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Obesity and the human microbiome

Ruth E. Ley
Department of Microbiology, Cornell University, Ithaca, Purpose of review
New York, USA
Obesity was once rare, but the last few decades have seen a rapid expansion of the
Correspondence to Ruth E. Ley, Department of proportion of obese individuals worldwide. Recent work has shown obesity to be
Microbiology, 260 Wing Hall, Cornell University, Ithaca,
NY 14853, USA associated with a shift in the representation of the dominant phyla of bacteria in the gut,
Tel: +1 607 255 4954; fax: +1 607 255 3904; both in humans and animal models. This review summarizes the latest research into the
e-mail: rel222@cornell.edu
association between microbial ecology and host adiposity, and the mechanisms by
Current Opinion in Gastroenterology 2010, which microbes in the gut may mediate host metabolism in the context of obesity.
26:5–11
Recent findings
Studies of the effect of excess body fat on the abundances of different bacteria taxa in
the gut generally show alterations in the gastrointestinal microbiota, and changes during
weight loss. The gastrointestinal microbiota have been shown to impact insulin
resistance, inflammation, and adiposity via interactions with epithelial and endocrine
cells.
Summary
Large-scale alterations of the gut microbiota and its microbiome (gene content) are
associated with obesity and are responsive to weight loss. Gut microbes can impact
host metabolism via signaling pathways in the gut, with effects on inflammation, insulin
resistance, and deposition of energy in fat stores. Restoration of the gut microbiota to a
healthy state may ameliorate the conditions associated with obesity and help maintain a
healthy weight.

Keywords
gut microbial ecology, inflammation, insulin resistance, metagenomics, microbiota,
obesity

Curr Opin Gastroenterol 26:5–11


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0267-1379

Introduction Patterns of microbial diversity in relation to


Up until the last few decades, obesity has been a obesity
rare physiological state. Now however, the number of The initial link between gut microbial ecology and
obese or overweight humans has come to outnumber obesity was made in leptin-deficient mice (mice homo-
those suffering from malnutrition [1]. This is an unpre- zygous for an aberrant leptin gene, ob/ob) by Ley et al. [2].
cedented state for our species, resulting from a mis- Results from a 16S rRNA gene sequence survey revealed
match between our evolutionary biology and our that the bacterial communities in the ceca of ob/ob mice
modern environment. The human body is a complex had a different proportion of bacteria belonging to the
system, made all the more complex through its inter- two dominant phyla when compared with those of lean
actions with the trillions of microorganisms that coat wild-type (þ/þ) or heterozygous (ob/þ) mice, with a
the body surface and densely populate the gut. Recent greater representation of Firmicutes and fewer Bacter-
work has shown that the microbes of the gut may oidetes characterizing the obese host microbiota. A sub-
play a role in human metabolism and adiposity. Because sequent metagenomic analysis of these same microbial
they are environmentally acquired, microbes constitute communities, which was based on shotgun sequencing of
one part of our environment that may contribute to the the microbial community DNA, showed an enrichment
obese state. This review discusses the most recent in genes involved in energy extraction from food in the
findings and insights into the relationship between obese host’s microbiome relative to that of the lean host’s
the human microbiota, obesity, and obesity-associated microbiome. A microbiota with greater energy extraction
diseases. efficiency resulted in less energy left over in feces and

0267-1379 ß 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins DOI:10.1097/MOG.0b013e328333d751

