
that are shuttled through the epithelial barrier, such as amino acids, sugars, and vitamins,
may be actively transported by the corresponding transporters. Lastly, pinocytosis, the
ingestion of fluid into cells, may allow metabolite uptake. One example of transcellular
transport by facilitated diffusion is glucose, which is taken up on the apical side of the lumen
by a Na
+
/Glucose symporter and transported from the basolateral side by the glucose
transporter-2 (GLUT2). SCFAs, on the other hand, may be transported into epithelial cells
and possibly through the epithelial barrier either actively by monocarboxylate transporters
(e.g., SLC5A8, SLC16A1) or by diffusion (
Ganapathy et al., 2013
).
Some metabolites that cannot be absorbed by transcellular transport (whether active or
passive) are taken up by paracellular transport. This type of transport is regulated by tight-
junction proteins. These proteins, primarily claudins, exclude molecules based on size and
charge (see review by
Van Itallie and Anderson, 2006
). Microbial metabolites may be
actively transported or diffuse through the healthy epithelial barrier, or conversely, cross the
barrier through paracellular transport when the epithelial barrier is breached. “Leaky gut”,
namely gut barrier dysfunction, is the result of dysbiosis and inflammation (
Marchiando et
al., 2010
). Interleukin-6 (IL-6), interferon-
γ
(IFN
γ
) and IL-1
β
-induced barrier dysfunction
(
Suzuki et al., 2011
;
Al-Sadi et al., 2010
) is a known characteristic of IBD (
Hollander et al.,
1986
). Conversely, several probiotics have been shown to decrease gut barrier permeability
(
Scaldaferri et al., 2012
), and SCFAs alone were sufficient to explain this effect (
Elamin et
al., 2013
).
The gut lumen is a challenging environment for metabolites such as peptides and small
molecules. Before crossing the epithelial barrier, a metabolite may be degraded or taken up
by microbes in the gut, or may undergo various modifications. The rate of these processes
and the rate of a metabolite’s absorption to circulation interact to determine its
bioavailability. Subsequently, metabolites, as do drugs, may undergo detoxification by the
liver and kidney, and be excreted from circulation. Xenobiotic metabolism may also alter the
physiology and gene expression of the host. Microbial metabolism of drugs is exploited to
convert prodrugs to active ingredients, and is also known to be associated with drug-induced
toxicity (
Li and Jia, 2013
,
Maurice, 2013
). Alternatively, microbial metabolism of
xenobiotics may inactivate drugs. Digoxin, a cardiac drug, is metabolized by
Eggerthella
lenta
, a gut bacterium (
Haiser et al., 2013
). Interestingly, dietary protein inhibits digoxin
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metabolism by this bacterium
in vivo
, and increases digoxin concentration in serum and
urine.
The circulatory system is structured such that any blood flowing from the gut flows to the
liver via the portal vein, through a network of liver sinusoids, and out of the hepatic veins to
the vena cava and circulation. The liver filters any particulate matter and bacteria that enter
through the intestines. The route of absorption differs for different metabolites; soluble
metabolites and nutrients are absorbed and enter the circulation through the portal vein, but
insoluble, fat-based metabolites are most commonly absorbed into the lymphatic system and
into the bloodstream through the thoracic duct (
Hall and Guyton, 2010
).
Taken together, the pharmacokinetic properties of a metabolite, from production and
survival in the gut through absorption and excretion, define its window of opportunity to act
in driving health or disease in the mammalian host.
Specialized microbial metabolites that mediate disease
The microbiome plays an important role in health and disease (previously reviewed by Kee
and Mazmanian, 2010;
Clemente et al., 2012
). A shift in balance between a healthy and
diseased microbiome leads to pathologic and metabolic conditions including obesity, colon
cancer, and IBD. Host-microbial interactions are in part mediated by the immune response
(
Round and Mazmanian, 2009
), and possibly via specialized metabolites (
Ursell et al.,
2014
). The gut microbiota is a virtual endocrine organ (
Clarke et al., 2014
) that produces
myriad secondary metabolites. Some of these metabolites have positive effects on the
mammalian host, as in the case of SCFAs and antibiotics. Although dysbiosis of the host-
associated microbiota has been implicated in various conditions (Kee and Mazmanian, 2010;
Clemente et al., 2012
), the mechanisms by which specific microbes, or microbial
communities, induce disease remain largely unknown. It is possible that specialized
metabolites may mediate many physiological states of well being and illness (Figure 3).
Microbial metabolites and cardiovascular disease
Gut microbes contribute to atherosclerosis from dietary consumption of red meat, providing
a compelling example of microbial metabolism leading to disease in the human host (
Wang
et al., 2011
;
Koeth et al., 2013
). Comparative levels of choline, trimethylamine N-oxide
(TMAO), and betaine, three metabolites of dietary phosphatidylcholine, predicted
cardiovascular disease risk in a clinical cohort, and promote atherosclerosis in mice.
Concentrations of these metabolites also correlated with microbial activity in the gut –
administration of antibiotics suppressed their production, and conventionalization with
mouse gut microbes rescued the phenotype (
Wang et al., 2011
). Trimethylamine (TMA), the
precursor of TMAO, is also the product of microbial metabolism of L-carnitine, a compound
abundant in red meat (
Koeth et al., 2013
). Interestingly, vegans and vegetarians consuming
L-carnitine produced much less TMAO than omnivores. Specific gut bacterial taxa also
correlated with plasma TMAO levels. Finally, supplementing mouse diets with L-carnitine
markedly increased plasma levels of TMA and TMAO, and accelerated atherosclerosis. The
mechanism by which TMAO accelerates atherosclerosis is unknown, but it may contribute
to forward cholesterol transport via upregulation of macrophage scavenger receptors. These
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studies demonstrate how a metabolite made by the gut bacterial community enters
circulation and contributes to disease. Moreover, ‘western’ (high-fat) diets have been
associated with intestinal permeability (
Martinez-Medina et al., 2014
), which would
facilitate the absorption of microbial metabolites into the circulatory system.
