Although genetic variants have been associated with susceptibility to developing obesity and type 2 diabetes, the heritability of these variants is fairly modest. The gut microbiota has recently been recognized as a key environmental factor driving metabolic diseases. In fact, the gut microbiota is even seen as a separate endocrine organ, which is involved, through a molecular crosstalk with the host, in the maintenance of host energy homeostasis and in the stimulation of host immunity [32]. Shifts in gut microbial composition caused by external factors can result in a dramatic alteration of the symbiotic relationship between gut bacteria and the host, which promotes the development of metabolic diseases. In particular, the gut microbiota is believed to contribute to metabolic diseases via stimulation of low-grade inflammation [13].

The gut microbiota affects calorie harvest and energy homeostasis

A body of evidence shows that the gut microbiota helps to harvest energy and increase host fat storage [33, 34]. Germ-free mice have 40 % less total body fat than conventional mice although they ingest 29 % more calories than their conventionally raised littermates [33]. Germ-free mice also gain less weight than conventionally raised mice and they are protected against diet-induced glucose intolerance and the development of insulin resistance [28]. In addition, fecal microbiota transplanted from conventionally raised mice to germ-free mice triggered a 57 % increase in the amount of body fat and a dramatic increase in hepatic triglyceride levels and insulin resistance without modifying the amount of food consumed [11]. The expression of host genes involved in energy homeostasis, lipid metabolism, and mitochondrial metabolism in different parts of the gut, as well as in the liver and adipose tissues, is markedly different in germ-free mice and conventionally raised mice [35].

Studies in germ-free and conventionally raised mice have revealed several mechanisms linking gut bacteria and energy metabolism (Fig. 2):

Fig. 2 Metabolic and immune interactions between gut microbes and the host in obesity and the metabolic syndrome. The gut microbiota is involved in a molecular crosstalk with the host that modulates host physiology, metabolism, and inflammatory status. In particular, the gut microbiota participates in the physiology and motility of the digestive tract and in the digestion of polysaccharides, which directly influences host energy availability. The gut microbiota inhibits fasting-induced adipose factor (FIAF) in the intestine and monophosphate activated protein kinase (AMPK) in several organs such as the brain and muscle, which results in increasing fat deposition. The short-chain fatty acids (SCFAs) produced by bacteria from polysaccharides interact with G protein-coupled receptors (GPCRs; GPR41, GPR43, and GPR109A), which stimulates gut motility and host immunity. The gut microbiota also contributes to fat deposition through the regulation of the farnesoid X receptor (FXR), the bile acid receptor responsible for the regulation of bile acid synthesis and hepatic triglyceride accumulation. The gut microbiota converts choline to trimethylamine, thus influencing the bioavailability of choline for host use and indirectly affecting phosphatidylcholine production and hepatic triglyceride transport by very-low-density lipoproteins (VLDLs) Full size image

