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Hallmarks of the human intestinal microbiome on liver maturation and function

  • Joana I. Almeida
    Affiliations
    Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain

    Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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  • Author Footnotes
    ‡ Present address of Miguel F. Tenreiro is Department of Bioengineering and iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
    Miguel F. Tenreiro
    Footnotes
    ‡ Present address of Miguel F. Tenreiro is Department of Bioengineering and iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
    Affiliations
    Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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  • Lucía Martinez-Santamaria
    Affiliations
    Carlos III University of Madrid. Bioengineering and Aerospace Engineering, Madrid, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, ISCIII), Madrid, Spain

    Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
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  • Sara Guerrero-Aspizua
    Affiliations
    Carlos III University of Madrid. Bioengineering and Aerospace Engineering, Madrid, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, ISCIII), Madrid, Spain
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  • Javier P. Gisbert
    Affiliations
    Gastroenterology Department. Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
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  • Paula M. Alves
    Affiliations
    Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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  • Author Footnotes
    † Equal contribution
    Margarida Serra
    Footnotes
    † Equal contribution
    Affiliations
    Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
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  • Author Footnotes
    † Equal contribution
    Pedro M. Baptista
    Correspondence
    Corresponding author. Address: Instituto de Investigación Sanitaria Aragón (IIS Aragon), Avda San Juan Bosco, 13, 50009 Zaragoza, Spain.
    Footnotes
    † Equal contribution
    Affiliations
    Instituto de Investigación Sanitaria Aragón (IIS Aragón), Zaragoza, Spain

    Carlos III University of Madrid. Bioengineering and Aerospace Engineering, Madrid, Spain

    Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain

    Fundación ARAID, Zaragoza, Spain
    Search for articles by this author
  • Author Footnotes
    † Equal contribution
    ‡ Present address of Miguel F. Tenreiro is Department of Bioengineering and iBB – Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.
Published:October 26, 2021DOI:https://doi.org/10.1016/j.jhep.2021.10.015

      Summary

      As one of the most metabolically complex systems in the body, the liver ensures multi-organ homeostasis and ultimately sustains life. Nevertheless, during early postnatal development, the liver is highly immature and takes about 2 years to acquire and develop almost all of its functions. Different events occurring at the environmental and cellular levels are thought to mediate hepatic maturation and function postnatally. The crosstalk between the liver, the gut and its microbiome has been well appreciated in the context of liver disease, but recent evidence suggests that the latter could also be critical for hepatic function under physiological conditions. The gut-liver crosstalk is thought to be mediated by a rich repertoire of microbial metabolites that can participate in a myriad of biological processes in hepatic sinusoids, from energy metabolism to tissue regeneration. Studies on germ-free animals have revealed the gut microbiome as a critical contributor in early hepatic programming, and this influence extends throughout life, mediating liver function and body homeostasis. In this seminar, we describe the microbial molecules that have a known effect on the liver and discuss how the gut microbiome and the liver evolve throughout life. We also provide insights on current and future strategies to target the gut microbiome in the context of hepatology research.

