Short-Chain Fatty Acids as Key Bacterial Metabolites

Leading Edge
Review
From Dietary Fiber to Host Physiology:
Short-Chain Fatty Acids as Key Bacterial Metabolites
Ara Koh, 1 Filipe De Vadder, 1 Petia Kovatcheva-Datchary, 1 and Fredrik Ba ̈ ckhed 1,2, *
1Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine,
Institute of Medicine, University of Gothenburg, 413 45 Gothenburg, Sweden
2Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology,
Faculty of Health Sciences, University of Copenhagen, 2200 København, Denmark
*Correspondence: [e-mail]
http://dx.doi.org/10.1016/j.cell.2016.05.041
A compelling set of links between the composition of the gut microbiota, the host diet, and host
physiology has emerged. Do these links reflect cause-and-effect relationships, and what might
be their mechanistic basis? A growing body of work implicates microbially produced metabolites
as crucial executors of diet-based microbial influence on the host. Here, we will review data sup-
porting the diverse functional roles carried out by a major class of bacterial metabolites, the
short-chain fatty acids (SCFAs). SCFAs can directly activate G-coupled-receptors, inhibit histone
deacetylases, and serve as energy substrates. They thus affect various physiological processes
and may contribute to health and disease.
Introduction
The human microbiota is the collection of microbes that live on
and in our body, with the largest and most diverse cluster of
microorganisms inhabiting the gut. The gut microbiota has
co-evolved with the host, which provides the microbes with
a stable environment while the microbes provide the host
with a broad range of functions such as digestion of complex
dietary macronutrients, production of nutrients and vitamins,
defense against pathogens, and maintenance of the immune
system. Emerging data have demonstrated that an aberrant
gut microbiota composition is associated with several dis-
eases, including metabolic disorders and inflammatory bowel
disorder (IBD). One of the mechanisms in which microbiota af-
fects human health and disease is its capacity to produce
either harmful metabolites associated with development of
disease or beneficial metabolites that protect against disease.
Diet drives gut microbiota composition and metabolism, mak-
ing microbes a link between diet and different physiological
states via their capacity to generate microbial metabolites de-
pending on dietary intake. Some studies representing evi-
dence of the interplay between diet, microbial composition,
and physiology are described in the next paragraph, and the
Review will then focus on a particularly versatile class of
microbial metabolite short-chain fatty acids (SCFAs) that
are derived from microbial fermentation of dietary fibers and
are likely to have broad impacts on various aspects of host
physiology.
Human populations with a diet enriched in complex carbo-
hydrates, such as the Hadza hunter gatherers from Tanzania,
have increased diversity of the gut microbiota (Schnorr et al.,
2014). In contrast, long-term intake of high-fat and high-su-
crose diet can lead to the extinction of several taxa of the
gut microbiota (Sonnenburg et al., 2016). Barley kernel-based
bread consumption improved glucose tolerance in healthy in-
dividuals with normal body mass index (BMI) in association
with enrichment of Prevotella copri and increased capacity
to ferment complex polysaccharides (Kovatcheva-Datchary
et al., 2015). Improved postprandial glucose response and
enrichment of butyrate-producing bacteria were found after
3 months intake of a mixture of inulin and oligofructose in
obese women (Dewulf et al., 2013), and in mice that are
obese due to either genetic manipulation or diet, supplemen-
tation with inulin-type fructans (fructo-oligosaccharides [FOS])
induced a remarkable increase of the number of Bifidobacte-
rium spp, which is inversely correlated with adiposity and
glucose intolerance (Cani et al., 2007).
Microbial Fermentation Products: Short-Chain Fatty
Acids
Dietary fibers, but also proteins and peptides, which escape
digestion by host enzymes in the upper gut, are metabolized
by the microbiota in the cecum and colon (Macfarlane and
Macfarlane, 2012). The major products from the microbial
fermentative activity in the gut are SCFAs—in particular, ace-
tate, propionate, and butyrate (Cummings et al., 1987). How-
ever, when fermentable fibers are in short supply, microbes
switch to energetically less favorable sources for growth
such as amino acids from dietary or endogenous proteins,
or dietary fats (Cummings and Macfarlane, 1991; Wall et al.,
2009), resulting in reduced fermentative activity of the micro-
biota and SCFAs as minor end products (Russell et al.,
2011). Protein fermentation can contribute to the SCFA pool
but mostly gives rise to branched-chain fatty acids such as
isobutyrate, 2-methylbutyrate, and isovalerate, exclusively
originating from branched-chain amino acids valine, isoleu-
cine, and leucine (Smith and Macfarlane, 1997), which are
implicated in insulin resistance (Newgard et al., 2009). Further
supplementation of diet rich in protein or fat with dietary fiber
1332 Cell 165, June 2, 2016 ª 2016 Elsevier Inc.

restores the levels of beneficial microbes, lowers the levels of
toxic microbial metabolites, and increases SCFAs (Sanchez
et al., 2009).