1. The gut microbiota can have a role in the development of the gut epithelium by increasing the density of small intestinal villi capillaries and by influencing gut physiology and gut motility, thus promoting caloric extraction from the diet [6, 36]. 2. Polysaccharides are not digested in the proximal intestine of humans and rodents; instead, they are transformed into digestible compounds such as sugars or SCFAs by the gut microbiota in the distal intestine. These energy substrates are used by colonocytes in particular and the host in general [37]. 3. The gut microbiota downregulates the intestinal expression of fasting-induced adipose factor (FIAF), which inhibits lipoprotein lipase in adipose tissues. FIAF activates the breakdown of lipoprotein-contained triacylglycerol into free fatty acids to be used by muscle and adipose tissues. Therefore, the inhibition of FIAF promotes triglyceride deposition in adipocytes [11]. 4. The gut microbiota suppresses the release of adenosine monophosphate-activated protein kinase (AMPK), which is primarily expressed in skeletal muscle, brain, and liver in response to metabolic stress (for example, hypoxia, glucose deprivation, exercise). AMPK inhibition promoted by gut bacteria leads to downregulation of mitochondrial fatty acid oxidation, ketogenesis, glucose uptake, and insulin secretion and up-regulation of lipogenesis and cholesterol and tryglyceride synthesis [34, 38]. 5. SCFAs are ligands for GPCRs such as GPR41, GPR43, and GPR109A, which are expressed in gut enteroendocrine cells. These specialized cells have essential endocrine functions in the intestine or pancreas. Upon SCFA production, GPCRs stimulate peptide YY (PYY), which leads to changes in gut motility and facilitation of nutrient absorption. Samuel and colleagues [34] showed that GPR41-deficient mice have more lean body mass and less body fat than their wild-type littermates. However, a more recent study had contrasting results, with GPR41 knockout mice showing increased amounts of body fat and decreased energy expenditure in comparison with wild-type mice [39]. GPR43 activation is also thought to reduce fat accumulation and regulate energy metabolism by suppressing insulin sensitivity in adipose tissues and increasing insulin sensitivity in liver and muscle [9, 11]. The gut microbiota also regulates the adaptive immune system in the gut and maintains colonic health in mice through the SCFA-dependent activation of GPR43 [40]. 6. Parseus and colleagues [41] proposed that the gut microbiota contributes to the high-fat-diet-induced obesity phenotype through the regulation of the farnesoid X receptor (FXR), the bile acid receptor responsible for the regulation of bile acid synthesis and hepatic triglyceride accumulation. 7. Choline is an essential nutrient for the synthesis of phosphatidylcholine, which is a major component of cell and mitochondrial membranes. Phosphatidylcholine is also a major component of very‐low‐density lipoproteins (VLDL), which are responsible for export of triglycerides to the organs [42]. Defective export of triglycerides by VLDL leads to their accumulation in hepatocytes, which is the central mechanism in the development of hepatic steatosis [43]. The gut microbiota, through its ability to convert choline to trimethylamine, regulates the bioavailability of choline and indirectly affects the storage of triglycerides in the liver [44].

Shifts in the gut microbial ecosystem in obesity

Human studies and animal models have been used to demonstrate that the gut microbiota is altered in obesity. A comparison of bacterial composition in the gut of lean, wild-type, and obese mice (leptin-deficient ob/ob mice, in which obesity is induced by a deficiency in leptin, the hormone that controls satiety) showed differences in the abundance of the phyla Bacteroidetes and Firmicutes. In particular, the Firmicutes:Bacteroidetes ratio positively correlated with the obese phenotype independently of diet [45]. Turnbaugh and colleagues [33] also compared the gut microbiota of lean mice and mice with diet-induced obesity and found an increase in the abundance of Firmicutes that was associated with diet-induced obesity. However, the observed differences were related to the growth of a specific class within the Firmicutes phylum, the Mollicutes class, in animals with diet-induced obesity. Moreover, these compositional changes were completely reversed after a return to a normal diet, which suggests that diet is the main contributing factor to obesity-associated changes in the gut microbiota. These observations were supported by the findings of Murphy and colleagues [46], who identified an increase in the Firmicutes:Bacteroidetes ratio in ob/ob mice and in mice fed a high-fat diet compared with lean mice. Of note, this increase was more significant in the high-fat-diet fed mice than in the ob/ob mice.

More recently, Ridaura and colleagues [47] have established causal links between gut microbial communities and obesity by transplanting fecal samples from co-twins discordant for obesity into separate groups of germ-free mice. They found that mice colonized with the fecal microbiota of co-twins with obesity had a greater increase in body weight and amount of adipose tissue than the mice colonized with the fecal microbiota of lean co-twins. In addition, obese mice co-housed with lean mice also experienced a lower weight gain than those co-housed with obese mice and a shift in gut microbiota composition towards a lean-like status. In particular, growth of Bacteroidetes was stimulated in obese mice co-housed with lean mice and was associated with the increased expression of proteins involved in branched-chain amino acid catabolism and increased production of SCFAs [47]. It is important to note that although SCFAs are a source of calories for the host, their intestinal production has been mostly associated with reduced inflammation and increased satiety and with overall positive metabolic effects [32, 48]. Altogether, these results show that the lean or obese gut microbial ecosystem in the mouse model is mostly influenced by the diet and to a lesser extent by co-housing with littermates. The effects of co-housing the obese and lean mice were highly transferable in germ-free mice, thus contributing to the protection or the onset of obesity in these mice.