Microbial metabolites and cancer
Gut microbes also play a role in carcinogenesis, especially in colorectal cancer (see reviews
by
Schwabe and Jobin, 2013
and
Sears and Garrett, 2014
). Both the whole gut microbial
community and specific bacteria at specific times, play a role in initiating or exacerbating
cancer (
Kostic et al., 2012
;
Kostic et al., 2013
;
Zackular et al., 2013
; Ahn et al., 201;
Belcheva et al., 2014
).
Fusobacterium nucleatum
is enriched in human colonic adenomas
relative to surrounding tissue, suggesting that it may play a role in early initiation of
colorectal cancer (
Kostic et al., 2012
;
Kostic et al., 2013
). Further supporting this idea,
F.
nucleatum
colonization promoted and exacerbated tumorigenesis in the gut of
APC
min/+
mice, although the mechanism of pathogenesis remains unknown.
Microbes might promote cancer by producing metabolites that increase disease
susceptibility and incidence. Risk factors for colorectal cancer include high alcohol
consumption and low folate intake.
Homann et al (2000)
fed rats normal diets, and
administered high ethanol with or without antibiotics. Ethanol led to increased acetaldehyde
and decreased folate in the colon. This effect was prevented by antibiotic treatment,
suggesting that ethanol degradation by gut microbes might play a role in inducing colon
cancer. Similarly, liver cancer likely involves a complex interaction between obesity, gut
microbes, and their metabolites. In a model for liver cancer where neonate mice were
injected with a chemical carcinogen (7,12-Dimethylbenz-alpha-anthracene), genetic- or diet-
induced obesity led to changes in the gut microbiome of treated mice, and increased levels
of the metabolite deoxycholic acid (DCA), a known DNA damaging agent. The induction of
hepatocellular cancer could be prevented by treatment with a cocktail of four antibiotics, or
by vancomycin alone. DCA levels were significantly increased by high-fat diet (or in
ob/ob
mice), compared to wild type animals, and addition of DCA to antibiotic-treated mice
rescued the tumor phenotype in these mice (
Yoshimoto et al., 2013
). These studies reveal a
chemical link between gut microbes and cancer, and also suggest a potential new treatment
modality for disease by targeting microbial processes during carcinogenesis.
Microbial metabolites and cystic fibrosis
In cystic fibrosis (CF), the airway is abnormally colonized by polymicrobial communities
that vary among patients. These communities are affected by the conditions and nutrients
available in CF lungs. Different microbial communities differ in physiology and metabolite
production: even the same microbe may produce different metabolites in the context of
different communities. For example, an increase in 2,3-butanedione concentrations was
observed in four of seven CF patients when compared to healthy and ambient air controls
(
Whiteson et al., 2014
); the three patients with normal levels were undergoing antibiotic
treatments. Similarly, 2,3-butanedione levels decreased when the other patients also
underwent antibiotic treatment, suggesting that microbes are involved in the production of
this compound.
Streptococcus
spp. was the dominant species carrying genes encoding 2,3-
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butanedione biosynthesis, whereas genes for utilizing butanedione pathway products were
encoded by
Pseudomonas aeruginosa
and
Rothia mucilaginosa
. Co-culture experiments
suggested that
P. aeruginosa
, upon consumption of 2,3-butanedione produced by
Streptococcus
spp, enhanced the production of redox carriers, namely phenazines.
Phenazines likely increase reactive oxygen species and provide additional electron acceptors
to the colonizing microbial community of the CF lung as oxygen is depleted (
Whiteson et
al., 2014
).
A recent study based on metagenomes and metatranscriptomes of microbial communities in
sputum of CF-patients suggested a gradient of different communities, and hence of which
biochemical pathways were operational, based on oxygen availability (
Quinn et al., 2014
).
Of particular interest is the shift of pathways corresponding to microaerophilic respiration
by
Pseudomonas
spp. to denitrification by
Pseudomonas
and
Rothia
spp., and anaerobic
respiration via reduction of various sulphur species on depletion of oxygen. Other anaerobic
pathways corresponded to acetate, butyrate and butanediol fermentation. Furthermore,
enrichment in amino acid catabolism correlated with elevated ammonia concentration,
previously observed in the sputum of CF patients. Interestingly, genes encoding folate
biosynthesis pathways were abundant in samples from the CF population, but absent in
healthy controls. The CF microbial community may thus evolve in response to the
administration of sulphonamide drugs, which target folate biosynthesis. These findings
demonstrate how to evaluate likely physiological roles and biochemical pathways of a
microbial community and its adaptation to disease environments.
Microbial metabolites and behavior
The gut microbiome-brain axis is an active area of research (Bravo et al., 2012;
Borre et al.,
2014
;
De Palma et al., 2014
), and has received much attention recently. Observations that
brain development and behavior are influenced by the gut microbiota (
Diaz Heijtz et al.,
2011
;
Neufeld et al., 2011
;
Gareau et al., 2011
;
Bravo et al., 2011
and others), and that this
impact may be transmitted from the enteric nervous system to the central nervous system via
the vagus nerve (e.g.;
Bravo et al., 2011
), make gut metabolites immediate suspects for
mediating gut microbiota-brain interactions.