      Keywords

      Introduction

      A fully mature liver is able to perform up to 500 different functions, including anabolic and catabolic metabolism of macronutrients, detoxification of xenobiotics, bile acid homeostasis, urea and plasma protein synthesis, destruction of old or faulty red blood cells, and even immune surveillance. This is made possible by the non-homogeneous division of metabolic pathways along the acinus, in which hepatocytes and other non-parenchymal cell types radiate outward from the central vein to the portal triads. The liver and its processes, when fully developed and matured, are imperative for life. While many authors have extensively reviewed the development of the liver,
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      Regulatory phases of early liver development: paradigms of organogenesis.
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      Liver development update: new embryo models, cell lineage control, and morphogenesis.
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      Orchestrating liver development.
      giving important insights into organ and tissue morphogenesis, much less is known regarding the acquisition of hepatic functions and the mechanisms behind foetal to neonatal to adult liver remodelling.
      In parallel with hepatic development, another complex entity is being established – the gut microbiome. The gut microbiome comprises trillions of microbes and their metabolites that influence host homeostasis in countless physiological ways.
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      Human Microbiome Project Consortium
      Structure, function and diversity of the healthy human microbiome.
      Due to recent advances in high-throughput characterisation techniques (i.e., shotgun metagenomic sequencing) and analytic methods (i.e., metagenomic profiling), host-microbiome interactions are gradually beginning to be understood. These interactions are especially relevant in hepatology, since the liver is anatomically and physiologically connected to the gut (and its microbiome) by the biliary tract, portal vein and several molecules that travel between them. Although research on the gut-liver axis has focused primarily on disease, a new research trend has started to consider this crosstalk as a determinant for the acquisition and maintenance of hepatic functions throughout life. In this review, we pinpoint key microbial molecules that have known effects on the liver, as well as their hepatic-specific molecular targets. We discuss how the microbiome evolves from the perinatal period into adulthood and provide evidence that the events that determine microbiome diversification and transformation are potentially linked to the acquisition of hepatic maturation and homeostasis. Finally, the potential of targeting the human microbiome in the context of hepatology research and clinical translation is also addressed.