Human studies also indicated an alteration of the gut microbial ecosystem with obesity. Turnbaugh and colleagues [33] observed differences in the distal gut microbiota of individuals with obesity compared to lean individuals and the relative abundance of Bacteroidetes increased as individuals lost weight when undergoing either a fat-restricted or a carbohydrate-restricted low-calorie diet. The decreased Bacteroidetes:Firmicutes ratio found in people with obesity is thought to lead to more efficient hydrolysis of non-digestible polysaccharides in the intestinal lumen and may lead to more calories and fat being extracted from food than occurs in lean individuals [11]. However, other human studies in which gut bacterial composition was compared between lean individuals and individuals with obesity have failed to confirm the association between obesity and a decreased Bacteroidetes:Firmicutes ratio [49, 50]. A recent report has suggested that the microbiota of people with obesity and those who are lean responds differently to the calorie content in the diet [51]. Nutrient absorption induced a shift in the gut microbial composition in lean individuals but not in those with obesity, increasing the relative abundance of Firmicutes while decreasing the relative abundance of Bacteroidetes [50]. Microbial gene richness might also have a role in the inflammatory status of the host, which is related to obesity. Individuals with obesity who have a high bacterial gene count were found to carry a higher proportion of species associated with an anti-inflammatory status (for example, F. prausnitzii) and a lower proportion of species associated with a proinflammatory status (for example, Bacteroides spp.). Also, the bacterial gene count for genes associated with oxidative stress was higher in individuals with low bacterial gene count than in those with high bacterial gene count [51]. As carrying out a controlled dietary intervention study in humans is difficult, the complex interaction between diet, age, host environment, and host genetic background in the modulation of gut microbial ecosystems is not fully understood. Nevertheless, a recent report suggests that alteration of the gut microbiota by behavioral changes, including new dietary habits [52] and use of antibiotics, could be the main driver of the obesity pandemic [53, 54].

Chronic inflammation links the gut microbiota to obesity and insulin resistance

One of the hallmarks of obesity and obesity-related pathologies is the occurrence of chronic low-grade inflammation [22]. Lipopolysaccharides (LPS), also called endotoxins, which are derived from the outer cell membrane of Gram-negative bacteria, have been thought to initiate the inflammation-related processes associated with the onset of obesity and insulin resistance (Fig. 3) [23]. LPS contain lipid A in their structure and are able to cross the gastrointestinal mucosa via leaky intestinal tight junctions or by infiltrating chylomicrons, the lipoproteins responsible for the absorption of dietary triglycerides and cholesterol from the intestine to the plasma [23, 55, 56]. Once they reach the systemic circulation, LPS infiltrate tissues such as the liver or adipose tissues, triggering an innate immune response [23]. In particular, LPS bind the plasma LPS-binding protein (LBP), which activates the receptor protein CD14 that is located in the plasma membrane of macrophages [56]. The complex thus generated binds Toll-like receptor 4 (TLR4) at the surface of macrophages, which triggers transduction signals that activate the expression of genes encoding several inflammatory effectors, such as nuclear factor κB (NF-κB) and activator protein 1 (AP-1) [56, 57]. LPS also regulate the nucleotide oligomerization domain (NOD)-like receptors present in macrophages and dendritic cells, which cooperate with TLRs to induce NF-κβ. In addition, LPS participate in the recruitment of other effector molecules, such as nucleotide-binding domain leucine-rich repeat containing (NLR) protein, adaptor protein ASC, and caspase-1, which are components of the inflammasome, a multiprotein oligomer that activates the innate immune system [27].

Fig. 3 Induction of inflammatory signals in proinflammatory macrophages and their connection with insulin pathways. a After translocation of gut bacteria to other tissues, the bacterial lipopolysaccharides (LPS) in the circulation and organs activate the transcription of cytokines via Toll-like receptor (TLR)4. Activated TLR4 mediates inflammatory signals involving myeloid differentiation primary response gene 88 (MyD88)-dependent pathways. The downstream responses trigger the activation of mitogen-activated protein kinase (MAPK) pathways, including those involving extracellular signal-regulated protein kinases 1 and 2 (ERK1/2), c-Jun-N-terminal kinases (JNK), p38, and inhibitor of IκB kinase complex (IKKβ). These pathways participate in the activation of transcription factors nuclear factor κB (NF-κB) and activator protein 1 (AP-1) and cytokine production. ERK1/2 and JNKs are also involved in the induction of insulin signaling pathways. b Pattern-recognition receptors such as TLR4, TLR2, and TLR8 are activated by LPS, cytokines, or lipotoxicity. The intracellular nucleotide oligomerization domain (NOD)-like receptors also recognize LPS, which leads to induction of thioredoxin-interacting protein (which is encoded by TXNIP) and recruitment of other effector molecules such as those that are components of inflammasome pathways [28]. Inflammasomes are multiprotein complexes composed of three proteins: nucleotide-binding domain leucine-rich repeat containing (NLR) protein, adaptor protein ASC, and caspase-1. Inflammasome activation contributes to the maturation of the cytokines interleukin (IL)-1β and IL-8 Full size image