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6 Gastrointestinal infections

greater levels of short-chain fatty acids (SCFAs) in the of association between microbial taxa and host weight
cecum. Furthermore, when the luminal contents from raise the question of how much impact the differences in
the ceca of obese or lean mice were provided to lean methodology can have on the patterns observed. Biases
germ-free recipients, the mice receiving the microbes are inherent to all of the methods employed in studies of
from the obese donors gained more weight over a 2-week microbial ecology, and the degree of bias can vary
period than recipients of the lean microbes, despite between samples within a study. For instance, several
equivalent food intake [3]. In a study extending these of the studies listed in Table 1 use fluorescent in-situ
observations to humans, 12 obese participants were hybridization (FISH) with group-specific oligonucleotide
randomly assigned to either carbohydrate-restricted or probes targeting the ribosomal RNA as a starting point to
fat-restricted diets, and on average, the proportion of enumerate (by microscopic counts or cell sorting) cells
Bacteroidetes bacteria enumerated via 16S rRNA gene belonging to specific microbial taxa. FISH reveals a
sequencing increased over time, mirroring reductions in limited fraction of cells (roughly 20–30% of bacterial
host weight but not changes in diet [4]. Together these cells in a given sample cannot be stained with FISH
studies showed that the gut microbiota was generally [6,9]) either due to cell permeability or probe mismatch
altered in the obese host and could contribute to host issues. In addition, any method that relies on specific
adiposity in humans and mice. oligonucleotide probes (e.g., qPCR and FISH) is inher-
ently limited by the fact that without a 16S rRNA gene-
Metagenomics and obesity based survey of the overall diversity within a sample, the
A subsequent and much larger study of the microbiome specificity of the selected probes will be uncertain.
associated with obesity conducted with humans also Indeed, each time a new participant’s microbiota is
showed that obesity was associated with a depletion of surveyed, novel diversity is described: the overall diver-
Bacteroidetes, together with an enrichment in carbo- sity of humanity’s microbial diversity is far from circum-
hydrate and lipid-utilizing genes in the microbiome as scribed. It would be highly informative for all of these
a whole. Turnbaugh et al. [5] focused on twins to assess common methods to be applied together within a single
the gut microbiota’s relationship to host weight. The study so that we can begin to understand how they relate.
fecal microbial communities of young adult female In addition, researchers are calling for standardized
monozygotic (n ¼ 31) and dizygotic (n ¼ 23) twin pairs approaches for sample processing [15,16].
concordant for either leanness or obesity were compared,
along with those of their mothers (n ¼ 46), using a com- Animal vs. human studies
bination of traditional 16S rRNA gene clone libraries and In contrast to studies performed in humans, studies of gut
high-throughput metagenomic analyses of the micro- microbial ecology and obesity conducted in animals tend
biome. Fecal samples were obtained from the majority to have less variable outcomes. Studies in rats and pigs
of participants at an initial time point and then again have reported greater abundances of Bacteroidetes
2 months later. Comparisons between all 154 participants associated with the lean state [16–18,19], as observed
showed obesity to be associated with reduced bacterial in ob/ob mice. In a systems-biology approach, Waldram
diversity and reduced representation of the Bacteroi- et al. [20] studied a rat model of obesity, characterizing
detes. Furthermore, the microbiome differed between gut microbiotas in parallel with metabolites. Results
obese and lean hosts in much the same way it had in the broadly support patterns of greater Firmicutes/Bacteroi-
obese mouse model, with obese host microbiomes detes ratios observed in other animal studies. In addition,
enriched in gene categories involved in carbohydrate specific bacteria were associated with the obese phenotype
and lipid metabolism. (Halomonas and Sphingomonas), as were lower total bac-
terial counts and lower Bifodobacterial counts; further-
Varied patterns of microbial ecology in relation to more, differences in microbial community composition
weight correlated with differences in metabotypes [20].
This and other patterns of fecal microbial ecology in
relation to body weight in humans have been reported Is the variation in outcomes of human studies related to
recently [4,5,6–9,10,11,12,13,14], and these are the complexity of the human lifestyle? In animal studies,
summarized in Table 1. In studies that examine the diet can be controlled precisely – this precludes any
effect of weight loss on the abundance of Bacteroides- potentially modulating effects of variations in diet
related taxa, the relationship has been reported as between participants (e.g., see [21] where specific
positive [12], neutral [9], and negative [11]. It is note- microbial taxa respond to changes in a diet’s content of
worthy that rather than using broad 16S rRNA gene specific carbohydrates). Yet, average human diets that
surveys or metagenomics to assess the composition of are not designed for weight loss may add noise to data
microbial communities, these studies enumerated rather than skew results one way or another. Indeed, in a
specific taxa using probes, which can differ between comparison of human vegetarians and omnivores allowed
studies (e.g., [11] vs. [9]). Thus, the varying patterns to eat their normal diet, Tap et al. [22] did not note any