SCFA Biosynthesis, Absorption, and Distribution
The microbial conversions of dietary fiber to monosaccharides
in the gut involve a number of principal events (reactions)
mediated by the enzymatic repertoire of specific members of
the gut microbiota (Figure 1 and Table 1). Major end products
from these fermentations are the SCFAs. One of the major
SCFAs, acetate, can be produced from pyruvate by many
gut bacteria either via acetyl-CoA or via the Wood-Ljungdahl
pathway in which acetate is synthesized via two branches:
(1) the C 1 -body branch (also known as Eastern branch) via
reduction of CO 2 to formate and (2) the carbon monoxide
branch (the Western branch) via reduction of CO 2 to CO,
which is further combined with a methyl group to produce
acetyl-CoA (Ragsdale and Pierce, 2008). Another major
SCFA, propionate, is produced from succinate conversion to
methylmalonyl-CoA via the succinate pathway. Propionate
can also be synthesized from acrylate with lactate as a
precursor through the acrylate pathway (Hetzel et al., 2003)
and via the propanediol pathway, in which deoxyhexose
sugars (such as fucose and rhamnose) are substrates
(Scott et al., 2006). The third major SCFA, butyrate is formed
from the condensation of two molecules of acetyl-CoA and
subsequent reduction to butyryl-CoA, which can be converted
to butyrate via the so-called classical pathway, by phospho-
transbutyrylase and butyrate kinase (Louis et al., 2004).
Butyryl-CoA can also be transformed to butyrate by the
butyryl-CoA:acetate CoA-transferase route (Duncan et al.,
2002). Some microbes in the gut can use both lactate and
acetate to synthesize butyrate (Table 1), which prevents
Figure 1. Known Pathways for Biosynthesis of SCFAs from Carbohydrate Fermentation and Bacterial Cross-Feeding
The microbial conversion of dietary fiber in the gut results in synthesis of the three major SCFAs, acetate, propionate, and butyrate. Acetate is produced from
pyruvate via acetyl-CoA and also via the Wood-Ljungdahl pathway. Butyrate is synthesized from two molecules of acetyl-CoA, yielding acetoacetyl-CoA, which is
further converted to butyryl-CoA via b-hydroxybutyryl-CoA and crotonyl-CoA. Propionate can be formed from PEP through the succinate pathway or the acrylate
pathway, in which lactate is reduced to propionate. Microbes can also produce propionate through the propanediol pathway from deoxyhexose sugars, such as
fucose and rhamnose. PEP, phosphoenolpyruvate; DHAP, dihydroxyacetonephosphate.
Cell 165, June 2, 2016 1333

accumulation of lactate and stabilizes the intestinal environ-
ment. Analysis of metagenome data also suggested that buty-
rate can be synthesized from proteins via the lysine pathway
(Vital et al., 2014), further suggesting that microbes in the
gut can adapt to nutritional switches in order to maintain the
synthesis of essential metabolites such as SCFAs.
The concentration of SCFAs varies along the length of
the gut, with highest levels in the cecum and proximal
colon, while it declines toward the distal colon (Cummings
et al., 1987). Reduced SCFA concentrations may be explained
by increased absorption through the Na + -coupled mono-
carboxylate transporter SLC5A8 and the H + -coupled low-af-
finity monocarboxylate transporter SLC16A1. Butyrate is the
preferred energy source for colonocytes and is locally
consumed, whereas other absorbed SCFAs drain into the por-
tal vein. Propionate is metabolized in the liver and thus is only
present at low concentration in the periphery, leaving acetate
as the most abundant SCFA in peripheral circulation (Cum-
mings et al., 1987) (Table 2). Furthermore, acetate can cross
the blood-brain barrier and reduce appetite via a central ho-
meostatic mechanism (Frost et al., 2014). Despite the low
concentration in the periphery, propionate and butyrate affect
peripheral organs indirectly by activation of hormonal and ner-
vous systems. In the next sections, we discuss recent findings
on microbially produced SCFAs and how they affect host
physiology and pathology.