Some bacteria can produce neuroactive metabolites, ranging from serotonin and gamma-
aminobutyric acid (GABA), to dopamine and norepinephrine, to acetylcholine and histamine
(see
Lyte, 2013
; Roshchina 2010;
Wall et al., 2014
). GABA, for example, is an inhibitory
neurotransmitter that regulates and participates in various functions in the central nervous
system in mammals, and is involved in anxiety and depression. Barrett et al (2012) reported
the production of GABA through metabolism of monosodium glutamate by
Bifidobacteria
and
lactobacillus
spp. isolated from the human gut. However, GABA from the gut cannot
cross an unbreached blood-brain barrier (Van Gelder and Elliott, 1958). Another connection
is that probiotic treatment with
Lactobacillus rhamnosus
increases GABA receptor
expression in the hippocampus, and reduces anxiety- and depression-related behaviors in a
mouse model (
Bravo et al., 2011
).
No complete bacterium-metabolite-target pathway has yet been definitively linked to
behavioral changes. However, differences in microbial communities are often correlated
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with changes in the metabolite profile, and perhaps behavior (e.g.;
Daniel et al., 2014
;
Hsiao
et al., 2013
). In a maternal immune activation (MIA) mouse model for autism spectrum
disorders (ASD), both fecal bacterial communities and serum metabolomic profiles are
different between animals displaying altered versus normal behavior (
Hsiao et al., 2013
).
MIA mice also exhibit autistic-like behavioral phenotypes (increased anxiety, increased
repetitive behavior, decreased sociability, and decreased vocalization), and increased gut
barrier dysfunction. Interestingly, administration of a probiotic,
Bacteroides fragilis
NTCC
9343, corrected some of the behavioral deficits and restored levels of some serum
metabolites. One of these metabolites, namely 4-ethylphenylsulfate (4-EPS), was sufficient
to induce anxiety-like behaviors in mice when injected into the circulation, and one
probiotic,
B. fragilis
, which contributes to a gut microbial community that produces less 4-
EPS, could also ameliorate some of the negative effects of potentially neurotoxic
metabolites.
The beneficial role of SCFAs in gut health has long been appreciated, but they also play a
role in host behavior. For example, acetate crosses the blood-brain barrier, where it is taken
up and activates hypothalamic neurons (
Frost et al., 2014
). Intraperitoneal administration of
acetate suppressed appetite and led to weight loss. However, although butyrate and acetate
were mostly beneficial, propionate may be pathogenic.
Comparisons between a propionic acid-based animal model of ASD with acquired
mitochondrial disorder and a cohort of 213 children with autism specific disorder suggested
abnormalities in acyl carnitines via the mitochondrial tricarboxylic acid cycle (
Frye et al.,
2013
). When injected intraventricularly in rats, propionate induces behavior with certain
features of autism (
MacFabe et al., 2007
).
The role of microbial communities in health and disease has been studied extensively in the
past decade, but the microbial mechanisms driving many of these processes, and their targets
in the mammalian host are yet unknown. Specialized microbial metabolites originating from
the oral, urogenital tract, gastrointestinal tract, and skin microbiota may be the next frontier
in elucidating molecular mechanisms of pathogenesis and symbiosis (Figure 1, Figure 3).
Specialized metabolites from microbial isolates
Chemical crosstalk, represented by molecular signaling between host and associated
microbiota, is among the most fascinating new areas in the realm of the human microbiome.
The bioactive molecules produced by the microbiota are likely an important factor
governing the establishment of specific microbial communities in humans. These molecules
have been mostly studied
in vitro
in pure cultures or co-cultures, enabling investigations of
their biological significance. Workflows focused on directly investigating these natural
products from human or animal samples urgently need to be developed.
Some isolated examples showing what might be possible in a unified framework include the
following. The quorum-sensing pentapeptide, competence and sporulating factor (CSF),
from
Bacillus subtilis
helps maintain intestinal homeostasis when taken up by the organic
cation transporter-2. After uptake by the transporter, CSF induces expression of heat shock
protein 27 and survival pathways such as p38 MAP kinase and protein kinase B (Akt)
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pathways in cultured human colonic epithelial cells (
Fujiya et al., 2007
). Similarly, bacterial
peptidic pheromones called competence stimulating peptides produced by human-derived
Streptococcus spp
. in co-culture experiments regulate uptake of environmental DNA and
prevent hyphal formation by the oral cavity coinhabitant
Candida albicans
(
Jarosz et al.,
2009
). Other signaling molecules such as homoserine lactones mediate interactions between
P. aeruginosa
and
C. albicans
, co-inhabitants of the CF lung community (
Hogan et al.,
2004
). Biotransformation of CF-associated
P. aeruginosa
phenazines by
Aspergillus
fumigatus
has effects on growth and production of siderophores by
A. fumigatus
(
Moree et
al., 2012
). Thus, quorum sensing molecules likely dictate the status of the microbiota and
the resulting dynamics.
Although quorum sensing molecules have been largely explored in the context of their
important roles in host-microbe or microbe-microbe interactions, ribosomally and non-
ribosomally synthesized peptides and polyketide classes of specialized metabolites derived
from the human microbiota have not yet been extensively studied. The biosynthetic
pathways encoding these specialized metabolites are widely present in the genomes of
microbial species, including bacterial species in the human gut (Cimermancic et al., 2014).
Roles of these specialized metabolites identified in microbial isolates include transition of
C.
albicans
from yeast to mycelium by a hybrid nonribosomal peptide-polyketide peptide
mutanobactin A produced by oral bacterium
Streptococcus mutans
(
Joyner et al., 2010
).
