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Nonalcoholic Fatty Liver Disease and the Intestinal Microbiome: An Inseparable Link

  • Maria Effenberger,
  • Christoph Grander,
  • Felix Grabherr and
  • Herbert Tilg* 
 Author information
Journal of Clinical and Translational Hepatology   2023;11(7):1498-1507

doi: 10.14218/JCTH.2023.00069


Nonalcoholic fatty liver disease (NAFLD) particularly affects patients with type 2 diabetes and obesity. The incidence of NAFLD has increased significantly over the last decades and is now pandemically across the globe. It is a complex systemic disease comprising hepatic lipid accumulation, inflammation, lipotoxicity, gut dysbiosis, and insulin resistance as main features and with the potential to progress to cirrhosis and hepatocellular carcinoma (HCC). In numerous animal and human studies the gut microbiota plays a key role in the pathogenesis of NAFLD, NAFLD-cirrhosis and NAFLD-associated HCC. Lipotoxicity is the driver of inflammation, insulin resistance, and liver injury. Likewise, western diet, obesity, and metabolic disorders may alter the gut microbiota, which activates innate and adaptive immune responses and fuels hereby hepatic and systemic inflammation. Indigestible carbohydrates are fermented by the gut microbiota to produce important metabolites, such as short-chain fatty acids and succinate. Numerous animal and human studies suggested a pivotal role of these metabolites in the progression of NAFLD and its comorbidities. Though, modification of the gut microbiota and/or the metabolites could even be beneficial in patients with NAFLD, NAFLD-cirrhosis, and NAFLD-associated HCC. In this review we collect the evidence that exogenous and endogenous hits drive liver injury in NAFLD and propel liver fibrosis and the progressing to advanced disease stages. NAFLD can be seen as the product of a complex interplay between gut microbiota, the immune response and metabolism. Thus, the challenge will be to understand its pathogenesis and to develop new therapeutic strategies.

Graphical Abstract


Nonalcoholic fatty liver disease, NAFLD, Microbiome, Metabolome


Nonalcoholic fatty liver disease (NAFLD) is the most prevalent liver disease worldwide and affects almost 25% of the population worldwide.1 NAFLD presents as phenotypes of varying severity ranging from steatosis to nonalcoholic steatohepatitis (NASH), liver fibrosis, cirrhosis, and hepatocellular carcinoma. One-third of patients present with inflammation and/or fibrosis,1 but liver histology can distinguish NASH from simple steatosis in most patients. NAFLD, especially NASH, has a crucial role in many systemic diseases, especially cardiovascular disease and malignancy.2–4 It increases the long-term complications of these diseases and results in increased mortality.5,6 Thus far, no medical therapies have been approved for the treatment of NAFLD.7 This is reflected by an increasing need for liver transplantation because of NAFLD-associated cirrhosis and/or hepatocellular carcinoma (HCC),8 in high-income and medically advanced countries.

The underlying mechanisms for development and progression of NAFLD are complex and multifactorial. Initially a two hits hypothesis was proposed, in which the first hit was the hepatic accumulation of lipids as result of lack of physical activity along with a high-fat diet (HFD) and insulin resistance, making the liver more sensitive to further insult. The second hit was activation of the inflammatory cascade and stimulation of fibrogenesis.9 That hypothesis was supported by a model of obesity in ob/ob mice in which a second hit after increased hepatic lipid accumulation,10 was necessary to initiate inflammation and fibrosis. Many human studies have shown that the complexity of the NAFLD was not explained by this hypothesis. Multiple co-influencing factors are involved in the development and progression of this disease. As a result, a multiple hit hypothesis has replaced the two-hit hypothesis for the progression of NAFLD.11 The view that steatosis always precedes inflammation has also changed. It is not the sum of hepatic hits, but more important, genetic, external, internal, and intracellular factors trigger different pathways that lead to steatosis and NASH.12 In this review, we discuss two novel players in the pathophysiology of NAFLD, the altered gut microbiome and the related modification of its metabolites.

Pathogenesis of NAFLD

Insulin resistance has a crucial role in NAFLD and is more pronounced in NASH than in simple steatosis.13 Patients without type 2 diabetes mellitus (T2DM) but with hepatic steatosis and NASH have decreased insulin sensitivity.14,15 Resistance to insulin appears to predispose to the development of NAFLD and further propels the progression to NASH,9 by activating the inflammatory cascade, inducing oxidative stress, and improving lipotoxiciy.9 In addition, environmental and genetic factors interact with the insulin receptor signaling cascade. Interaction of these factors contributes to the worsening of insulin resistance in patients with NAFLD.16 Inflammatory signal transducers such as c Jun N-terminal protein kinase 1 (JNK1), nuclear factor B kinase inhibitor (IKKb),16 nuclear factor-kappa B activation (NF-kB) or suppressors of cytokine signaling all affect insulin signaling in patients with NAFLD.17 Activation of transcription factors such as carbohydrate response element-binding protein (ChREBP), sterol regulatory element-binding protein-1 (SREBP-1), and peroxisome proliferator-activated receptor (PPAR)-γ increase de novo hepatic lipogenesis (DNL).18 In patients with NAFLD, both DNL and nocturnal plasma free fatty-acid levels are increased compared with controls, and importantly, are not suppressed by fasting.19

Activated insulin receptors substrate 2 (IRS-2) influences DNL by regulating of SREBP-1c.20 In insulin resistance, SREBP-1c is overexpressed and DNL is up-regulated, but IRS-2 is down-regulated.21 Enhanced insulin levels in insulin resistance also inhibit β-oxidation of free fatty-acids and promote hepatic lipid accumulation.22 In this vicious cycle, free fatty-acids in hepatocytes alter insulin signaling by activating serine kinases that increase insulin resistance.23 As insulin suppresses lipolysis in adipose tissue, insulin resistance results in an increased efflux of free fatty-acids to the liver.24

In addition, endoplasmic reticulum (ER) stress promotes DNL and steatohepatitis via different pathways.25,26 Reduced synthesis or secretion of very low density lipoprotein (VLDL) and other fat disposal pathways, such as impaired hepatic fatty acid oxidation, are thought to be of less importance for fat accumulation and lipotoxicity in NAFLD,27 but they are not irrelevant nor neglectable. It is also important to mention that lipid regulation by autophagy is decreased in liver steatosis, which contributes to a vicious cycle of the suppression of autophagy and lipid accumulation.28,29 Other factors, including mitochondrial dysfunction, genetic determinants, adipose tissue dysfunction, and dietary factors in this context have been extensively reviewed elsewhere.30,31

NAFLD and microbiota: preclinical and human evidence

The gut microbiome is increasingly seen as participating in NAFLD pathogenesis through the gut-liver axis. The evidence points toward involvement of the microbiome-gut-liver axis in NAFLD pathogenesis,32 and the microbiome-gut-liver axis seems to have a pivotal role in the progression of NAFLD to more advanced disease.32 Data describing the relationship of the gut microbiota and NAFLD development derive from fecal transplantation and murine studies. Housing of mice with genetically modified inflammasome pathways together with wild-type mice demonstrated that NASH developed following coprophagia.33 In another study, fecal microbiota transplantation (FMT) from weight-matched obese mice with or without steatosis to germ-free (GF) controls led to increased expression of genes involved in lipid uptake, altered lipogenesis, fatty acid catabolism, and VLDL export in liver tissue and increased hepatic triglycerides.34 These phenotypes were traced to an increase in Lachnospiraceae and the relative abundance of Barnesiella intestine hominis.34 Transfer of these findings from bench to bedside is challenging because the microbiota of mice and humans differ substantially.35 First, some genera and species in humans are not present in mice. And some that are present in mice are absent in humans.35 Second, the digestive tracts of mice and humans have differences that influence the composition of the gut microbia.35 To avoid those problems, FMT from NAFLD patients to GF mice was performed to produce the patient hepatic phenotype.36 FMT led to hepatic steatosis and inflammation in the mice, and the artificial phenotype was promoted by the feeding of an HFD.36 Inflammation and immunologic balance influence development of metabolic disease, but GF mice,37 does not have such a balance. To study the role of microbiota in murine models, conventional mouse models for FMT studies might be an alternative. Interestingly, hepatic triglycerides were increased within 14 days in conventional mice fed a chow diet after FMT from obese women.38 Despite some limitations, the existing evidence from mouse studies supports the idea that the gut microbiota contributes to NAFLD development. The results of these studies indicate that increased intestinal permeability leads to lipopolysaccharide (LPS) release, which triggers tissue and systemic inflammation. In the long run, that enhances production of microbial metabolites such as trimethylamine N-oxide (TMAO), choline, or ethanol and bile acid signaling, which also interact with the host immunity.39,40