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Obesity and the human microbiome Ley 7

Table 1 Human studies of gut microbial ecology in relation to body weight


Author Participants Method (sample type) Finding

Ley et al. [2] 12 obese participants on one 16S rRNA surveys by Proportion of Bacteroidetes sequences
of two diets, carbohydrate or Sanger sequencing (feces) increased over time, on average, and
fat-reduced, for 1 year; correlated with weight loss. No difference
two lean controls between diets
Turnbaugh et al. [5] 154 participants, MZ and DZ twins 16S by Sanger and 454 Reduced levels of diversity, and reduced
and mothers, obese or lean pyrosequencing, levels of Bacteroidetes in obese participants;
metagenomics (feces) metagenomes of obese participants enriched
in energy-harvesting genes
Schwiertz et al. [6] 30 lean, 35 overweight, 33 obese qPCR for Bacteroidetes, More Bacteroidetes in overweight and obese
participants Actinobacteria, Archaea vs. lean participants, and more
(feces) Methanobrevibacter in lean participants
Collado et al. [7] Women before and during pregnancy, FISH/flow cytometry Higher levels of Bacteroidetes and S. aureus in
18 overweight participants and qPCR (feces) overweight, positive correlation between
and 36 controls Bacteroides levels and weight gain over
pregnancy
Sotos et al. [8] 8 obese and overweight adolescents FISH (feces) Enterobacteriaceae and sulfate-reducing
during weight loss bacteria reduced in group with greatest
weight loss. Reduced levels of
Roseburia–Eubacterium in those with
less weight loss
Duncan et al. [9] Participants on weight loss diets FISH counts (feces) No difference in Bacteroidetes levels between
over 8 weeks vs. groups; reduced levels of Roseburia
weight maintenance and Eubacterium, and increased levels of
Clostridium spp., correlate with reduced
carbohydrate intake
Kalliomaki et al. [10] Obese and overweight children qRT-PCR and FISH/flow Children remaining lean at age 7 had higher
(n ¼ 25) and normal cytometry (feces) levels of Bifidobacteria and lower levels of
weight children (n ¼ 24); S. aureus, as infants
prospective study
Santacruz et al. [11] 36 adolescents on diet and physical qPCR (feces) Bacteroides fragilis abundance correlated
activity, 10 weeks with carbohydrate intake. Levels of
Bacteroides and Lactobacillus increased
with weight loss
Nadal et al. [12] 39 adolescents on diet and physical qPCR (feces) Clostridium histolyticum and E. rectale–C.
activity, 10 weeks coccoides reduced with weight gain;
increase in Bacteroides–Prevotella in
high weight loss group
Sabate et al. [13] 137 obese patients, 40 healthy Glucose-hydrogen breath test Bacterial overgrowth in small intestine
controls (for H2) and liver biopsy more common in obese vs. lean participants
(breath, liver)
Zhang et al. [14] 3 lean, three obese, and three Sanger and 454 sequencing of Firmicutes more abundant in lean participants,
postgastric bypass 16S rDNAs, qPCR (feces) lowest after gastric bypass. Gamma-
participants Proteobacteria and Verrucomicrobia enriched
after gastric bypass; higher Archaea in obese
participants; overall communities of gastric
bypass and obese participants more similar
to each other than to lean participants
DZ, dizygotic; FISH, fluorescent in-situ hybridization; MZ, monozygotic.