E.
coli
harboring the
pks
gene locus for biosynthesis of colibactin, a putative hybrid
nonribosomal peptide-polyketide genotoxin, increases tumor growth in colorectal cells by
enhancing the emergence of senescent cells when compared with
pks
−
(deletion) strains
(
Cougnoux et al., 2014
). These senescent cells expressed higher levels of growth factors
leading to proliferation of non-infected cells and hence colorectal tumor promotion. A
highly conserved biosynthetic gene cluster for burkholderic acid, a polyketide, was found in
the genomes of the human pathogens
Burkholderia mallei
and
Burkholderia pseudomallei
(
Franke et al., 2012
). These pathogens are considered biowarfare agents because they can
cause high mortality, and are rich in biosynthetic pathways encoding specialized metabolites
(
Nierman et al., 2004
;
Vial et al., 2007
). The
Burkholderia cepacia
complex (Bcc) has been
demonstrated to produce a large number of secondary metabolites (
Vial et al., 2007
). When
Bcc infections occur in CF patients, the sputum was shown to display reduced diversity of
the polymicrobial infection. These findings encouraged
in vitro
studies, and screening of the
Bcc for antimicrobial properties (
Lipuma, 2010
). These investigations lead to the discovery
of enacyclins, a polyene class of antibiotics, that displayed potent activity against CF
pathogens.
The ribosomally synthesized lantibiotics salivaricins, such as salivaricin A2, salivaricin B,
and salivaricin D among others have been isolated from oral bacterium
Streptococcus
salivarius
from healthy individuals.
S. salivarius
has been suggested to have beneficial
properties (
Hyink et al., 2007
;
Birri et al., 2012
) and whether these peptides mediates some
of the probiotic effects is unknown. Streptolysin S from
Streptococcus pyogenes
is another
example of ribosomally produced peptide that enhanced virulence and occurrence of
necrotic lesions in animal models (
Betschel et al., 1998
;
Lee et al., 2008
). Using
comparative genomic analysis, biosynthetic pathways similar to the one utilized for
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streptolysin S production was found in the genomes of major food-borne pathogens and lead
to the
characterization
of the biotoxin clostridiolysin S from
Clostridium botulinum
and its
cousin
C. sporogenes
, a soil bacterium that can colonize hosts (
Gonzalez et al., 2010
;
Wikoff et al., 2009
). Pyroglutamic dipeptides produced by member of the gastrointestinal
tract
Lactobacillus plantarum
have been shown to reduce production of pro-inflammatory
cytokine IFN
γ
(Zvanych et al., 2014).
Ascaris suum
nematode peptidic molecule, cecropin
P1, isolated from pig intestines and found in various other insects as well as cysteine-rich
A.
suum
antibacterial factor peptides isolated from the human pathogen,
Ascaris lumbricoides
,
have been shown to possess antimicrobial activity and may help these pathogens colonize
the intestines of associated hosts (
Lee et al., 1989
,
Andersson et al., 2003
). Furthermore,
in
silico
analyses of genome sequences revealed various biosynthetic pathways for peptidic
specialized metabolites such as thiopeptides in human commensal vaginal bacteria
Lactobacillus gasseri
and human pathogen
Streptococcus pneumonia
(
Li et al., 2012
).
Whether or not members of the microbiota use this biosynthetic potential to colonize
humans and affect health remains an open question. Human commensal and pathogenic
microbes also harbor biosynthetic gene clusters for aryl polyenes and caratenoids that may
confer protection against oxidative stress (Cimermancic et al., 2014). A tri-terpenoid
cartenoid associated with human pathogen
Staphylococcus aureus
, staphyloxanthin,
enhances survival under oxidative stress and prevents killing by neutrophils (
Liu et al.,
2005
;
Clauditz et al., 2006
).
Thus, various specialized metabolites are associated with the human microbiome. Although
in silico
DNA sequence-based and
in vitro
methods have been exploited to investigate
metabolites that the human microbiota may produce, and to gain insights into the
biosynthetic potential and metabolic functions of these organisms, direct identification of
such molecules in the complex environment of the associated host has not yet been
accomplished. Such
in silico
methods and experiments performed in pure cultures or co-
culture experiments do not represent the true metabolic capacity of the microbiome
in situ
.
Thus, future efforts to develop strategies for metabolic profiling that focus specifically on
natural products in fecal matter, biological fluids such as serum, urine, and intact diseased
host tissues are needed. In this regard, imaging mass spectrometry can be especially valuable
in direct molecular analysis of gut tissue sections (
Rath et al., 2012
), enabling spatial
investigation of host-microbiome interactions. Molecular networking is an effective strategy
for differentiating metabolites of microbial and human origin (
Garg et al., 2014
) from the
complex environment of a CF-associated human lung. Since most specialized metabolites
have associated biosynthetic pathways that are unique to an organism or a class of
organisms, a combination of metagenome and metatranscriptome sequencing (
Quinn et al.,
2014
), and high resolution mass spectrometry-based molecular networking analysis
combined with statistical approaches will allow the investigation of specialized metabolite
associated crosstalk between a microbiome and its host. Although limited to small volatile
molecules, gas chromatography-mass spectrometry is also useful in connecting metabolites
and their origin to physiologically relevant diseased states (
Pleil et al., 2014
,
Amann et al.,
2014
). One potential challenge for future integration of such methodology resides in
developing platforms and algorithms for co-analysis of large volumes of high density “Big
data” generated on different mass spectrometry based analytical platforms.