Systemic LPS are found at low concentrations in healthy individuals but reach high concentrations in individuals with obesity, a condition called metabolic endotoxemia [23]. Several mechanisms linking obesity and metabolic endotoxemia have been proposed: during consumption of a high-fat diet, the gut microbiota is modified, which leads to increases in gut permeability and in the systemic levels of bacterial products such as LPS [23]. Additionally, excess fat intake triggers an increase in chylomicrons in the intestine during the postprandial period (following a meal), which favors LPS infiltration into the circulation [58]. Impaired lipoprotein metabolism in patients with type 2 diabetes has also been found to reduce LPS catabolism and might increase endotoxemia-related inflammation [59]. The importance of metabolic endotoxemia in the physiopathology of insulin resistance and obesity has been further highlighted by Shi and colleagues [50], who showed that mice lacking TLR4 were protected against insulin resistance induced by a high-fat diet. Results from another study revealed that LPS infusion into genetically identical male mice for 4 weeks induced a comparable weight gain to that observed in mice consuming a high-fat diet [23]. Furthermore, an interesting animal model, the immunoprotein CD14 knockout ob/ob mouse, which is unable to induce LPS-mediated inflammatory pathways, was resistant to weight gain and was insulin-hypersensitive, despite being fed with the same diet as leptin-deficient ob/ob mice [60]. In humans, circulating endotoxin levels were found to increase by 20 % in individuals with obesity or glucose intolerance and by 125 % in individuals with type 2 diabetes compared with the levels in lean individuals [61]. Circulating endotoxin levels were also associated with elevated TNF-α and IL-6 concentrations in adipocytes [62]. In addition, a high-fat or high-carbohydrate diet, but not a diet rich in fiber and fruit, activated systemic LPS secretion, as well as the expression of TLR4, NF-κB, and suppressor of cytokine (SOC) 3, which are factors also involved in pathways that regulate insulin secretion [62]. Together, these results show the important role LPS-mediated inflammatory pathways have in obesity and obesity-related pathologies.

Other microbial-derived metabolites produced from aromatic amino acids (tyrosine, tryptophan, and phenylalanine) have been suggested to interact with host signaling pathways and thus affect host immunity. Indole was identified as one of the major tryptophan-derived microbial metabolites [63], produced by the action of bacterial tryptophanase (which is present in Bacteroides thetaiotaomicron, Proteus vulgaris, and Escherichia coli, among other species) [64]. Upon absorption, indole can be sulfated in the liver, which results in the production of 3-indoxylsulfate, or can undergo further bacterial metabolism, leading to the production of a range of related compounds, including indole-3-pyruvate, indole-3-lactate, and indole-3-acetate [65]. These metabolites bind human pharmacological targets, which puts the impact of bacterial metabolism of tryptophan in human health and disease into a wider perspective. In particular, 3-indoxylsulfate and indole-3-propionate have been thought to interact with inflammation-related processes in the human host [66]. 3-Indoxylsulfate activates the aryl hydrocarbon receptor (AhR), thus regulating the transcription of IL-6 and several enzymes from the P450 superfamily complex (for example, CYP1A1, CYP1A2, and CYP2S1) [67]. Indole-3-propionate is a pregnane X receptor (PXR) agonist with a beneficial role in gut barrier function, which takes place either through up-regulation of the expression of junctional proteins or by downregulation of TNF-α production in enterocytes [66]. By improving intestinal barrier permeability, indole-3-propionate also indirectly limits the translocation of antigens and pathogens, and LPS infiltration, into the circulation and, therefore, might reduce metabolic endotoxemia and host inflammation [68]. Therefore, a healthy or dysbiotic gut microbiota affects the gut and metabolic health of the host through modulation of gut physiology and LPS infiltration, calorie intake, fat accumulation, and insulin action (Fig. 4).