major differences between gut microbiotas for the two approach to this question has been to control the com-
diet groups. Rather than the composition of the diet, position of the initial microbial community directly. This
another factor that may be important to consider is how is accomplished by administering whole microbiotas of
the food is ingested throughout the day, for instance, how known composition by oral gavage straight into the
long the fasting periods last. Fasted mice have been stomach of germ-free (usually mouse) recipients housed
shown to harbor a greater proportion of Bacteroidetes in asceptic isolators. As mentioned above, the result of
in their ceca compared with unfasted mice with equiv- such ‘transplantation’ of the gut microbes from obese
alent body fat [23]. Thus, the frequency with which food (genetic or diet-induced models) to lean germ-free reci-
enters the bowel and its transit time may be important pient mice is greater weight gain for mice that received
factors to control for, or at least note, when comparing obese-microbiotas [3,19]. Although these transplan-
studies in humans. tation experiments are highly artificial, they show that
a microbiota can predispose the host to greater weight
Prospective studies gain, and recent studies have shown these findings to be
The question of whether or not a microbial community relevant to human health. Kalliomaki et al. [10] com-
can predispose a host to weight gain or loss has been pared groups of children over time and observed that
addressed in animal models and human studies. One those who became overweight by age 7 had had lower

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8 Gastrointestinal infections

levels of Bifidobacteria and higher levels of Staphylococcus metabolism throughout the body. Germ-free mice raised
aureus as infants compared with those that kept a healthy in asceptic isolators are significantly leaner than conven-
weight. These researchers had banked samples over time tionally raised mice despite their considerably greater
and were able to go back to interrogate the microbiota of food intake, and, in addition, they are resistant to diet-
the same individuals prospectively. In shorter-term induced obesity and insulin resistance [27,28]. Presence
study, Santacruz et al. [11] found that the response of of a microbiota increases serum levels of glucose and
overweight adolescents to a diet and exercise weight-loss SCFAs, which can induce triglyceride production in the
program was dependent on the initial microbiota prior to liver, and is associated with greater adiposity and reduced
the treatment. Both of these studies demonstrate that the glucose tolerance [28].
microbiota are differentiated between people prior to the
change in weight, which suggests that therapeutic inter- Bäckhed et al. [27] showed that the gut microbiota
ventions aimed at reshaping the gut microbiota may be regulates an important gut-derived regulator of host
beneficial for weight loss as well as preventive against lipid metabolism, angiopoietin-like protein 4 (Angptl4),
weight gain. also known as Fiaf, or fasting-induced adipose factor.
Angptl4 regulates fatty acid oxidation in both muscle
Other body habitats and adipose tissue [29]. When a normal mouse microbiota
Clearly, obesity can be associated with a dysbiosis of the is administered to germ-free mice, Angptl4 production is
microbiota from the lower intestinal tract; recently, suppressed in the intestine and a greater proportion of
researchers have extended this observation to other parts triglycerides are deposited in adipose tissue. Further-