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Conclusion
With the development of a three-pronged strategy combining metagenomics,
metatranscriptomics and metabolomics, we are now entering the new era where we can
begin to address the physiological role of the human microbiome in health and disease in
relation to end products of primary metabolism and secondary metabolites, with recently
emerging emphasis on microbial natural products, also termed specialized metabolites in
this Perspective. Although a small set of such metabolites have been shown to modulate host
physiology, the vast majority of such metabolites in humans (suggested to be present by
metagenome sequencing) have not been investigated. We propose that the identification of
specialized metabolites, their biotransformations by the microbiome and the host, transport,
and their origin via metatranscriptomics, and metabolomics in combination with
metagenomics will open new avenues to investigate underlying mechanisms by which the
human microbiome influences health and microbial community development. Subsequent
in
vivo
studies may further substantiate the role of these metabolites and provide insights into
such mechanisms. Finally, a deeper understanding of the complex chemical crosstalk
between the gut microbiota and humans may advance potentially revolutionary therapies for
immune, metabolic, and neurologic disorders.
Acknowledgements
We thank Dr. Hiutung Chu for comments on the manuscript. Supported by Human Frontiers Science Program –
Long-term fellowship (for G.S). Work in the authors’ laboratories are supported by funding from the NIH, the
Crohn’s and Colitis Foundation of America, and the Howard Hughes Medical Institute (to R.K.); a metabolomics
supplement to parent grant GM095384, UCSD Clinical and Translational Research Institute Pilot award
UL1TR000100 and NIH AI095125 (to P.C.D.); and the Crohn’s and Colitis Foundation of America, Autism Speaks
and the NIH DK078938; GM099535; MH100556 (to S.K.M.).
References
Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L. Human gut
microbiome and risk for colorectal cancer. J. Natl. Cancer Inst. 2013; 105:1907–1911. [PubMed:
24316595]
Al-Sadi R, Ye D, Said HM, Ma TY. IL-1beta-induced increase in intestinal epithelial tight junction
permeability is mediated by MEKK-1 activation of canonical NF-kappaB pathway. Am. J. Pathol.
2010; 177:2310–2322. [PubMed: 21048223]
Amann A, Costello B, de L, Miekisch W, Schubert J, Buszewski B, Pleil J, Ratcliffe N, Risby T. The
human volatilome: volatile organic compounds (VOCs) in exhaled breath, skin emanations, urine,
feces and saliva. J. Breath Res. 2014; 8:034001. [PubMed: 24946087]
Andersson M, Boman A, Boman HG. Ascaris nematodes from pig and human make three antibacterial
peptides: isolation of cecropin P1 and two ASABF peptides. Cell. Mol. Life Sci. 2003; 60:599–606.
[PubMed: 12737319]
Belcheva A, Irrazabal T, Robertson SJ, Streutker C, Maughan H, Rubino S, Moriyama EH, Copeland
JK, Kumar S, Green B, et al. Gut Microbial Metabolism Drives Transformation of Msh2-Deficient
Colon Epithelial Cells. Cell. 2014; 158:288–299. [PubMed: 25036629]
Bellahcene M, O’Dowd JF, Wargent ET, Zaibi MS, Hislop DC, Ngala RA, Smith DM, Cawthorne
MA, Stocker CJ, Arch JRS. Male mice that lack the G-protein-coupled receptor GPR41 have low
energy expenditure and increased body fat content. Br. J. Nutr. 2013; 109:1755–1764. [PubMed:
23110765]
Berger M, Gray Ja, Roth BL. The expanded biology of serotonin. Annu. Rev. Med. 2009; 60:355–366.
[PubMed: 19630576]
Sharon et al.
Page 13
Cell Metab
. Author manuscript; available in PMC 2015 February 23.
NIH-PA Author Manuscript
NIH-PA Author Manuscript
NIH-PA Author Manuscript
Berggren AM, Nyman EM, Lundquist I, Björck IM. Influence of orally and rectally administered
propionate on cholesterol and glucose metabolism in obese rats. Br. J. Nutr. 1996; 76:287–294.
[PubMed: 8813902]
Betschel SD, Borgia SM, Barg NL, Low DE, De Azavedo JC. Reduced virulence of group A
streptococcal Tn916 mutants that do not produce streptolysin S. Infect. Immun. 1998; 66:1671–
1679. [PubMed: 9529097]
Birri DJ, Brede DA, Nes IF. Salivaricin D, a novel intrinsically trypsin-resistant lantibiotic from
Streptococcus salivarius 5M6c isolated from a healthy infant. Appl. Environ. Microbiol. 2012;
78:402–410. [PubMed: 22101034]
Blumberg R, Powrie F. Microbiota, disease and back to health: a metastable journey. Sci Transl Med.
2012; 4:137.
Borre YE, O’Keeffe GW, Clarke G, Stanton C, Dinan TG, Cryan JF. Microbiota and
neurodevelopmental windows: implications for brain disorders. Trends Mol. Med. 2014
Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG, Bienenstock J, Cryan JF.
Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor
expression in a mouse via the vagus nerve. Proc. Natl. Acad. Sci. U. S. A. 2011; 108:16050–
16055. [PubMed: 21876150]
Brestof JR, Artis D. Commensal bacteria at the interface of host metabolism and the immune system.
Nat Rev Immunol. 2013; 14:676–684.
Brown AJ, Goldsworthy SM, Barnes AA, Eilert MM, Tcheang L, Daniels D, Muir AI, Wigglesworth
MJ, Kinghorn I, Fraser NJ, et al. The Orphan G protein-coupled receptors GPR41 and GPR43 are
activated by propionate and other short chain carboxylic acids. J. Biol. Chem. 2003; 278:11312–
11319. [PubMed: 12496283]
Clarke G, Stilling RM, Kennedy PJ, Stanton C, Cryan JF, Dinan TG. Gut Microbiota: The Neglected
Endocrine Organ. Mol. Endocrinol. 2014; 28:me20141108.
Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser JN. Recognition of peptioglycan from
the microbiota by Nod1 enhances systemic innate immunity. Nat. Med. 2010; 16:228–231.