Bacterial dysbiosis in NAFLD

Based on the above murine studies, the composition of the gut microbiota and microbiota-related metabolite signatures were studied in patients with NAFLD, NASH, and NAFLD cirrhosis and compared with each other and healthy controls.41 The microbiota of NAFLD patients compared with healthy controls had consistently altered microbiome signatures at the phylum,38,42–45 family,42,45 and genus levels.38,46 When comparing them with patients with NASH,38,43,47 some concordant microbial signatures were observed at the,42–44 family,42,43,45 and genus levels.42,44,45 The signatures overlapped in NASH and NAFLD patients. The microbiome signatures in NAFLD fibrosis have not been extensively studied. The role of the gut microbiome in NAFLD fibrosis progression was investigated in a randomized trial,42 and distinct microbial patterns have been found in cases with advanced fibrosis.42,43,48Bacteroides vulgatus and Escherichia coli were the most abundant species,42 and increases of B. vulgatus correlate with mild–moderate to advanced fibrosis in NAFLD.42 Interestingly, in the presence of metabolic alterations, the same signature of B. vulgatus has been reported, with increased abundance correlated with body mass index, hemoglobin A1c level, and insulin resistance.49 Similarly, an abundance of E. coli has been seen in patients with T2DM and there was a strong connection between NAFLD and metabolic disorders.50 Dysbiosis and NAFLD seem to create a complex network and are linked to each other. This is consistently shown and in several studies,39,44,46,51,52 that highlighted external factors such as socioeconomic status.53Ruminococcaceae and Veillonellaceae were identified in a recent study as the main microbiota species associated with fibrosis severity in 171 Asian nonobese subjects.54 In addition, a Finnish study including more than 6,000 patients found a strong association between the fatty liver index and a specific microbiome signature mostly belonging to order Lachnospirales and Oscillospirales.55 Frost et al.56 showed that fatty liver disease and diabetes mellitus, which are cofactors of the metabolic syndrome, were associated with the greatest microbiome signature variability. Enterobacteriaceae or Escherichia/Shigella were more abundant in metabolic syndrome-associated diseases. High initial alpha diversity identified the greatest microbial stability. The gut microbiome has shown promise as a predictive biomarker for various diseases, and the potential clinical validity of gut metagenomic sequencing to complement conventional risk factors for prediction of liver diseases was convincingly demonstrated in a recent study.57 Therefore, clinical trials to modulate the gut microbiome, for instance with FMT, and improve NAFLD have been performed. Unfortunately, FMT did not improve insulin resistance or increase the hepatic proton density fat fraction, but it did improve intestinal permeability.58 Similar effects were shown with symbiotics in NAFLD,59 and physical exercise.60,61 A Mediterranean diet, restricted in processed and/or red meat and enriched with green plant-based proteins/polyphenols like green tea, and walnuts, seems to be the best strategy for intrahepatic fat loss compared with other diets. It has been shown to reduce NAFLD by half.62 Furthermore, disulfiram, a drug commonly used to treat chronic alcoholism, had promising results in the treatment of NAFLD.63

Bacterial dysbiosis in liver cirrhosis

In patients with liver cirrhosis, there is convincing evidence that the progression of NAFLD, alcoholic liver disease, or viral hepatitis is strongly associated with gut microbiome dysbiosis. Cirrhotic microbial signatures are characterized by an increase in pathogenic taxa and a decrease in metabolically beneficial taxa.64–66 In multiple preclinical NAFLD and alcoholic liver disease studies, a clear association between the degree of liver disease and dysbiosis was described.67–71 Some human and animal studies demonstrated that the microbiome also influenced the progression from early chronic liver disease (CLD) to cirrhosis, pointing out a key role of dysbiosis in the development of end-stage liver disease.68,69,72,73 As mentioned above, the microbial composition in patients with advanced NAFLD and cirrhosis is characterized by a decrease of beneficial bacteria and an increase in potentially pathogenic bacteria.66,74 The gut microbial composition was studied in patients with cirrhosis caused by different underlying liver diseases. Some of the microbial alterations overlapped in cirrhosis of different etiologies. This suggests that features of end-stage liver disease drive the microbial alterations. An abundance of Veillonella or Streptococcus and a decrease of order Clostridiales are commonly found in patients with end-stage liver disease and cirrhosis.66 The gut microbiome of patients with cirrhosis presents with a relative reduction in Bacteroidetes and an increase in Proteobacteria and Fusobacteria, but changes in Firmicutes mimicked the microbiome from healthy individuals.75 Furthermore, there are differences at the family level, with Streptococcaceae and Veillonellaceae. Streptococcaceae positively and Lachnospiraceae negatively correlated to cirrhosis severity. Another research group has confirmed these differences in a large population of cirrhosis patients.64,75

Microbial composition differs between patients with compensated or decompensated cirrhosis, which suggests that microbial alterations are more influenced by cirrhosis stage rather than by the underlying liver disease.72 Bacterial’s overgrowth in the upper gastrointestinal tract has a pivotal role along with shifts in microbial signatures when it comes to the increase of circulating LPS levels.76 Various studies investigated the qualitative and quantitative bacterial changes in the duodenal and salivary microbiota, comparing healthy individuals and patients with cirrhosis. Bacterial shifts in the upper gastrointestinal tract may influence the microbial signature in the lower gastrointestinal tract and might therefore have a key role in the pathophysiology of CLD as well as in the development of HCC.77

These cirrhosis-related alterations in the microbiome are not only evident in feces, but also in serum, saliva, small intestine mucosa, ascites, colon mucosa, and liver tissue.64,75,78,79 The intestinal metabolic shift in cirrhosis seems to influence a cascade of mucosal immune changes and vice versa. It is also associated with the main cirrhosis comorbidities like spontaneous bacterial peritonitis, hepatic encephalopathy, organ failure and finally death.64,72,80,81 The most common components of the microbiota are bacteria, but there is evidence of the importance of fungi, archaea, and viruses, especially bacteriophages.82 In a recent study, fungal diversity in patients with cirrhosis was linked to bacterial diversity, and suggests that fungi can affect hospitalizations in conjunction with bacterial indices.83,84

Recent studies indicate that specific changes of the gut microbiota are promising markers in different stages of liver disease and liver disease progression. The findings underline the hypothesis that the microbiota is a key factor in the complex pathophysiology of NAFLD disease and disease progression from mild fibrosis to severe fibrosis, cirrhosis and finally HCC.42,43,48 It was already proposed to use microbiome signatures for the diagnosis of NAFLD fibrosis, but confirmation and validation in independent cohorts and across geographical regions is necessary.65 Further studies are needed to accurately and precisely describe the constituents of the entire microbiome in liver disease. Nevertheless, studies including patients with non-NAFLD, NAFLD without advanced fibrosis, or NAFLD cirrhosis are needed to define potentially diagnostic microbial signatures (Fig. 1).42,71

Gut microbiota-derived metabolites are involved in the progression of nonalcoholic fatty liver disease.
Fig. 1  Gut microbiota-derived metabolites are involved in the progression of nonalcoholic fatty liver disease.

AhR, aryl hydrocarbon receptor; AMPK, AMP-activated protein kinase; CYP2E1, cytochrome P450 2E1, CYP7A1, cytochrome P450 7A1; FAS, fatty acid synthase; FGF21, fibroblast growth factor 21; FXR, farnesoid X receptor; FGF19, fibroblast growth factor 19; GPBAR1, G-protein-coupled bile acid receptor 1; GLP-1, glucagon-like peptide-1; GPR41/43, G-protein-coupled receptor 41 and 43, HDAC, histone deacetylase; I3A-indole-3-acetic acid; IPA, indole-3-propionic acid; mTORC1, mammalian target of rapamycin complex 1; NF-κB, nuclear factor-kappa B; PFKFB3, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3; PPARα, peroxisome proliferator-activated receptor α; PXR, pregnane X receptor; SHP, short heterodimer partner; SREBP1c, sterol regulatory element-binding protein 1c; TLR4, Toll-like receptor 4; TMA, trimethylamine; TMAO, trimethylamine-N-oxide.