of the body. In a study of the oral microbiota, Goodson more, germ-free mice lacking Angptl4 are no longer
et al. [24] show differences in the diversity and abun- protected against diet-induced obesity [27]. The
dances of salivary bacteria between overweight and relevance of these findings to human health is under-
healthy weight people. Specifically, they found that scored by population genetic and metabolic studies in
Prevotellas (a group within the Bacteroidetes phylum) humans. Functional variants of the ANGPTL4 gene
were in greater abundance in the overweight and Sele- were found to be more prevalent in individuals with
nomonas was present only in the overweight individuals, comparatively low triglyceride levels [30]. In addition,
suggesting that these taxa could be biomarkers for excess in a study of 108 participants, ANGPTL4 plasma levels
adiposity. Traveling further down the gastrointestinal correlated with fasting fatty acid levels and adipose tissue
tract, bacterial overgrowth in the small intestine has been lypolysis [31]. Thus, ANGPTL4 may be an important
shown to be more common in morbidly obese patients regulator of lipid metabolism in humans as well, and
than in healthy weight individuals [13]. Although pre- research that investigates the role of the gut microbes
liminary, these studies indicate that obesity may be in regulating its expression in the human intestine
associated with a dysbiosis of the normal microbiota is warranted.
throughout the body.
Gut microbes, inflammation, and insulin resistance
Low-grade metabolic inflammation is recognized as an
Mechanisms linking the microbiota to obesity important component of obesity and metabolic syndrome
Obesity is associated with a number of chronic con- [32]. Metabolic systems are integrated functionally and
ditions, including inflammation, insulin resistance, type molecularly with immune responses, for instance, the
II diabetes, hepatic steatosis, and cardiovascular disease. increase in pro-inflammatory cytokines, such as tumor
A number of recent studies have focused on the mechan- necrosis factor-a (TNF-a), typical of obesity-related
istic links between gut microbes and specific conditions inflammation, has been shown to result in insulin resist-
associated with obesity (for more in-depth reviews see ance [33]. Recent work has shown that gut bacteria can
[25,26]). Combining studies of host–microbial inter- initiate the inflammation and insulin resistance associ-
actions relevant to obesity with studies of microbial ated with obesity.
diversity should lead to a more comprehensive under-
standing of which microbes, or microbial products, are the One of the ways bacteria can impact inflammation and
best targets for interventions (such as pharmaceutical insulin resistance is through the activity of lipopolysac-
mimicry) aimed at improving health, aiding weight loss, charide (LPS), an essential component of the cell walls of
or preventing weight gain. Gram-negative bacteria such as the Bacteroidetes. Cani
et al. [34] have shown that subcutaneous infusion of LPS
Gut microbes and host metabolism can cause weight gain and insulin resistance in mice
The microbiota can influence host adiposity through without altering energy intake. In accordance with this,
energy extraction from the diet, with variable efficiency mice lacking Toll-like receptor 4 (TLR4), which recog-
depending on community composition; furthermore, the nizes LPS, are resistant to diet-induced obesity and
microbiota can also affect host adiposity by influencing insulin resistance [35].