[PubMed: 20081863]
Clauditz A, Resch A, Wieland K-P, Peschel A, Götz F. Staphyloxanthin plays a role in the fitness of
Staphylococcus aureus and its ability to cope with oxidative stress. Infect. Immun. 2006; 74:4950–
4953. [PubMed: 16861688]
Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an
integrative view. Cell. 2012; 148:1258–1270. [PubMed: 22424233]
Cougnoux A, Dalmasso G, Martinez R, Buc E, Delmas J, Gibold L, Sauvanet P, Darcha C, Déchelotte
P, Bonnet M, et al. Bacterial genotoxin colibactin promotes colon tumour growth by inducing a
senescence-associated secretory phenotype. Gut. 2014
Cummings JH. Fermentation in the human large intestine: evidence and implications for health.
Lancet. 1983; 1:1206–1209. [PubMed: 6134000]
Daniel H, Moghaddas Gholami A, Berry D, Desmarchelier C, Hahne H, Loh G, Mondot S, Lepage P,
Rothballer M, Walker A, et al. High-fat diet alters gut microbiota physiology in mice. ISME J.
2014; 8:295–308. [PubMed: 24030595]
Delzenne NM, Williams CM. Prebiotics and lipid metabolism. Curr. Opin. Lipidol. 2002; 13:61–67.
[PubMed: 11790964]
De Palma G, Collins SM, Bercik P, Verdu EF. The microbiota-gut-brain axis in gastrointestinal
disorders: stressed bugs, stressed brain or both? J. Physiol. 2014; 592:2989–2997. [PubMed:
24756641]
Diaz Heijtz R, Wang S, Anuar F, Qian Y, Björkholm B, Samuelsson A, Hibberd ML, Forssberg H,
Pettersson S. Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad.
Sci. U. S. A. 2011; 108:3047–3052. [PubMed: 21282636]
Dosselaere F, Vanderleyden J. A metabolic node in action: chorismate-utilizing enzymes in
microorganisms. Crit. Rev. Microbiol. 2001; 27:75–131. [PubMed: 11450855]
Elamin EE, Masclee AA, Dekker J, Pieters H-J, Jonkers DM. Short-chain fatty acids activate AMP-
activated protein kinase and ameliorate ethanol-induced intestinal barrier dysfunction in Caco-2
cell monolayers. J. Nutr. 2013; 143:1872–1881. [PubMed: 24132573]
Sharon et al.
Page 14
Cell Metab
. Author manuscript; available in PMC 2015 February 23.
NIH-PA Author Manuscript
NIH-PA Author Manuscript
NIH-PA Author Manuscript
Evans DF, Pye G, Bramley R, Clark AG, Dyson TJ, Hardcastle JD. Measurement of gastrointestinal
pH profiles in normal ambulant human subjects. Gut. 1988; 29:1035–1041. [PubMed: 3410329]
Franke J, Ishida K, Hertweck C. Genomics-driven discovery of burkholderic acid, a noncanonical,
cryptic polyketide from human pathogenic Burkholderia species. Angew. Chem. Int. Ed. Engl.
2012; 51:11611–11615. [PubMed: 23055407]
Frost G, Sleeth ML, Sahuri-Arisoylu M, Lizarbe B, Cerdan S, Brody L, Anastasovska J, Ghourab S,
Hankir M, Zhang S, et al. The short-chain fatty acid acetate reduces appetite via a central
homeostatic mechanism. Nat. Commun. 2014; 5:3611. [PubMed: 24781306]
Frye RE, Melnyk S, Macfabe DF. Unique acyl-carnitine profiles are potential biomarkers for acquired
mitochondrial disease in autism spectrum disorder. Transl. Psychiatry. 2013; 3:e220. [PubMed:
23340503]
Fujiya M, Musch MW, Nakagawa Y, Hu S, Alverdy J, Kohgo Y, Schneewind O, Jabri B, Chang EB.
The Bacillus subtilis quorum-sensing molecule CSF contributes to intestinal homeostasis via
OCTN2, a host cell membrane transporter. Cell Host Microbe. 2007; 1:299–308. [PubMed:
18005709]
Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, Tobe T, Clarke JM, Topping DL,
Suzuki T, et al. Bifidobacteria can protect from enteropathogenic infection through production of
acetate. Nature. 2011; 469:543–547. [PubMed: 21270894]
Ganapathy V, Thangaraju M, Prasad PD, Martin PM, Singh N. Transporters and receptors for short-
chain fatty acids as the molecular link between colonic bacteria and the host. Curr. Opin.
Pharmacol. 2013; 13:869–874. [PubMed: 23978504]
Garg N, Kapono CA, Lim YW, Koyama N, Vermeij MJA, Conrad D, Rohwer F, Dorrestein PC. Mass
spectral similarity for untargeted metabolomics data analysis of complex mixtures. Int. J. Mass
Spectrom. 2014
Gareau MG, Wine E, Rodrigues DM, Cho JH, Whary MT, Philpott DJ, Macqueen G, Sherman PM.
Bacterial infection causes stress-induced memory dysfunction in mice. Gut. 2011; 60:307–317.
[PubMed: 20966022]
Gill SR, Pop M, Deboy RT, Eckburg PB, Peter J, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett
CM, Nelson KE. Metagenomic Analysis of the Human Distal Gut Microbiome. Science. 2006;
312:1355–1359. [PubMed: 16741115]
Gonzalez DJ, Lee SW, Hensler ME, Markley AL, Dahesh S, Mitchell DA, Bandeira N, Nizet V, Dixon
JE, Dorrestein PC. Clostridiolysin S, a post-translationally modified biotoxin from Clostridium
botulinum. J. Biol. Chem. 2010; 285:28220–28228. [PubMed: 20581111]
Greenblum S, Turnbaugh PJ, Borenstein E. Metagenomic systems biology of the human gut
microbiome reveals topological shifts associated with obesity and in fl ammatory bowel disease.