HCC and microbiota: preclinical evidence

Evidence that changes in the gut microbial composition participate in the development of liver disease and HCC is increasing. High levels of circulating LPS in mouse models and humans with CLD or HCC indicate the presence of an altered intestinal barrier during multiple stages of CLD and hepatocarcinogenesis.85–87 Functional experiments in GF mice lacking the toll-like receptor (TLR) 4 and treated with LPS had evidence of a leaky gut essentially contributes to hepatocarcinogenesis.88 Furthermore, chronic liver inflammation and increased rates of infectious complications in end-stage liver disease, are associated with a leaky gut and increased bacterial translocation. Microbe-associated molecular pattern MAMPs) and host pattern recognitions receptors (PRRs), specifically TLRs, interact in the hepatic inflammatory cascade.89 The development of HCC in a murine model can be triggered by chronic infusion of low-dose LPS via osmotic pumps.88 Furthermore, the administration of dextran sulfate sodium leads to a disruption of the intestinal barrier and higher levels of systemic LPS, which worsened liver fibrosis and promoted HCC development.90,91 In accordance with these findings, liver inflammation, fibrosis and HCC formation in mice and rats can be suppressed via inhibition of TLR4 signaling.92,93 TLR4 is expressed in multiple hepatic cell lines, including hepatic stellate cells (HSCs), endothelial cells, Kupffer cells, and hepatocytes. TLR4 in hepatocytes, HSCs and Kupffer cells drive hepatic fibrogenesis and hepatocarcinogenesis.88 Activation of the TLR4 cascade leads to NF-κB-mediated upregulation of the potent hepatomitogen epiregulin (EPR), an epidermal growth factor family member, in HSCs.88,94 Increased LPS levels resulting from a disrupted gut barrier have multiple cellular targets, such as Kupffer cells and HSCs, participate in hepatocarcinogenesis.

NF-κB mediated prevention of hepatocyte apoptosis,88 has a key role in hepatocarcinogenesis and is promoted via the LPS-TLR4 pathway. Hepatocyte proliferation, reduced oxidative stress, and apoptosis in Kupffer cells can also be mediated by tumor necrosis factor (TNF) and interleukin (IL)6, where transcription and release of TNF and IL6 are activated by the LPS-TLR4 pathway.93 In HCC cell lines TLR4 is activated by LPS. This trigger promotes invasiveness and epithelial mesenchymal transition in these cell lines.95 Together, these data show that an impaired intestinal barrier via MAMP-TLR-mediated signals contributes to hepatocarcinogenesis.96 Dysbiosis and the impaired intestinal barrier are closely related. Furthermore, in HCC there seems to be a shift toward bacterial species with an increased likelihood of translocation across the gut barrier.97 In a murine HCC model, antibiotic depletion of the host microflora suppressed tumor formation with a significant reduction in the number and size of HCC nodules in treated mice compared to control animals.93

Furthermore, dysbiosis promotes development of HCC by altering the bile acid metabolism. In a model of NASH-associated HCC, an HFD rich in saturated fatty acids and cholesterol (STHD-01), was fed to specific pathogen-free (SPF) C57BL/6J mice. The accumulation of cholesterol and secondary bile acids caused hepatic inflammation and injury, which in turn contributed to carcinogenesis.98 In another mouse model of HCC, tumor growth was significantly reduced by administering probiotics, thus decreasing the number of activated Th17 cells and their production of the proinflammatory IL17. Probiotic treatment also slowed the growth of established tumors and reduced tumor size.99

Inflammation has a key role in carcinogenesis and dysbiosis can create a proinflammatory environment that favors HCC development. Regulatory T cells (Tregs) are a subpopulation of T cells that act to suppress immune responses not only by producing anti-inflammatory IL10. The number of Tregs. in peripheral blood and liver tissue has been associated with increases of Alistipes, Butyricimonas, Mucispirillum, Oscillibacter, Parabacteroides, Paraprevotella, and Prevotella. Parabacteroides are known to inhibit inflammation by inhibiting the secretion of inflammatory cytokines and promoting the release of anti-inflammatory cytokines like IL10.99,100 Such microbial changes are found in the feces of SPF mice having a normal spectrum of commensal microorganisms but not in microbiota-deficient mice treated with broad-spectrum antibiotics or in GF mice.99 In a murine model of streptozotocin-high fat diet (STZ-HFD) induced NASH-HCC, Akkermansia muciniphila, Bacteroides fragilis, Parabacteroides distasonis, and Alistipes shahii were significantly enriched.101,102Alistipes shahii tends to modulate the gut by ablating tumor growth and Bacteroides fragilis acts by stimulating Treg cells via induction of IL10.103

HCC and microbiota: human evidence

There are only a few clinical trials correlating microbiota with HCC, and they found different alterations of the gut microbiota in patients with HCC. In one study the presence of HCC in cirrhotic patients was associated with increased fecal E. coli, and intestinal overgrowth of these bacteria was thought to have contributed to hepatocarcinogenesis.104 In a more recent study, HCC patients with hepatitis B virus/hepatitis C virus infection harbored increased populations of potential pro-inflammatory bacteria (Escherichia, Shigella, Enterococcus) and had reduced populations of Faecalibacterium, Ruminococcus, and Ruminoclostridium, which resulted in a decrease of potentially anti-inflammatory short-chain fatty acids (SCFAs).105 Patients with NAFLD-related cirrhosis and HCC, NAFLD-related cirrhosis without HCC, and healthy controls were also compared. Plasma IL8, IL13, chemokine ligand (CCL) 3, CCL4, and CCL5 were increased in the HCC group and were associated with activation of circulating monocytes. The fecal microbiota of patients with cirrhosis had a higher abundance of Enterobacteriaceae and Streptococcus and a reduction in Akkermansia. Bacteroides and Ruminococcaceae were increased in the HCC group and Bifidobacterium was reduced.106 In another study 75 patients with early HCC were compared to patients with cirrhosis and healthy controls. In this investigation, fecal microbial diversity increased from cirrhosis to cirrhosis with early HCC. Specifically, phylum Actinobacteria and 13 genera including Gemmiger and Parabacteroides were increased in early HCC. The microbiota pattern showed an increase in LPS-producing species, such as Parabacteroides, and a decrease in butyrate-producing species, such as Actinobacteriae, compared with healthy individuals. Therefore, current evidence suggests that a specific microbiota pattern for patients with HCC might exist.107

Gut-derived metabolites and pathways in NAFLD

Numerous studies have defined metabolomic signatures associated with NAFLD.108 The signatures include molecules produced by bacteria such as LPS100 or SCFAs. The SCFAs, butyrate, propionate and acetate,39 and products derived from bile acid metabolism act on farnesoid X receptors (FXRs) within the liver or the intestine.109 Changes in the composition of these metabolites are thought to be involved in the pathophysiology of liver injury (Fig. 1). Multiple studies found that these metabolites have an effect in obesity and metabolic alterations in T2DM. The activation of insulin resistance pathways can be promoted by LPS in obesity.110 Furthermore, SCFAs may increase weight gain by energy harvesting despite their benefits in metabolic health and disease.111 SCFAs were found to be increased in fecal samples of obese individuals compared with a healthy corhort.112


Higher liver fat accumulation and modified gut bacteria composition can be evoked by dietary choline reduction in mice.113 In a murine model of HFD-induced NAFLD, standard choline levels led to a decrease of systemic phosphatidylcholine along with NAFLD progression.114 The gut microbiota metabolizes dietary choline into trimethylamine (TMA), and the hepatic enzyme FMO3 converts TMA to TMAO.115,116 Increased TMAO levels are a biomarker of cardiovascular events and are positively correlated with increased abundance of fecal Deferribacteres and Tenericutes in murine models.11 Increased urinary levels of TMA and TMAO were associated with NAFLD severity in a murine model.114 However, other studies reported that dietary intake of choline and phosphatidylcholine were associated with increased TMA and TMAO production.115,116 These divergent data suggest that the role of TMA and TMAO in NAFLD is not fully understood and needs further investigation. One of the most likely hypotheses is that modification of the microbiota metabolism leads to reduced host choline bioavailability with methylamine production and as its urinary excretion.114

Bile acids

The gut microbiota deconjugates primary bile acids into secondary bile acids. Both, primary and secondary bile acids have endocrine functions in multiple metabolic pathways through different receptors.117 For example, primary bile acids facilitate the absorption of dietary fat and fat-soluble molecules and are involved in cholesterol metabolism.117,118 The G-protein-coupled bile acid receptor 1 (TGR1) participates in energy, glucose, and lipid metabolism. Secondary bile acids are the preferential ligands of TGR1. The gut microbiota interacts with bile acid pathways on multiple levels. In regulating the secondary bile acid metabolism, the microbiota reduces FXR inhibition, which in turn reduces hepatic synthesis of lipids.119 Hence, its composition influences the homeostasis and bile acid composition because it deconjugates, dehydrogenates, and dehydrates bile acids, which promotes NAFLD and NASH progression, as suggested by various studies.109 NAFLD is associated with decreased bile acid levels via TMAO production. CYP7A1 and CPY27A1, two enzymes involved in bile acid metabolism, are inhibited by TMAO. TMAO thus induces a decrease of total bile acids.120 Accordingly, patients with advanced cirrhosis have a gut microbiota composition that decreases the conversion of bile acids including abundant Enterobacteriaceae and relatively less abundant Lachnospiraceae, Ruminococcaceae, and Blautia.121,122