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Obesity and the human microbiome Ley 9

In addition to insulin resistance, Cani et al. [34] showed In humans, plasma LPS levels correlate positively with
that LPS also induces inflammation in mice and that mice total energy intake in healthy individuals [39]. Plasma
lacking CD14 (a co-receptor of TLR4) are resistant to the LPS levels are also higher in participants with type II
development of inflammation. One type of inflammatory diabetes [45]. At this time, the effect of energy intake and
molecule that appears to be induced by LPS are the diabetes on the gut microbiota is not known in humans,
serum amyloid A (SAA) proteins, which exhibit increased but based on the results in mice, it is likely that a
levels in the serum of obese persons [36]. The mouse dysbiosis exists under these conditions.
isoform SAA3 is the most abundant in adipose tissue [37].
Reigstad et al. [38] assessed the effects of the presence
of microbes on SAA3 levels in germ-free, conventionally Gut microbes and endocrine cells
raised and Myd88/ mice. Results showed that SAA3 is The gut communicates with the brain using endocrine
elevated in adipose tissue and colonic tissue in the signals to coordinate energy intake and expenditure.
presence of microbes. Decreased levels of SAA3 in Enteroendocrine cells respond to nutrient intake by
Myd88-deficient mice compared with controls and secreting incretin hormones, including glucagon-like
increased levels of TNF-a in colonic tissue in conven- peptides 1 and 2 (GLP-1 and GLP-2). GLP-1 stimulates
tionalized vs. germ-free mice indicate that microbiota can insulin release from the pancreas, slows gastric emptying,
partially mediate SAA3 through LPS-mediated TLR/ and promotes satiety and weight loss [25]; GLP-2 stimu-
Myd88/NF-kB signaling. lates intestinal glucose transport and reduces gut per-
meability [46]. An earlier report indicated that gut micro-
Evidence suggests that a high-fat diet can trigger the biota can regulate enteroendocrine cells and influence
steps that lead to metabolic inflammation by aiding the release of gut hormones [47]. Furthermore, the pre-
transport of LPS out of the gut. A diet rich in energy sence of microbes is necessary for the full complement of
can increase levels of plasma LPS in humans [39] and enteroendocrine cells to be present in zebrafish [48]. In a
mice [34]. Furthermore, SAA3 is upregulated in the series of studies, Cani et al. [49] have shown a connection
adipose tissue of mice fed a high-fat diet [37]. Myd88- between gut microbes and levels of both GLP-1 and
deficient mice fed a high-fat diet are leaner than wild- GLP-2. In rats, oligofructose treatment (which increases
type controls, further supporting the role of LPS-TLR the proportion of Bifidobacteria) has been associated with
signaling in SAA3 production [38]. The link between a a greater number of GLP-1 secreting enteroendocrine
high-fat diet, LPS, and inflammation was made by cells (L cells) in the colon. Ob/ob mice treated with
Ghoshal et al. [40], who showed that a high-fat diet can prebiotic carbohydrates had altered gut microbiotas
increase LPS absorption. Dietary fat is transported from and increased levels of GLP-1 and GLP-2 [44]. Thus,
the gut after its incorporation as triglycerides into enteroendocrine cells represent a direct signaling path-
chylomicrons, which also have a high affinity for LPS. way from gut microbes to host metabolism.
Thus, triglycerides form chylomicrons that move LPS
from gut cells into the circulation. In yet another distinct pathway, gut microbes have been
shown to stimulate gut hormones. Samuel et al. [50]
A high-fat diet may also modulate plasma LPS levels and recently showed that enteroendocrine cells express a
inflammation through changes in the gut microbiota. A receptor for SCFAs, GPR41, which is necessary for the
high-fat diet has been shown in mice to alter the proportion full metabolic effect of these microbial metabolites. Mice
of Bacteroides-related bacteria both positively and nega- lacking Gpr41 had reduced levels of the gut hormone
tively [19,41] (these studies used different enumer- PYY, greater gut transit time, lower recovery of SCFAs
ation methods), as well as to promote a bloom in Mollicutes from the diet, and lower fat accumulation in fat pads.
(phylum Firmicutes [19]), but perhaps most importantly SCFAs are products of bacterial fermentation of carbo-
to reduce the numbers of Bifidobacteria (Gram-positive, hydrates from the diet: thus, they function both as an
phylum Actinobacteria) [41]. The effect of a decrease in energy source and as a signaling molecule, and their
Bifidobacterial levels may be inferred by the inverse: abundance and type (e.g., butyrate, propionate, acetate)
augmenting levels of Bifidobacteria in the gut, either are directly related to the species composition of the
directly as an ingested probiotic or indirectly with bifido- microbiota and their syntrophic interactions. Again, it will
genic prebiotics, has been shown to reduce inflammation be interesting to see whether other signaling pathways
and improve glucose tolerance [42,43]. Greater levels of (such as through the SCFA receptor GPR43 for example)
Bifidobacteria have also been associated with reduced gut are similarly involved in host energy balance and whether
leakiness, allowing less LPS to translocate to the serum different microbial communities interact differently with
[44]. Thus, a high-fat diet is thought to modulate the these molecules.
composition of the gut bacteria (notably by reducing levels
of Bifidobacteria), which increases gut permeability and Anecdotal evidence suggests that the gut microbes also
allows higher LPS plasma levels [26]. affect gut hormones in humans. Gut hormones are

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10 Gastrointestinal infections

implicated in the reduction of appetite and weight after 5 Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in
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