PNAS. 2011; 109:594–599. [PubMed: 22184244]
Hague A, Elder D, Hicks D, Paraskeva C. Apoptosis in colorectal tumour cells: induction by the short
chain fatty acids butyrate, propionate and acetate and by the bile salt deoxycholate. Int J Cancer.
1995; 60:400–406. [PubMed: 7829251]
Haiser HJ, Gootenberg DB, Chatman K, Sirasani G, Balskus EP, Turnbaugh PJ. Predicting and
Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta. Science
(80-.). 2013; 341:295–298.
Hall, JE.; Guyton, AC. Guyton and Hall Textbook of Medical Physiology. Philadelphia: Saunders
Elsevier; 2010.
Havenaar R. Intestinal health functions of colonic microbial metabolites: a review. Benef. Microbes.
2011; 2:103–114. [PubMed: 21840809]
Hinnebusch BF, Meng S, Wu JT, Archer SY, Hodin RA. Nutrition and Cancer The Effects of Short-
Chain Fatty Acids on Human Colon Cancer Cell Phenotype Are Associated with Histone
Hyperacetylation 1. Nutr Cancer. 2002:1012–1017.
Hogan DA, Vik A, Kolter R. A Pseudomonas aeruginosa quorum-sensing molecule influences
Candida albicans morphology. Mol. Microbiol. 2004; 54:1212–1223. [PubMed: 15554963]
Hollander D, Vadheim CM, Brettholz E, Petersen GM, Delahunty T, Rotter JI. Increased intestinal
permeability in patients with Crohn’s disease and their relatives. A possible etiologic factor. Ann.
Intern. Med. 1986; 105:883–885. [PubMed: 3777713]
Sharon et al.
Page 15
Cell Metab
. Author manuscript; available in PMC 2015 February 23.
NIH-PA Author Manuscript
NIH-PA Author Manuscript
NIH-PA Author Manuscript
Homann N, Tillonen J, Salaspuro M. Microbially produced acetaldehyde from ethanol may increase
the risk of colon cancer via folate deficiency. Int. J. Cancer. 2000; 86:169–173. [PubMed:
10738242]
Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune
system. Science. 2012; 336:1268–1273. [PubMed: 22674334]
Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, Codelli JA, Chow J, Reisman SE,
Petrosino JF, et al. Microbiota modulate behavioral and physiological abnormalities associated
with neurodevelopmental disorders. Cell. 2013; 155:1451–1463. [PubMed: 24315484]
Hyink O, Wescombe PA, Upton M, Ragland N, Burton JP, Tagg JR. Salivaricin A2 and the novel
lantibiotic salivaricin B are encoded at adjacent loci on a 190-kilobase transmissible megaplasmid
in the oral probiotic strain Streptococcus salivarius K12. Appl. Environ. Microbiol. 2007;
73:1107–1113. [PubMed: 17194838]
Jarosz LM, Deng DM, van der Mei HC, Crielaard W, Krom BP. Streptococcus mutans competence-
stimulating peptide inhibits Candida albicans hypha formation. Eukaryot. Cell. 2009; 8:1658–
1664. [PubMed: 19717744]
Joyner PM, Liu J, Zhang Z, Merritt J, Qi F, Cichewicz RH. Mutanobactin A from the human oral
pathogen Streptococcus mutans is a cross-kingdom regulator of the yeast-mycelium transition.
Org. Biomol. Chem. 2010; 8:5486–5489. [PubMed: 20852771]
Kim MH, Kang SG, Park JH, Yanagisawa M, Kim CH. Short-chain fatty acids activate GPR41 and
GPR43 on intestinal epithelial cells to promote inflammatory responses in mice. Gastroenterology.
2013; 145:396–406. e10. [PubMed: 23665276]
Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, et al.
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.
Nat. Med. 2013; 19:576–585. [PubMed: 23563705]
Kolmeder CA, de Been M, Nikkilä J, Ritamo I, Mättö J, Valmu L, Salojärvi J, Palva A, Salonen A, de
Vos WM. Comparative metaproteomics and diversity analysis of human intestinal microbiota
testifies for its temporal stability and expression of core functions. PLoS One. 2012; 7:e29913.
[PubMed: 22279554]
Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ,
Tabernero J, et al. Genomic analysis identifies association of Fusobacterium with colorectal
carcinoma. Genome Res. 2012; 22:292–298. [PubMed: 22009990]
Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC,
Lochhead P, Hold GL, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and
modulates the tumor-immune microenvironment. Cell Host Microbe. 2013; 14:207–215.
[PubMed: 23954159]
Lan A, Lagadic-Gossmann D, Lemaire C, Brenner C, Jan G. Acidic extracellular pH shifts colorectal
cancer cell death from apoptosis to necrosis upon exposure to propionate and acetate, major end-
products of the human probiotic propionibacteria. Apoptosis. 2007; 12:573–591. [PubMed:
17195096]
Larsen PE, Scott N, Post AF, Field D, Knight R, Hamada Y, Gilbert JA. Satellite remote sensing data
can be used to model marine microbial metabolite turnover. ISME J. 2014
Le Poul E, Loison C, Struyf S, Springael J-Y, Lannoy V, Decobecq M-E, Brezillon S, Dupriez V,
Vassart G, Van Damme J, et al. Functional characterization of human receptors for short chain
fatty acids and their role in polymorphonuclear cell activation. J. Biol. Chem. 2003; 278:25481–
25489. [PubMed: 12711604]
LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin
suppliers to their host: a gut microbiota perspective. Curr. Opin. Biotechnol. 2013; 24:160–168.