Gut microbiota-derived ethanol production may also participate in NAFLD pathophysiology. In children with NAFLD, the gut microbiota contains more ethanol-producing bacteria than obese or healthy children.44 A recent study assayed ethanol concentration in the peripheral blood and in the portal vein while fasting and 120 min after a mixed meal test. In the presence of NAFLD, the ethanol concentration in the median portal vein was increased by 187 times, and continued to increase with disease progression.123 The abundance of Lactobacillaceae was positively correlated with postprandial peripheral blood ethanol concentrations in a prospective study.123 The results of these studies suggest that microbial ethanol production is associated with gut microbial disturbances acts as a hepatic toxin in the progression of NASH and NAFLD.31 A study in mice and humans identified Klebsiella pneumoniae as an ethanol-producing bacteria in the absence of any alcohol consumption.124


SCFAs have a key role in increasing liver triglyceride levels, which serve as energy storage and promote weight gain.125 In patients with NAFLD or NASH fecal levels of SCFAs were increased compared to healthy controls, going along with an increase in SCFAs producing bacteria. Accordingly, patients with NASH had reduced levels of resting regulatory T cells (CD4+, CD45RA+, CD25+) and an increased Th17/Treg ratio in peripheral blood, previously recognized as systemic immunological features of NASH. Decreased T cells were found to be associated with increased fecal SCFAs and changes in the microbial signature.126 However, SCFAs pathways are not fully understood. For example, the benefits of SCFAs include activation of G-protein-coupled receptor 43 (GPR43), which decreases hepatic T-cell infiltration and production of pro-inflammatory cytokines. Accordingly, GF and GPR43–/– mice express lower levels of SCFAs together with increased circulating T cells and colonic inflammation, a feature usually seen in NASH.127

Products of microbial protein fermentation

Some strains of the gut microbiota that ferment proteins may also have a role in NAFLD progression and proinflammatory pathways.32,128 Ammonia, hydrogen sulfide and phenolic compounds be involved in NAFLD progression by translocating proinflammatory compounds toward the enterohepatic pathway. A murine model of GF mice suggested there was a connection between products of gut microbial protein fermentation and NAFLD.34 GF mice fed an HFD and colonized with microbial strains from diabetes model mice developed hepatic macrovesicular steatosis. The control animals received microbiota from normoglycemic mice and developed only low-level steatosis. In the mice with macrovesicular steatosis, cecal concentrations of the branched-chain fatty acids isovalerate and isobutyrate were present and mainly derived from the microbial fermentation of branched-chain amino acids (BCAAs). Furthermore, insulin resistance and leptinemia were detected in those mice.34 On the other hand, the microbial metabolite indole, which is derived from the aromatic amino acid l-tryptophan by the microbiota-associated enzyme tryptophanase, preserved gut barrier dysfunction and decreased inflammation in the gut.129,130 Furthermore, orally administered indole reduced LPS-linked upregulation of proinflammatory cytokines in this murine model and proteins active in the hepatic NF-κB pathway were down-regulated in these experiments.131 However, there is a need to replicate the results of this study into a setting with patients with NAFLD, to determine potential beneficial effects. In women with morbid obesity, but without evidence of T2DM, fecal metagenome and the hepatic transcriptome were analyzed and the plasma and urine metabolomes were studied.38 In this setting, the grade of steatosis was significantly associated with dysregulation of microbial aromatic amino acid and BCAA metabolism. Another study identified a product of phenylalanine catabolism, phenylacetic acid, as a driver of steatosis progression in a murine model and in human hepatocytes. BCAA utilization in the tricarboxylic acid cycle increases lipid accumulation in the liver, potentially via phenylacetic acid.38 The development of hepatic steatosis seems fueled by proteolytic fermentation products, as shown in these studies. Accordingly, LPS and TMAO were identified as key players in the development in steatosis in this study. The findings support the microbial multihit hypothesis in metabolic diseases.

Preclinical and clinical studies in the last decade support the key role of the gut microbiome/metabolome in NAFLD. These studies suggest that a specific microbial signature is associated with NAFLD and provide an opportunity to uncover important mechanistic insights (Table 1).26,70,126,132–40 Ongoing research guided by previous results might identify distinct microbiome signatures and new bacterial metabolites as key players in liver disease. Because the gut microbiota plays this role, research was focused on the intestinal microbiota. It offered opportunities as well as challenges in understanding the pathogenesis and developing treatment options of NAFLD. Most published studies focused on 16sRNA sequencing with low resolution and limited to the genus level. With metagenomics sequencing techniques NAFLD-related microbes at a strain level can be identified, offering functional information of the gut microbiota in this expanding disease. Future research will aim to find direct causal relationships of NAFLD with intestinal microbial changes in murine and human studies. These future data should aim at microbiota-targeted therapeutics. The microbiome–host interaction in the development and progression of NAFLD, despite enormous advances in correlating microbial intestinal changes with NAFLD, remains largely elusive. Therefore, further studies to understand host-microbial interactions in patients with NAFLD are needed. These novel bacterial-derived pathways in disease progression will uncover novel treatment strategies.

Table 1

Changes in the gut microbiome and metabolites in different stages of NAFLD, including potential therapeutic options

Patient cohortControl cohortMicrobiome increaseMicrobiome decreaseMetabolitesPotential therapy
NASH126NAFLDEubacterium biforme, Fusobacteria, Fusobacteriaceae, Fusobacterium, Prevotellaα-diversity↓,Stool: propionate↑, butyrate↑, acetate↑Tributyrin. (Butyrate prodrug)132
NASH126Fusobacteriaceae; PrevotellaceaeStool: propionate↑, butyrate↑, acetate↑Tributyrin132
NAFLD126PrevotellaceaeStool: propionate↑, butyrate↑, acetate↑Tributyrin132
NAFLD G326NAFLD G0β-diversity, Christensenellaceae, Coprococcus,Odoribacter, Odoribacteraceae, Oscillospira, Ruminococcaceae,Not available
NAFLD cirrhosis70Catenibacterium, Faecalibacterium prausnitzii, Gallibacterium, Megasphaera,, Mogibacterium, Rikenellaceae, Streptococcus, PeptostreptococcaceaeBacillus↓, Lactococcus↓,Not available
Lean NAFLD133DoreaChristensenellaceae, MarvinbryantiaTotal BA↑, total primary BA↑, total secondary BA↑, CDCA↑, DCA↑FXR;134136 NGM282137
Increased NAFLD severity138Actinobacteria, Actinomycetaceae, Bacteroidetes, Firmicutes, Lachnospiraceae Proteobacteria,α-diversity Bacteroidaceae, BacteroidetesTotal BA↑, primary conjugated BA↑, GCA↑, secondary conjugated BA↑; stool: total BA↑, DCA↑FXR;134136 NGM282137
NAFLD-HCC139Enterobacteriaceae, ProteobacteriaErysipelotrichaceae, OscillospiraceaeStool: oxaloacetate↑, acetylphosphate↑, isocitrate↑, acetate↑, butyrate↑, formate↑ Serum: butyrate↑, propionate↑Tributyrin132
NAFLD-cirrhosis139EubacteriaceaeCoriobacteriaceae, Muribaculaceae, Odoribacteraceae, PrevotellaceaeNot available
NAFLD-HCC139NAFLD cirrhosisBacteroides caecimuris, Veillonella parvulaNot available
Nonobese F2-4 fibrosis140Babjeviella inositovora, C. albicans, Cyberlindnera jadinii, Mucor sp, Salinispora sp.Not available

NAFLD, as a multifactorial disease, needs novel clinical approaches. Zeevi et al.141 reported that individual glycemic responses can be predicted by combining personal, dietary, and microbiome characteristics, successfully targeting personalized nutrition. A individualized precision medicine based on diet and intestinal microbiota profiles could facilitate risk stratification and diagnostic accuracy, predict variable clinical phenotypes, and hopefully the therapeutic response of NAFLD. Gut-derived metabolites and metabolomic signatures have a pivotal role in NAFLD, and the gut microbiota may thus be a promising marker in diagnosis and progress prediction in NAFLD. Influencing gut microbial alterations will be a novel therapeutic strategy in the NAFLD pandemic in the future. To summarize, the underlying mechanisms for development and progression of NAFLD are multifactorial and very complex. Gut dysbiosis has a key role that is supported not only by preclinical studies, but also by large clinical datasets. However it is still not clear which bacterial strains are the big players in this context.



alcoholic liver disease


chemokine ligand


chronic liver disease


de novo lipogenesis


fecal microbiota transplantation




hepatic stellate cell


hepatocellular carcinoma


high fat diet




microbe associated molecular pattern


nonalcoholic fatty liver disease


nonalcoholic steatohepatitis


pattern recognition receptor


short chain fatty acids


toll like receptor




type 2 diabetes mellitus



This study is supported by the excellence initiative VASCage (Center for Promoting Vascular Health in the Aging Community), an R&D K-Center (COMET program Competence Centers for Excellent Technologies) funded by the Austrian Ministry for Transport, Innovation and Technology, the Austrian Ministry for Digital and Economic Affairs and the federal states Tyrol, Salzburg, and Vienna.