SCFAs as Signaling Molecules
HDAC Inhibitors
Histone acetylation emerges as a central switch that allows
interconversion between permissive (via acetylation) and
repressive chromatin structures (via deacetylation). Histone
acetylation, which takes place on the epsilon amino groups
of lysine residues on N-terminal tails of mainly histones 3
and 4, is thought to increase accessibility of the transcriptional
machinery to promote gene transcription. Acetyl groups are
added to histone tails by histone acetyltransferases (HATs)
and are removed by histone deacetylases (HDACs). HDAC in-
hibitors have been widely used for cancer therapy. Their anti-
inflammatory or immune-suppressive function has also been
reported. Butyrate and, to a lesser extent, propionate are
known to act as HDAC inhibitors (Johnstone, 2002); therefore,
SCFAs may act as modulators of cancer and immune homeo-
stasis.
Among the SCFAs, butyrate has been investigated most
extensively. Present at high levels (mM) in the gut lumen, buty-
rate is the primary energy source for colonocytes and also
protects against colorectal cancer and inflammation, at least
partly by inhibiting HDACs (Flint et al., 2012), altering the
expression of many genes with diverse functions, some of
which include cell proliferation, apoptosis, and differentiation.
In contrast to colorectal cancer cells, butyrate does not inhibit
cell growth when it is delivered to healthy colonic epithelium in
rodents or when it is added to noncancerous colonocytes
in vitro. Instead, butyrate has either no significant effect or
the opposite effect of stimulating cell growth under these con-
ditions by acting as an energy substrate (Lupton, 2004)—the
butyrate paradox. This may be explained by the fact that
butyrate is the preferred energy substrate for normal colono-
cytes, whereas cancerous colonocytes prefer glucose (aero-
bic glycolysis or Warburg effect). Compared to normal colono-
cytes that oxidize butyrate, butyrate is accumulated 3-fold in
nuclear extracts from cancer cells, generating higher concen-
trations of butyrate in cancerous epithelial cells, where it can
act as an efficient HDAC inhibitor (Donohoe et al., 2012).
Thus, butyrate may act as an HAT activator in normal cells
and as an HDAC inhibitor in cancerous cells. The butyrate
consumption of normal colonocytes protects stem/progenitor
cells in the colon from exposure to high butyrate concentra-
tions and alleviates butyrate-dependent HDAC inhibition and
impairment of stem cell function (Kaiko et al., 2016). In
contrast, butyrate-induced HDAC inhibition in small intestinal
stem cells promotes the stem cell population (Yin et al.,
2014). Taken together, the butyrate can induce different ef-
fects in a cell- and environment-specific context.
In addition to being an anti-tumor agent, SCFA-mediated
HDAC inhibition is also a potent anti-inflammatory agent.
Butyrate suppresses proinflammatory effectors in lamina
Table 1. SCFA Production by Microbes in the Gut
SCFAs Pathways/Reactions Producers References
Acetate from pyruvate via acetyl-CoA most of the enteric bacteria, e.g., Akkermansia muciniphila,
Bacteroides spp., Bifidobacterium spp., Prevotella spp.,
Ruminococcus spp.
Louis et al., 2014;
Rey et al., 2010
Wood-Ljungdahl pathway Blautia hydrogenotrophica, Clostridium spp., Streptococcus spp.
Propionate succinate pathway Bacteroides spp., Phascolarctobacterium succinatutens,
Dialister spp., Veillonella spp.
Louis et al., 2014;
Scott et al., 2006
acrylate pathway Megasphaera elsdenii, Coprococcus catus
propanediol pathway Salmonella spp., Roseburia inulinivorans, Ruminococcus obeum
Butyrate phosphotransbutyrylase/
butyrate kinase route
Coprococcus comes, Coprococcus eutactus Duncan et al., 2002;
Louis et al., 2014
butyryl-CoA:acetate CoA-
transferase route
Anaerostipes spp. (A, L), Coprococcus catus (A), Eubacterium
rectale (A), Eubacterium hallii (A, L), Faecalibacterium
prausnitzii (A), Roseburia spp. (A)
A, acetate is the substrate for producing butyrate; L, lactate is the substrate for producing butyrate.