      Liver development and remodelling after birth

      The human embryonic liver emerges by the 3rd to 4th week of gestation as a result of hepatic diverticulum (or liver bud) organogenesis, a process remarkably conserved across vertebrate species.
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      Regulatory phases of early liver development: paradigms of organogenesis.
      ,
      • Lemaigre F.
      • Zaret K.S.
      Liver development update: new embryo models, cell lineage control, and morphogenesis.
      ,
      • Roskams T.
      • Eyken P.V.
      • Desmet V.
      Human liver growth and development.
      Hepatic endoderm cells that form the hepatic diverticulum rapidly grow and invade the adjacent septum transversum mesenchyme, allowing for hepatic specification of the hepatic diverticulum (Fig. 1A). Remarkably, only approximately 56-80 days pass from the termination of hepatic lineage differentiation (by day 210 of gestation) up to the end of the gestational period (∼266-288 days), corresponding to the period of hepatocyte maturation in utero.
      • Gordillo M.
      • Evans T.
      • Gouon-Evans V.
      Orchestrating liver development.
      Is this enough time to mature the “metabolic factories” of the liver? Are hepatocytes functional during and after gestation?
      Figure thumbnail gr1
      Fig. 1Liver development and postpartum changes involved in hepatic maturation.
      (A) During embryogenesis, the first sign of human liver development corresponds to the formation of the hepatic diverticulum after the commitment of foregut endoderm. Throughout gestation these hepatic progenitor cells, known as hepatoblasts, differentiate into hepatocytes or cholangiocytes, which culminates with the development of hepatic lobules. The foetal liver also supports haematopoiesis, peaking at the 2nd trimester and declining until birth. The maturation of liver cells happens during the last moments before birth, which is definitely not sufficient to establish all hepatic functions that are imperative for adult competence.
      (B) Environmental, cellular and molecular factors that play a part in postpartum liver maturation. HMO, human milk oligosaccharide.
      During the gestational period, the foetal liver undergoes rapid volumetric growth (from approximately 3.09 g in foetuses aged 12-13th weeks to 161.94 g in foetuses aged 41st-42nd weeks
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      Volumetric growth of the liver in the human fetus: An Anatomical, Hydrostatic, and Statistical study.
      ) and becomes a pivotal organ involved in foeto-placental metabolism. However, most hepatic functions from the adult liver are absent in the foetus. For example, during the 5-6th week of gestation (10 mm embryo) the human foetal liver is colonised by haematopoietic progenitors, and by the 2nd trimester of gestation approximately 60-70% of the hepatic parenchyma is populated by haematopoietic cells
      • Chou S.
      • Lodish H.F.
      Fetal liver hepatic progenitors are supportive stromal cells for hematopoietic stem cells.
      (Fig. 1A). Additionally, the foetal liver has often been described as a “cardiovascular tissue”,
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      Functions and the Emerging Role of the Foetal Liver into Regenerative Medicine.
      since it receives oxygen-rich blood from the umbilical vein and shunts it via the ductus venosus to the inferior vena cava and then to the foetus’s heart. Foetal hepatic metabolism is also incapable of matching adult levels. For example, foetal cytochrome P450 (CYP450) expression represents only ∼30% of the levels detected in adulthood,
      • Ring J.A.
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      • Ching M.S.
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      • Morgan D.J.
      Fetal hepatic drug elimination.
      gluconeogenesis under physiological conditions has not been documented in utero,
      • Kalhan S.C.
      • D’Angelo L.J.
      • Savin S.M.
      • Adam P.A.
      Glucose production in pregnant women at term gestation: Sources of glucose for the human fetus.
      and the plasma concentrations of alpha-fetoprotein surpass those of albumin before birth.
      • Tomasi Jr., T.B.
      Structure and function of alpha-fetoprotein.
      This striking immaturity might be related to the foetus’s dependency on the maternal body to support basic foetal functions like nutrition and filtration, or simply because the acquisition of liver functions requires more time and stimuli that are not present during uterine life.
      The transition from a foetus to a newborn is the most complex adaptation that occurs in human experience.
      • Hillman N.H.
      • Kallapur S.G.
      • Jobe S.G.
      Physiology of transition from intrauterine to extrauterine life.
      The newborn liver is required to rapidly adapt and mature to face the challenges imposed by extrauterine life, in which several molecular, cellular and environmental factors contribute to its maturation, as previously identified by Chen et al.
      • Chen C.
      • Soto-Gutierrez A.
      • Baptista P.M.
      • Spee B.
      Biotechnology Challenges to In Vitro Maturation of Hepatic Stem Cells.
      (Fig. 1B). For instance, relevant molecular hallmarks pivotal to hepatocyte maturation are postpartum polyploidisation (up to 8n)
      • Gentric G.
      • Celton-Morizur S.
      • Desdouets C.
      Polyploidy and liver proliferation.
      and foetal-to-adult isoform switching (mediated by alternative splicing events).
      • Sen S.
      • Jumaa H.
      • Webster N.J.G.
      Splicing factor SRSF3 is crucial for hepatocyte differentiation and metabolic function.
      Degeneration of elements that participated in foetal circulation due to the cessation of placental circulation and cord clamping, equally induce significant changes in the hepatic parenchyma. In particular, the decrease of oxygen consumption can explain not only whole-organ morphological changes
      • Meyer W.W.
      • Lind J.
      Postnatal changes in the portal circulation.
      but also the establishment of functional heterogeneity within the hepatic niche.
      • Wölfle D.
      • Schmidt H.
      • Jungermann K.
      Short-term modulation of glycogen metabolism, glycolysis and gluconeogenesis by physiological oxygen concentrations in hepatocyte cultures.
      ,
      • Jungermann K.
      • Kietzmann T.
      Role of oxygen in the zonation of carbohydrate metabolism and gene expression in liver.
      The neonatal diet greatly differs from the foetal diet.
      • Girard J.
      Metabolic adaptations to change of nutrition at birth.
      Milk and later solid food intake bring higher nutritional richness and force the neonate to take control over its metabolic needs, thereby programming postpartum hepatic metabolism.
      • Marsac C.
      • Saudubray J.M.
      • Moncion A.
      • Leroux J.P.
      Development of Gluconeogenic Enzymes in the Liver of Human Newborns.
      • Pégorier J.P.
      • Châtelain F.
      • Thumelin S.
      • Girard J.
      Role of long-chain fatty acids in the postnatal induction of genes coding for liver mitochondrial β-oxidative enzymes.
      • Bougneres P.F.
      • Lemmel C.
      • Ferré P.
      • Bier D.M.
      Ketone body transport in the human neonate and infant.
      Lastly, after birth, microbial colonisation of the neonate’s gut,
      • Tamburini S.
      • Shen N.
      • Wu H.C.
      • Clemente J.C.
      The microbiome in early life: implications for health outcomes.
      in association with an increase in portal venous blood flow,
      • Meyer W.W.
      • Lind J.
      Postnatal changes in the portal circulation.
      can supply a wide range of microbial molecules that affect the hepatic niche in multiple ways.
      A fully developed and mature liver can perform over 500 life-sustaining functions.
      The influence of the gut microbiome on liver maturation, function and homeostasis is a relatively new concept. In this review, we unravel how the gut microbiome can impact the liver throughout life, providing a detailed overview of this physiological interaction and identifying key mediators that participate in this crosstalk.