[PubMed: 22940212]
Lee YK, Mazmanian SK. Has the microbiota played a critical role in the evolution of the adaptive
immune system? Science. 2010; 330:1768–1773. [PubMed: 21205662]
Lee J, Boman A, Sun C, Andersson M, Jornvall H, Mutt V, Boman H. Antibacterial peptides from pig
intestine: isolation of a mammalian cecropin. PNAS. 1989a; 86:9159–9162. [PubMed: 2512577]
Sharon et al.
Page 16
Cell Metab
. Author manuscript; available in PMC 2015 February 23.
NIH-PA Author Manuscript
NIH-PA Author Manuscript
NIH-PA Author Manuscript
Lee JY, Boman A, Sun CX, Andersson M, Jörnvall H, Mutt V, Boman HG. Antibacterial peptides
from pig intestine: isolation of a mammalian cecropin. Proc. Natl. Acad. Sci. U. S. A. 1989b;
86:9159–9162. [PubMed: 2512577]
Lee SW, Mitchell DA, Markley AL, Hensler ME, Gonzalez D, Wohlrab A, Dorrestein PC, Nizet V,
Dixon JE. Discovery of a widely distributed toxin biosynthetic gene cluster. Proc. Natl. Acad. Sci.
U. S. A. 2008; 105:5879–5884. [PubMed: 18375757]
Levy R, Borenstein E. Metagenomic systems biology and metabolic modeling of the human
microbiome. 2014:1–6.
Li H, Jia W. Cometabolism of microbes and host: implications for drug metabolism and drug-induced
toxicity. Clin. Pharmacol. Ther. 2013; 94:574–581. [PubMed: 23933971]
Li J, Qu X, He X, Duan L, Wu G, Bi D, Deng Z, Liu W, Ou H-Y. ThioFinder: a web-based tool for the
identification of thiopeptide gene clusters in DNA sequences. PLoS One. 2012; 7:e45878.
[PubMed: 23029291]
Lim YW, Schmieder R, Haynes M, Furlan M, Matthews TD, Whiteson K, Poole SJ, Hayes CS, Low
DA, Maughan H, et al. Mechanistic model of Rothia mucilaginosa adaptation toward persistence
in the CF lung, based on a genome reconstructed from metagenomic data. PLoS One. 2013;
8:e64285. [PubMed: 23737977]
Lipuma JJ. The changing microbial epidemiology in cystic fibrosis. Clin. Microbiol. Rev. 2010;
23:299–323. [PubMed: 20375354]
Liu GY, Essex A, Buchanan JT, Datta V, Hoffman HM, Bastian JF, Fierer J, Nizet V. Staphylococcus
aureus golden pigment impairs neutrophil killing and promotes virulence through its antioxidant
activity. J. Exp. Med. 2005; 202:209–215. [PubMed: 16009720]
Lyte M. Microbial endocrinology in the microbiome-gut-brain axis: how bacterial production and
utilization of neurochemicals influence behavior. PLoS Pathog. 2013; 9:e1003726. [PubMed:
24244158]
MacFabe DF, Cain DP, Rodriguez-Capote K, Franklin AE, Hoffman JE, Boon F, Taylor AR,
Kavaliers M, Ossenkopp K-P. Neurobiological effects of intraventricular propionic acid in rats:
possible role of short chain fatty acids on the pathogenesis and characteristics of autism spectrum
disorders. Behav. Brain Res. 2007; 176:149–169. [PubMed: 16950524]
Marchiando AM, Graham WV, Turner JR. Epithelial barriers in homeostasis and disease. Annu. Rev.
Pathol. 2010; 5:119–144. [PubMed: 20078218]
Marcobal A, Kashyap PC, Nelson TA, Aronov PA, Donia MS, Spormann A, Fischbach MA,
Sonnenburg JL. A metabolomic view of how the human gut microbiota impacts the host
metabolome using humanized and gnotobiotic mice. ISME J. 2013; 7:1933–1943. [PubMed:
23739052]
Martens JH, Barg H, Warren MJ, Jahn D. Microbial production of vitamin B12. Appl. Microbiol.
Biotechnol. 2002; 58:275–285. [PubMed: 11935176]
Martinez-Medina M, Denizot J, Dreux N, Robin F, Billard E, Bonnet R, Darfeuille-Michaud A,
Barnich N. Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host
barrier function favouring AIEC colonisation. Gut. 2014; 63:116–124. [PubMed: 23598352]
Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis
D, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor
GPR43. Nature. 2009; 461:1282–1286. [PubMed: 19865172]
Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics Shape the Physiology and Gene Expression of the
Active Human Gut Microbiome. Cell. 2013; 152:39–50. [PubMed: 23332745]
McCarren J, Becker JW, Repeta DJ, Shi Y, Young CR, Malmstrom RR, Chisholm SW, DeLong EF.
Microbial community transcriptomes reveal microbes and metabolic pathways associated with
dissolved organic matter turnover in the sea. Proc. Natl. Acad. Sci. U. S. A. 2010; 107:16420–
16427. [PubMed: 20807744]
Moree WJ, Phelan VV, Wu C-H, Bandeira N, Cornett DS, Duggan BM, Dorrestein PC. Interkingdom
metabolic transformations captured by microbial imaging mass spectrometry. Proc. Natl. Acad.
Sci. U. S. A. 2012; 109:13811–13816. [PubMed: 22869730]
Sharon et al.
Page 17
Cell Metab
. Author manuscript; available in PMC 2015 February 23.
NIH-PA Author Manuscript
NIH-PA Author Manuscript
NIH-PA Author Manuscript