Conflict of interest

The authors have no conflict of interests related to this publication.

Authors’ contributions

Design and writing of the paper (ME, HT), provision of critical feedback (HT), and manuscript preparation (CG, ME, FG, HT). All authors have made a significant contribution to this study and have approved the final manuscript.


  1. Diehl AM, Day C. Cause, Pathogenesis, and Treatment of Nonalcoholic Steatohepatitis. N Engl J Med 2017;377(21):2063-2072 View Article PubMed/NCBI
  2. Targher G, Mantovani A, Grander C, Foco L, Motta B, et al. Association between non-alcoholic fatty liver disease and impaired cardiac sympathetic/parasympathetic balance in subjects with and without type 2 diabetes-The Cooperative Health Research in South Tyrol (CHRIS)-NAFLD sub-study. Nutr Metab Cardiovasc Dis 2021;31(12):3464-3473 View Article PubMed/NCBI
  3. Targher G, Byrne CD, Tilg H. NAFLD and increased risk of cardiovascular disease: clinical associations, pathophysiological mechanisms and pharmacological implications. Gut 2020;69(9):1691-1705 View Article PubMed/NCBI
  4. Simon TG, Roelstraete B, Alkhouri N, Hagström H, Sundström J, Ludvigsson JF. Cardiovascular disease risk in paediatric and young adult non-alcoholic fatty liver disease. Gut 2023;72(3):573-580 View Article PubMed/NCBI
  5. Simon TG, Roelstraete B, Khalili H, Hagström H, Ludvigsson JF. Mortality in biopsy-confirmed nonalcoholic fatty liver disease: results from a nationwide cohort. Gut 2021;70(7):1375-1382 View Article PubMed/NCBI
  6. Sanyal AJ, Van Natta ML, Clark J, Neuschwander-Tetri BA, Diehl A, Dasarathy S, et al. Prospective Study of Outcomes in Adults with Nonalcoholic Fatty Liver Disease. N Engl J Med 2021;385(17):1559-1569 View Article PubMed/NCBI
  7. Diehl AM, Farpour-Lambert NJ, Zhao L, Tilg H. Why we need to curb the emerging worldwide epidemic of nonalcoholic fatty liver disease. Nat Metab 2019;1(11):1027-1029 View Article PubMed/NCBI
  8. Haldar D, Kern B, Hodson J, Armstrong MJ, Adam R, Berlakovich G, et al. Outcomes of liver transplantation for non-alcoholic steatohepatitis: A European Liver Transplant Registry study. J Hepatol 2019;71(2):313-322 View Article PubMed/NCBI
  9. Peverill W, Powell LW, Skoien R. Evolving concepts in the pathogenesis of NASH: beyond steatosis and inflammation. Int J Mol Sci 2014;15(5):8591-8638 View Article PubMed/NCBI
  10. Leamy AK, Egnatchik RA, Young JD. Molecular mechanisms and the role of saturated fatty acids in the progression of non-alcoholic fatty liver disease. Prog Lipid Res 2013;52(1):165-174 View Article PubMed/NCBI
  11. Tilg H, Adolph TE, Moschen AR. Multiple Parallel Hits Hypothesis in Nonalcoholic Fatty Liver Disease: Revisited After a Decade. Hepatology 2021;73(2):833-842 View Article PubMed/NCBI
  12. Yilmaz Y. Review article: is non-alcoholic fatty liver disease a spectrum, or are steatosis and non-alcoholic steatohepatitis distinct conditions?. Aliment Pharmacol Ther 2012;36(9):815-823 View Article
  13. Pagano G, Pacini G, Musso G, Gambino R, Mecca F, et al. Nonalcoholic steatohepatitis, insulin resistance, and metabolic syndrome: further evidence for an etiologic association. Hepatology 2002;35(2):367-372 View Article
  14. Sanyal AJ, Campbell-Sargent C, Mirshahi F, Gambino R, Mecca F, et al. Nonalcoholic steatohepatitis: association of insulin resistance and mitochondrial abnormalities. Gastroenterology 2001;120(5):1183-1192 View Article PubMed/NCBI
  15. Cortez-Pinto H, Camilo ME, Baptista A, De Oliveira AG, De Moura MC. Non-alcoholic fatty liver: another feature of the metabolic syndrome?. Clin Nutr 1999;18(6):353-358 View Article PubMed/NCBI
  16. Sabio G, Das M, Mora A, Zhang Z, Jun JY, Ko HJ, et al. A stress signaling pathway in adipose tissue regulates hepatic insulin resistance. Science 2008;322(5907):1539-1543 View Article PubMed/NCBI
  17. Taniguchi CM, Emanuelli B, Kahn CR. Critical nodes in signalling pathways: insights into insulin action. Nat Rev Mol Cell Biol 2006;7(2):85-96 View Article
  18. George J, Liddle C. Nonalcoholic fatty liver disease: pathogenesis and potential for nuclear receptors as therapeutic targets. Mol Pharm 2008;5(1):49-59 View Article
  19. Lambert JE, Ramos-Roman MA, Browning JD, Parks EJ. Increased de novo lipogenesis is a distinct characteristic of individuals with nonalcoholic fatty liver disease. Gastroenterology 2014;146(3):726-735 View Article PubMed/NCBI
  20. Schreuder TC, Verwer BJ, van Nieuwkerk CM, Mulder CJ. Nonalcoholic fatty liver disease: an overview of current insights in pathogenesis, diagnosis and treatment. World J Gastroenterol 2008;14(16):2474-2486 View Article PubMed/NCBI
  21. Tilg H, Moschen AR, Roden M. NAFLD and diabetes mellitus. Nat Rev Gastroenterol Hepatol 2017;14(1):32-42 View Article PubMed/NCBI
  22. Rosso C, Kazankov K, Younes R, Esmaili S, Marietti M, et al. Crosstalk between adipose tissue insulin resistance and liver macrophages in non-alcoholic fatty liver disease. J Hepatol 2019;71(5):1012-1021 View Article PubMed/NCBI
  23. Parlakgül G, Arruda AP, Pang S, Cagampan E, Min N, Güney E, et al. Regulation of liver subcellular architecture controls metabolic homeostasis. Nature 2022;603(7902):736-742 View Article PubMed/NCBI
  24. Lewis GF, Carpentier A, Adeli K, Giacca A. Disordered fat storage and mobilization in the pathogenesis of insulin resistance and type 2 diabetes. Endocr Rev 2002;23(2):201-229 View Article PubMed/NCBI
  25. Latif MU, Schmidt GE, Mercan S, Rahman R, Gibhardt CS, Stejerean-Todoran I, et al. NFATc1 signaling drives chronic ER stress responses to promote NAFLD progression. Gut 2022;71(12):2561-2573 View Article PubMed/NCBI
  26. Kim JY, Garcia-Carbonell R, Yamachika S, Zhao P, Dhar D, Loomba R, et al. ER Stress Drives Lipogenesis and Steatohepatitis via Caspase-2 Activation of S1P. Cell 2018;175(1):133-145.e15 View Article PubMed/NCBI
  27. Khan RS, Bril F, Cusi K, Newsome PN. Modulation of Insulin Resistance in Nonalcoholic Fatty Liver Disease. Hepatology 2019;70(2):711-724 View Article PubMed/NCBI
  28. Ueno T, Komatsu M. Autophagy in the liver: functions in health and disease. Nat Rev Gastroenterol Hepatol 2017;14(3):170-184 View Article PubMed/NCBI
  29. Allaire M, Rautou PE, Codogno P, Lotersztajn S. Autophagy in liver diseases: Time for translation?. J Hepatol 2019;70(5):985-998 View Article PubMed/NCBI
  30. Buzzetti E, Pinzani M, Tsochatzis EA. The multiple-hit pathogenesis of non-alcoholic fatty liver disease (NAFLD). Metabolism 2016;65(8):1038-1048 View Article PubMed/NCBI
  31. Tilg H, Adolph TE, Dudek M, Knolle P. Non-alcoholic fatty liver disease: the interplay between metabolism, microbes and immunity. Nat Metab 2021;3(12):1596-1607 View Article PubMed/NCBI
  32. Tilg H, Adolph TE, Trauner M. Gut-liver axis: Pathophysiological concepts and clinical implications. Cell Metab 2022;34(11):1700-1718 View Article PubMed/NCBI
  33. Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 2012;482(7384):179-185 View Article PubMed/NCBI
  34. Le Roy T, Llopis M, Lepage P, Bruneau A, Rabot S, et al. Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice. Gut 2013;62(12):1787-1794 View Article PubMed/NCBI
  35. Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research?. Dis Model Mech 2015;8(1):1-16 View Article PubMed/NCBI