1334 Cell 165, June 2, 2016

Table 2. Microbial Metabolites and Their Cognate Receptors
GPR43/FFAR2
(Gi , Gq )
Ligand EC50 Systemic/Portal Conc References
acetate (C2),
propionate (C3)
259537 mM 70 mM /250 mM for C2; 5 mM /88 mM for C3 Brown et al., 2003;
Kimura et al., 2013;
Maslowski et al., 2009;
Nøhr et al., 2013; Smith
et al., 2013; Tolhurst
et al., 2012
Expression Function Microbial Metabolite-
Mediated Signaling a
colonic, small intestinal epithelium, EEC,
colonic LP cells (mast cells, neutrophils,
eosinophils, and colonic Tregs), leukocytes
in small intestinal LP, polymorphonuclear
cells, adipocytes, skeletal muscle, heart,
and spleen
Metabolism: anti-lipolysis, increased
insulin sensitivity and energy expenditure,
GLP-1 and PYY secretion, preadipocyte
differentiation, and appetite control; Cancer
and IBD: protection against IBD, resolution
of inflammation in animal models of colitis,
and apoptosis of human colon cancer cell
line; Immune: expansion and differentiation
of Tregs, increase of Teff against
pathogenic bacteria, neutrophil
chemotaxis, reduced leukemia cell
proliferation, and resolution of arthritis and
asthma; Ect: electrolyte and fluid secretion
yes in intestinal epithelium
and in LP cells; yes in
adipocytes after consuming
dietary fiber
GPR41/
FFAR3 (G i )
Ligand EC50 Systemic/Portal Conc References
propionate (C3),
butyrate (C4),
(C3>C4>>C2)
12274 mM for C3 5 mM /88 mM for C3; 4 mM /29 mM for C4 Brown et al., 2003;
De Vadder et al., 2014;
Kimura et al., 2011;
Le Poul et al., 2003;
Nøhr et al., 2015; Samuel
et al., 2008; Trompette
et al., 2014
Expression Function Microbial Metabolite-
Mediated Signaling a
colonic, small intestinal epithelium,
colonic LP cells (mast cells but not in
neutrophils), spleen, bone marrow, lymph
nodes, adipose tissue, periportal afferent
system, peripheral nervous system,
peripheral blood monocuclear cells,
pancreas, and co-expressed with GLP-1
in EECs located in the crypts and lower
part of the villi
Metabolism: increased energy expenditure,
oxygen consumption rate, leptin
expression, decrease of food intake,
increased PYY expression, and intestinal
gluconeogenesis (IGN); Immune:
hematopoiesis of DCs from bone marrow,
increased Treg cells and DC precursors
alleviating asthma, and protective immunity
yes in periportal afferent
system, DC precursors
in bone marrow, and
intestinal epithelium
GPR109A/
HCA2 (G i, Gbg)
Ligand EC50 Systemic/Portal Conc References
niacin, b-D-OHB,
butyrate (C4)
0.8 mM (h) and
0.3 mM (m) for
b-D-OHB; 0.7 mM
(h) and 1.6 mM (m)
for butyrate
<0.1 mM for niacin; 1–2 mM (2–3 days
of fasting) for b-D-OHB; 4 mM /29 mM
for C4
Macia et al., 2015; Singh
et al., 2014; Taggart et al.,
2005; Thangaraju et al.,
2009; Tunaru et al., 2003;
Wise et al., 2003
Expression Function Microbial Metabolite-
Mediated Signaling a
apical membrane of colonic/small
intestinal epithelium (silenced in colon
cancer and microbiota-dependent
expression), macrophages, monocytes,
neutrophils, DCs; but not in lymphocytes,
adipocytes (white and brown), epidermal
Langerhans cells, and retinal pigment
epithelium
Metabolism: anti-lipolysis and triglyceride
lowering; Cancer and IBD: protection
against colitis and CRC, improved epithelial
barrier function, and tumor suppressor in
mammary gland; Immune: increase of Treg
generation (FoxP3 expression), IL-10-
producing T cells, and decrease of pro-
inflammatory Th17 cells (only in colonic LP)
no evidence for niacin and
b-D-OHB; yes in intestinal
epithelium and DCs for
butyrate
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Cell 165, June 2, 2016 1335