      Unravelling crosstalk between the gut and liver

      The term “gut-liver axis”, first described in the 1980s,
      • Bjorneboe M.
      • Prytz H.
      • Orskov F.
      Antibodies to intestinal microbes in serum of patients with cirrhosis of the liver.
      ,
      • Volta U.
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      • Bianchi F.B.
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      • Pisi E.
      IgA Antibodides to dietary antigens in liver cirrhosis.
      refers to the bidirectional communication between the gut (with its microbiota) and the liver, in which there is an active participation of signals from dietary, genetic and environmental origin (Fig. 2A). In the past decade, strong evidence from both animal models and clinical studies has suggested that perturbations to the gut-liver axis influence liver disease progression, namely in non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis, alcohol-related liver disease, cirrhosis and hepatocellular carcinoma.
      • Schnabl B.
      • Brenner D.A.
      Interactions between the intestinal microbiome and liver diseases.
      The burden of these gastrointestinal-associated liver diseases has, consequently, placed the gut-liver axis on the scientific agenda. While much is known about its role in disease,
      • Albillos A.
      • de Gottardi A.
      • Rescigno M.
      The gut-liver axis in liver disease: Pathophysiological basis for therapy.
      its physiological contribution to liver development and homeostasis is less appreciated.
      Figure thumbnail gr2
      Fig. 2The gut-liver axis.
      (A) The bidirectional communication between gut and liver is intensified soon after birth and persists throughout life.
      (B) The liver is anatomically connected with the gut via the hepatopancreatic ampulla (or ampulla of Vater) and provides it with bile acids to ease lipidic nutrient digestion and absorption and antimicrobial molecules to prevent bacterial overgrowth. In turn, microbes inhabiting the gut produce a wide variety of compounds (e.g., short-chain fatty acids, amino acid catabolites, secondary bile acids, vitamins, and small bioactive peptides) that are absorbed across the (C) intestinal lumen and reach (D,E) hepatic sinusoids in the liver via portal vein circulation. (F) These microbial-derived metabolites are sensed by receptors localised at the plasma membrane of hepatocytes, influencing the parenchyma in multiple ways. FXR, farnesoid X receptor; GPCRs, G protein-coupled receptors; SCFAs, short-chain fatty acids; TLRs, Toll-like receptor.
      The liver and the gut are connected by the biliary tract and the portal venous system. The common bile duct joins the pancreatic duct at the anatomical transition from foregut to midgut, known as the hepatopancreatic ampulla, where both bile and pancreatic enzymes are allowed to enter the major duodenal papilla during the postprandial period (Fig. 2B). In particular, the bile contains bile acids that aid lipid and fat-soluble vitamin emulsification, solubilisation and absorption along the ileum. Due to its finger-like evaginations (i.e., villi), the gut is one of the body’s largest interfaces, where host, environmental factors, antigens and microorganisms interact (Fig. 2C). Among the players involved, bile acids, for instance, can instruct enterocytes to produce antimicrobial agents during periods of increased microbial exposure, and so mediate gut eubiosis.
      • Inagaki T.
      • Moschetta A.
      • Lee Y.K.
      • Peng L.
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      • Downes M.
      • et al.
      Regulation of antibacterial defense in the small intestine by the nuclear bile acid receptor.
      Most of these bile acids (∼95%) will return to the liver through the portal venous system to be recycled and secreted back to the biliary tract, completing the so-called enterohepatic circulation. The portal venous system is established early on, between the 4th and 12th weeks of gestation,
      • Lee W.-K.
      • Chang S.D.
      • Duddalwar V.A.
      • Comin J.M.
      • Perera W.
      • Lau W.-F. E.
      Imaging assessment of congenital and acquired abnormalities of the portal venous system.
      ,
      • Carneiro C.
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      • Bilreiro C.
      • Barros M.
      • Bahia C.
      • Santiago I.
      • et al.
      All about portal vein: a pictorial display to anatomy, variants and physiopathology.
      and is responsible for toxin and nutrient drainage from the gastrointestinal tract to the liver. In fact, portal blood flow represents 75% of the total hepatic blood flow, with approximately one litre of blood reaching the liver per minute in healthy individuals.
      • Da Costa J.D.
      • Leão A.R.D.S.
      • Santos J.E.M.
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      • Sebastianes P.M.
      • D’Ippolito G.
      Measurement of portal blood flow in healthy individuals: a comparison between magnetic resonance imaging and Doppler ultrasound.
      Apart from reabsorbed bile acids, nutrients and minerals, a rich repertoire of microbial metabolites also travels along the portal circulation (Fig. 2D). Once they reach the liver, these molecules are sensed by specific hepatocyte receptors and initiate distinct signal transduction pathways that result in multiple cellular responses (Fig. 2E,F). Below, we briefly introduce the microbial communities that inhabit the gut and discuss the compounds that they produce which might reach and influence the liver parenchyma.