  36. Chiu CC, Ching YH, Li YP, Liu JY, Huang YT, Huang YW, et al. Nonalcoholic Fatty Liver Disease Is Exacerbated in High-Fat Diet-Fed Gnotobiotic Mice by Colonization with the Gut Microbiota from Patients with Nonalcoholic Steatohepatitis. Nutrients 2017;9(11):1220 View Article PubMed/NCBI
  37. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 2008;57(6):1470-1481 View Article PubMed/NCBI
  38. Hoyles L, Fernández-Real JM, Federici M, Serino M, Abbott J, Charpentier J, et al. Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women. Nat Med 2018;24(7):1070-1080 View Article PubMed/NCBI
  39. Leung C, Rivera L, Furness JB, Angus PW. The role of the gut microbiota in NAFLD. Nat Rev Gastroenterol Hepatol 2016;13(7):412-425 View Article PubMed/NCBI
  40. Brandl K, Schnabl B. Intestinal microbiota and nonalcoholic steatohepatitis. Curr Opin Gastroenterol 2017;33(3):128-133 View Article PubMed/NCBI
  41. Aron-Wisnewsky J, Vigliotti C, Witjes J, Le P, Holleboom AG, et al. Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders. Nat Rev Gastroenterol Hepatol 2020;17(5):279-297 View Article PubMed/NCBI
  42. Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, et al. Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. Cell Metab 2019;30(3):607 View Article PubMed/NCBI
  43. Shen F, Zheng RD, Sun XQ, Ding WJ, Wang XY, et al. Gut microbiota dysbiosis in patients with non-alcoholic fatty liver disease. Hepatobiliary Pancreat Dis Int 2017;16(4):375-381 View Article PubMed/NCBI
  44. Zhu L, Baker SS, Gill C, Liu W, Alkhouri R, et al. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology 2013;57(2):601-609 View Article PubMed/NCBI
  45. Del Chierico F, Nobili V, Vernocchi P, Russo A, De Stefanis C, et al. Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta-omics-based approach. Hepatology 2017;65(2):451-464 View Article PubMed/NCBI
  46. Boursier J, Mueller O, Barret M, Machado M, Fizanne L, Araujo-Perez F, et al. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota. Hepatology 2016;63(3):764-775 View Article PubMed/NCBI
  47. Wong VW, Wong GL, Chan RS, Shu SS, Cheung BH, et al. Beneficial effects of lifestyle intervention in non-obese patients with non-alcoholic fatty liver disease. J Hepatol 2018;69(6):1349-1356 View Article PubMed/NCBI
  48. Hernández-Ceballos W, Cordova-Gallardo J, Mendez-Sanchez N. Gut Microbiota in Metabolic-associated Fatty Liver Disease and in Other Chronic Metabolic Diseases. J Clin Transl Hepatol 2021;9(2):227-238 View Article PubMed/NCBI
  49. Aron-Wisnewsky J, Prifti E, Belda E, Ichou F, Kayser BD, Dao MC, et al. Major microbiota dysbiosis in severe obesity: fate after bariatric surgery. Gut 2019;68(1):70-82 View Article PubMed/NCBI
  50. Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2015;528(7581):262-266 View Article PubMed/NCBI
  51. Tilg H, Adolph TE. Influence of the human intestinal microbiome on obesity and metabolic dysfunction. Curr Opin Pediatr 2015;27(4):496-501 View Article PubMed/NCBI
  52. Mouzaki M, Comelli EM, Arendt BM, Bonengel J, Fung SK, et al. Intestinal microbiota in patients with nonalcoholic fatty liver disease. Hepatology 2013;58(1):120-127 View Article PubMed/NCBI
  53. Saki N, Hashemi SJ, Hosseini SA, Rahimi Z, Rahim F, Cheraghian B. Socioeconomic status and metabolic syndrome in Southwest Iran: results from Hoveyzeh Cohort Study (HCS). BMC Endocr Disord 2022;22(1):332 View Article PubMed/NCBI
  54. Lee G, You HJ, Bajaj JS, Joo SK, Yu J, Park S, et al. Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD. Nat Commun 2020;11(1):4982 View Article PubMed/NCBI
  55. Ruuskanen MO, Åberg F, Männistö V, Havulinna AS, Méric G, Liu Y, et al. Links between gut microbiome composition and fatty liver disease in a large population sample. Gut Microbes 2021;13(1):1-22 View Article PubMed/NCBI
  56. Frost F, Kacprowski T, Rühlemann M, Pietzner M, Bang C, Franke A, et al. Long-term instability of the intestinal microbiome is associated with metabolic liver disease, low microbiota diversity, diabetes mellitus and impaired exocrine pancreatic function. Gut 2021;70(3):522-530 View Article PubMed/NCBI
  57. Liu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, et al. Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting. Cell Metab 2022;34(5):719-730.e4 View Article PubMed/NCBI
  58. Craven L, Rahman A, Nair Parvathy S, Beaton M, Silverman J, et al. Allogenic Fecal Microbiota Transplantation in Patients With Nonalcoholic Fatty Liver Disease Improves Abnormal Small Intestinal Permeability: A Randomized Control Trial. Am J Gastroenterol 2020;115(7):1055-1065 View Article PubMed/NCBI
  59. Scorletti E, Afolabi PR, Miles EA, Smith DE, Almehmadi A, Alshathry A, et al. Synbiotics Alter Fecal Microbiomes, But Not Liver Fat or Fibrosis, in a Randomized Trial of Patients With Nonalcoholic Fatty Liver Disease. Gastroenterology 2020;158(6):1597-1610.e7 View Article PubMed/NCBI
  60. Hughes A, Dahmus J, Rivas G, Hummer B, Chen See JR, Wright JR, et al. Exercise Training Reverses Gut Dysbiosis in Patients With Biopsy-Proven Nonalcoholic Steatohepatitis: A Proof of Concept Study. Clin Gastroenterol Hepatol 2021;19(8):1723-1725 View Article PubMed/NCBI
  61. Cheng R, Wang L, Le S, Yang Y, Zhao C, Zhang X, et al. A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease. Nat Commun 2022;13(1):2555 View Article PubMed/NCBI
  62. Yaskolka Meir A, Rinott E, Tsaban G, Zelicha H, Kaplan A, Rosen P, et al. Effect of green-Mediterranean diet on intrahepatic fat: the DIRECT PLUS randomised controlled trial. Gut 2021;70(11):2085-2095 View Article PubMed/NCBI
  63. Lei Y, Tang L, Chen Q, Wu L, He W, Tu D, et al. Disulfiram ameliorates nonalcoholic steatohepatitis by modulating the gut microbiota and bile acid metabolism. Nat Commun 2022;13(1):6862 View Article PubMed/NCBI
  64. Bajaj JS, Heuman DM, Hylemon PB, Sanyal AJ, White MB, Monteith P, et al. Altered profile of human gut microbiome is associated with cirrhosis and its complications. J Hepatol 2014;60(5):940-947 View Article PubMed/NCBI
  65. Kwan SY, Jiao J, Joon A, Wei P, Petty LE, Below JE, et al. Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease. Hepatology 2022;75(4):955-967 View Article PubMed/NCBI
  66. Qin N, Yang F, Li A, Prifti E, Chen Y, et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014;513(7516):59-64 View Article PubMed/NCBI
  67. Yan AW, Fouts DE, Brandl J, Stärkel P, Torralba M, Schott E, et al. Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 2011;53(1):96-105 View Article PubMed/NCBI
  68. De Minicis S, Rychlicki C, Agostinelli L, Saccomanno S, Candelaresi C, et al. Dysbiosis contributes to fibrogenesis in the course of chronic liver injury in mice. Hepatology 2014;59(5):1738-1749 View Article PubMed/NCBI
  69. Acharya C, Sahingur SE, Bajaj JS. Microbiota, cirrhosis, and the emerging oral-gut-liver axis. JCI Insight 2017;2(19):94416 View Article PubMed/NCBI
  70. Caussy C, Tripathi A, Humphrey G, Bassirian S, Singh S, Faulkner C, et al. A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease. Nat Commun 2019;10(1):1406 View Article PubMed/NCBI
  71. Oh TG, Kim SM, Caussy C, Fu T, Guo J, Bassirian S, et al. A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis. Cell Metab 2020;32(5):878-888.e6 View Article PubMed/NCBI
  72. Bajaj JS, Betrapally NS, Gillevet PM. Decompensated cirrhosis and microbiome interpretation. Nature 2015;525(7569):E1-E2 View Article PubMed/NCBI
  73. Quigley EM, Stanton C, Murphy EF. The gut microbiota and the liver. Pathophysiological and clinical implications. J Hepatol 2013;58(5):1020-1027 View Article PubMed/NCBI
  74. Wei X, Jiang S, Chen Y, Zhao X, Li H, Lin W, et al. Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach. BMC Gastroenterol 2016;16(1):121 View Article PubMed/NCBI
  75. Chen Y, Yang F, Lu H, Wang B, Chen Y, Lei D, et al. Characterization of fecal microbial communities in patients with liver cirrhosis. Hepatology 2011;54(2):562-572 View Article PubMed/NCBI
  76. Bauer TM, Schwacha H, Steinbruckner B, Brinkmann FE, Ditzen AK, Aponte J, et al. Small intestinal bacterial overgrowth in human cirrhosis is associated with systemic endotoxemia. Am J Gastroenterol 2002;97(9):2364-2370 View Article PubMed/NCBI
  77. Bajaj JS, Betrapally NS, Hylemon PB, Heuman DM, Daita K, White MB, et al. Salivary microbiota reflects changes in gut microbiota in cirrhosis with hepatic encephalopathy. Hepatology 2015;62(4):1260-1271 View Article PubMed/NCBI
  78. Chen Y, Ji F, Guo J, Shi D, Fang D, Li L. Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology. Sci Rep 2016;6:34055 View Article PubMed/NCBI
  79. Chen Y, Guo J, Qian G, Fang D, Shi D, Guo L, et al. Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality. J Gastroenterol Hepatol 2015;30(9):1429-1437 View Article PubMed/NCBI
  80. Ahluwalia V, Betrapally NS, Hylemon PB, White MB, Gillevet PM, Unser AB, et al. Impaired Gut-Liver-Brain Axis in Patients with Cirrhosis. Sci Rep 2016;6:26800 View Article PubMed/NCBI
  81. Garcia-Lezana T, Raurell I, Bravo M, Torres-Arauz M, Salcedo MT, Santiago A, et al. Restoration of a healthy intestinal microbiota normalizes portal hypertension in a rat model of nonalcoholic steatohepatitis. Hepatology 2018;67(4):1485-1498 View Article PubMed/NCBI
  82. Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med 2016;8(1):51 View Article PubMed/NCBI
  83. Bajaj JS, Liu EJ, Kheradman R, Fagan A, Heuman DM, White M, et al. Fungal dysbiosis in cirrhosis. Gut 2018;67(6):1146-1154 View Article PubMed/NCBI
  84. Szabo G. Gut-Liver Axis Beyond the Microbiome: How the Fungal Mycobiome Contributes to Alcoholic Liver Disease. Hepatology 2018;68(6):2426-2428 View Article PubMed/NCBI
  85. Lin RS, Lee FY, Lee SD, Tsai YT, Lin HC, Lu RH, et al. Endotoxemia in patients with chronic liver diseases: relationship to severity of liver diseases, presence of esophageal varices, and hyperdynamic circulation. J Hepatol 1995;22(2):165-172 View Article PubMed/NCBI
  86. Zhang HL, Yu LX, Yang W, Tang L, Lin Y, Wu H, et al. Profound impact of gut homeostasis on chemically-induced pro-tumorigenic inflammation and hepatocarcinogenesis in rats. J Hepatol 2012;57(4):803-812 View Article PubMed/NCBI
  87. Nolan JP. The role of intestinal endotoxin in liver injury: a long and evolving history. Hepatology 2010;52(5):1829-1835 View Article PubMed/NCBI
  88. Dapito DH, Mencin A, Gwak GY, Pradere JP, Jang MK, Mederacke I, et al. Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. Cancer Cell 2012;21(4):504-516 View Article PubMed/NCBI
  89. Takeuchi O, Akira S. Pattern recognition receptors and inflammation. Cell 2010;140(6):805-820 View Article PubMed/NCBI
  90. Gabele E, Dostert K, Hofmann C, Wiest R, Schölmerich J, Hellerbrand C, et al. DSS induced colitis increases portal LPS levels and enhances hepatic inflammation and fibrogenesis in experimental NASH. J Hepatol 2011;55(6):1391-1399 View Article PubMed/NCBI
  91. Achiwa K, Ishigami M, Ishizu Y, Kuzuya T, Honda T, Hayashi K, et al. DSS colitis promotes tumorigenesis and fibrogenesis in a choline-deficient high-fat diet-induced NASH mouse model. Biochem Biophys Res Commun 2016;470(1):15-21 View Article PubMed/NCBI
  92. Seki E, De Minicis S, Osterreicher CH, Kluwe J, Osawa Y, Brenner DA, et al. TLR4 enhances TGF-beta signaling and hepatic fibrosis. Nat Med 2007;13(11):1324-1332 View Article PubMed/NCBI
  93. Yu LX, Yan HX, Liu Q, Yang W, Wu HP, Dong W, et al. Endotoxin accumulation prevents carcinogen-induced apoptosis and promotes liver tumorigenesis in rodents. Hepatology 2010;52(4):1322-1333 View Article PubMed/NCBI
  94. Toyoda H, Komurasaki T, Uchida D, Takayama Y, Isobe T, Okuyama T, et al. Epiregulin. A novel epidermal growth factor with mitogenic activity for rat primary hepatocytes. J Biol Chem 1995;270(13):7495-7500 View Article PubMed/NCBI
  95. Jing YY, Han ZP, Sun K, Zhang SS, Hou J, Liu Y, et al. Toll-like receptor 4 signaling promotes epithelial-mesenchymal transition in human hepatocellular carcinoma induced by lipopolysaccharide. BMC Med 2012;10:98 View Article PubMed/NCBI
  96. Venkatesh M, Mukherjee S, Wang H, Li H, Sun K, Benechet AP, et al. Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4. Immunity 2014;41(2):296-310 View Article PubMed/NCBI
  97. Brandi G, De Lorenzo S, Candela M, Pantaleo MA, Bellentani S, Tovoli F, et al. Microbiota, NASH, HCC and the potential role of probiotics. Carcinogenesis 2017;38(3):231-240 View Article PubMed/NCBI
  98. Yamada S, Takashina Y, Watanabe M, Nagamine R, Saito Y, Kamada N, et al. Bile acid metabolism regulated by the gut microbiota promotes non-alcoholic steatohepatitis-associated hepatocellular carcinoma in mice. Oncotarget 2018;9(11):9925-9939 View Article PubMed/NCBI
  99. Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J, deRoos P, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013;504(7480):451-455 View Article PubMed/NCBI
  100. Kverka M, Zakostelska Z, Klimesova K, Sokol D, Hudcovic T, Hrncir T, et al. Oral administration of Parabacteroides distasonis antigens attenuates experimental murine colitis through modulation of immunity and microbiota composition. Clin Exp Immunol 2011;163(2):250-259 View Article PubMed/NCBI
  101. Li J, Sung CY, Lee N, Ni Y, Pihlajamäki J, Panagiotou G, et al. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. Proc Natl Acad Sci U S A 2016;113(9):E1306-E1315 View Article PubMed/NCBI
  102. Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A 2010;107(27):12204-12209 View Article PubMed/NCBI
  103. Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Weingarten RA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 2013;342(6161):967-970 View Article PubMed/NCBI
  104. Grat M, Wronka KM, Krasnodebski M, Masior Ł, Lewandowski Z, Kosińska I, et al. Profile of Gut Microbiota Associated With the Presence of Hepatocellular Cancer in Patients With Liver Cirrhosis. Transplant Proc 2016;48(5):1687-1691 View Article PubMed/NCBI
  105. Liu Q, Li F, Zhuang Y, Xu J, Wang J, Mao X, et al. Alteration in gut microbiota associated with hepatitis B and non-hepatitis virus related hepatocellular carcinoma. Gut Pathog 2019;11:1 View Article PubMed/NCBI
  106. Ponziani FR, Bhoori S, Castelli C, Putignani L, Rivoltini L, Del Chierico F, et al. Hepatocellular Carcinoma Is Associated With Gut Microbiota Profile and Inflammation in Nonalcoholic Fatty Liver Disease. Hepatology 2019;69(1):107-120 View Article PubMed/NCBI
  107. Ren Z, Li A, Jiang J, Zhou L, Yu Z, Lu H, et al. Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma. Gut 2019;68(6):1014-1023 View Article PubMed/NCBI
  108. Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 2014;513(7516):59-64 View Article PubMed/NCBI
  109. Arab JP, Karpen SJ, Dawson PA, Arrese M, Trauner M. Bile acids and nonalcoholic fatty liver disease: Molecular insights and therapeutic perspectives. Hepatology 2017;65(1):350-362 View Article PubMed/NCBI
  110. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007;56(7):1761-1772 View Article PubMed/NCBI
  111. Canfora EE, Jocken JW, Blaak EE. Short-chain fatty acids in control of body weight and insulin sensitivity. Nat Rev Endocrinol 2015;11(10):577-591 View Article PubMed/NCBI
  112. Chambers ES, Byrne CS, Morrison DJ, Murphy KG, Preston T, Tedford C, et al. Dietary supplementation with inulin-propionate ester or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised cross-over trial. Gut 2019;68(8):1430-1438 View Article PubMed/NCBI
  113. Spencer MD, Hamp TJ, Reid RW, Fischer LM, Zeisel SH, Fodor AA. Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 2011;140(3):976-986 View Article PubMed/NCBI
  114. Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, et al. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A 2006;103(33):12511-12516 View Article PubMed/NCBI
  115. Tang WHW, Bäckhed F, Landmesser U, Hazen SL. Intestinal Microbiota in Cardiovascular Health and Disease: JACC State-of-the-Art Review. J Am Coll Cardiol 2019;73(16):2089-2105 View Article PubMed/NCBI
  116. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011;472(7341):57-63 View Article PubMed/NCBI
  117. Wahlström A, Sayin SI, Marschall HU, Bäckhed F. Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism. Cell Metab 2016;24(1):41-50 View Article PubMed/NCBI
  118. Wang D, Doestzada M, Chen L, Andreu-Sanchez S, van den Munckhof IC, Augustijn HE, et al. Characterization of gut microbial structural variations as determinants of human bile acid metabolism. Cell Host Microbe 2021;29(12):1802-1814.e5 View Article PubMed/NCBI
  119. Sayin SI, Wahlström A, Felin J, Jäntti S, Marschall HU, Bamberg K, et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 2013;17(2):225-235 View Article PubMed/NCBI
  120. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 2013;19(5):576-585 View Article PubMed/NCBI
  121. Kakiyama G, Pandak WM, Gillevet PM, Hylemon PB, Heuman DM, Daita K, et al. Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J Hepatol 2013;58(5):949-955 View Article PubMed/NCBI
  122. Chávez-Talavera O, Tailleux A, Lefebvre P, Staels B. Bile Acid Control of Metabolism and Inflammation in Obesity, Type 2 Diabetes, Dyslipidemia, and Nonalcoholic Fatty Liver Disease. Gastroenterology 2017;152(7):1679-1694.e3 View Article PubMed/NCBI
  123. Meijnikman AS, Davids M, Herrema H, Aydin O, Tremaroli V, Rios-Morales M, et al. Microbiome-derived ethanol in nonalcoholic fatty liver disease. Nat Med 2022;28(10):2100-2106 View Article PubMed/NCBI
  124. Yuan J, Chen C, Cui J, Lu J, Yan C, Wei X, et al. Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae. Cell Metab 2019;30(6):1172 View Article PubMed/NCBI
  125. Samuel BS, Shaito A, Motoike T, Rey FE, Backhed F, Manchester JK, et al. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci U S A 2008;105(43):16767-16772 View Article PubMed/NCBI
  126. Rau M, Rehman A, Dittrich M, Groen AK, Hermanns HM, Seyfried F, et al. Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease. United European Gastroenterol J 2018;6(10):1496-1507 View Article PubMed/NCBI
  127. Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 2009;461(7268):1282-1286 View Article PubMed/NCBI
  128. Canfora EE, Meex RCR, Venema K, Blaak EE. Gut microbial metabolites in obesity, NAFLD and T2DM. Nat Rev Endocrinol 2019;15(5):261-273 View Article PubMed/NCBI
  129. Bansal T, Alaniz RC, Wood TK, Jayaraman A. The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation. Proc Natl Acad Sci U S A 2010;107(1):228-233 View Article PubMed/NCBI
  130. Cervantes-Barragan L, Chai JN, Tianero MD, Di Luccia B, Ahern PP, Merriman J, et al. Lactobacillus reuteri induces gut intraepithelial CD4(+)CD8αα(+) T cells. Science 2017;357(6353):806-810 View Article PubMed/NCBI
  131. Beaumont M, Neyrinck AM, Olivares M, Rodriguez J, de Rocca Serra A, Roumain M, et al. The gut microbiota metabolite indole alleviates liver inflammation in mice. FASEB J 2018;32(12):fj201800544 View Article PubMed/NCBI
  132. Vinolo MA, Rodrigues HG, Festuccia WT, Crisma AR, Alves VS, Martins AR, et al. Tributyrin attenuates obesity-associated inflammation and insulin resistance in high-fat-fed mice. Am J Physiol Endocrinol Metab 2012;303(2):E272-E282 View Article PubMed/NCBI
  133. Chen F, Esmaili S, Rogers GB, Bugianesi E, Petta S, Marchesini G, et al. Lean NAFLD: A Distinct Entity Shaped by Differential Metabolic Adaptation. Hepatology 2020;71(4):1213-1227 View Article PubMed/NCBI
  134. Verbeke L, Farre R, Trebicka J, Komuta M, Roskams T, Klein S, et al. Obeticholic acid, a farnesoid X receptor agonist, improves portal hypertension by two distinct pathways in cirrhotic rats. Hepatology 2014;59(6):2286-2298 View Article PubMed/NCBI
  135. Neuschwander-Tetri BA, Loomba R, Sanyal AJ, Lavine JE, Van Natta ML, Abdelmalek MF, et al. Farnesoid X nuclear receptor ligand obeticholic acid for non-cirrhotic, non-alcoholic steatohepatitis (FLINT): a multicentre, randomised, placebo-controlled trial. Lancet 2015;385(9972):956-965 View Article PubMed/NCBI
  136. Traussnigg S, Schattenberg JM, Demir M, Wiegand J, Geier A, Teuber G, et al. Norursodeoxycholic acid versus placebo in the treatment of non-alcoholic fatty liver disease: a double-blind, randomised, placebo-controlled, phase 2 dose-finding trial. Lancet Gastroenterol Hepatol2 2019;4(10):781-793 View Article PubMed/NCBI
  137. Harrison SA, Rinella ME, Abdelmalek MF, Trotter JF, Paredes AH, Arnold L, et al. NGM282 for treatment of non-alcoholic steatohepatitis: a multicentre, randomised, double-blind, placebo-controlled, phase 2 trial. Lancet 2018;391(10126):1174-1185 View Article PubMed/NCBI
  138. Adams LA, Wang Z, Liddle C, Melton PE, Ariff A, Chandraratna H, et al. Bile acids associate with specific gut microbiota, low-level alcohol consumption and liver fibrosis in patients with non-alcoholic fatty liver disease. Liver Int 2020;40(6):1356-1365 View Article PubMed/NCBI
  139. Behary J, Amorim N, Jiang XT, Raposo A, Gong L, McGovern E, et al. Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma. Nat Commun 2021;12(1):187 View Article PubMed/NCBI
  140. Demir M, Lang S, Hartmann P, Duan Y, Martin A, Miyamoto Y, et al. The fecal mycobiome in non-alcoholic fatty liver disease. J Hepatol 2022;76(4):788-799 View Article PubMed/NCBI
  141. Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, et al. Personalized Nutrition by Prediction of Glycemic Responses. Cell 2015;163(5):1079-1094 View Article PubMed/NCBI
  • Journal of Clinical and Translational Hepatology
  • pISSN 2225-0719
  • eISSN 2310-8819
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Nonalcoholic Fatty Liver Disease and the Intestinal Microbiome: An Inseparable Link

Maria Effenberger, Christoph Grander, Felix Grabherr, Herbert Tilg
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