      The gut microbiome

      It is estimated that, during a lifetime, around 60 tons of food pass across the gut, along with large amounts of environmental toxins and microorganisms. These external inputs take part in the development of gastrointestinal immunity and establish its unique microbial community, the gut microbiome, which refers to the collection of bacteria (bacterial microbiome), archaea (archaeal microbiome), fungi (mycobiome), protists (meiofauna) and viruses (virome). The Human Microbiome Project was launched by the NIH in 2007 with the aim of comprehensively identifying and characterising the human microbiome.
      • Huttenhower C.
      • Gevers D.
      • Knight R.
      • Abubucker S.
      • Badger J.H.
      • Chinwalla A.T.
      • et al.
      Human Microbiome Project Consortium
      Structure, function and diversity of the healthy human microbiome.
      There are circa 100 trillion microorganisms inhabiting the human gut, which encompasses more than ∼10 times the number of human cells in the body.
      • Xu J.
      • Gordon J.I.
      Honor thy symbionts.
      Such an ecosystem is unique simply because it allows cooperative growth and maturation of many species that exist nowhere else together in nature. Some authors even acknowledge the gut microbiome as a ‘forgotten organ’ or ‘hidden organ’,
      • O’Hara A.M.
      • Shanahan F.
      The gut flora as a forgotten organ.
      since it collectively encodes 500 times more genes than the human genome,
      • Huttenhower C.
      • Gevers D.
      • Knight R.
      • Abubucker S.
      • Badger J.H.
      • Chinwalla A.T.
      • et al.
      Human Microbiome Project Consortium
      Structure, function and diversity of the healthy human microbiome.
      ,
      • Qin J.
      • Li R.
      • Raes J.
      • Arumugam M.
      • Burgdorf K.S.
      • Manichanh C.
      • et al.
      A human gut microbial gene catalogue established by metagenomic sequencing.
      and can regulate a complex framework of metabolic activities equal to a virtual organ.
      The organisation of microbes along the intestine is remarkable; it is determined by physiological variations along the length of the intestine, which include pH and oxygen gradients, antimicrobial concentration, nutrient competition with the host, and the establishment of an indirect contact with the intestinal epithelium.
      • Donaldson G.P.
      • Lee S.M.
      • Mazmanian S.K.
      Gut biogeography of the bacterial microbiota.
      The latter is sealed tightly together and is protected from microorganisms by a thick layer of mucus, thus avoiding local inflammation and systemic translocation. Nonetheless, this barrier is selectively permeable to a wide variety of microbial metabolic products, so-called postbiotics, that can influence the host in numerous ways, not only in the gut but also throughout the body, including in the liver.

      Microbial molecules from the gut and their effect on the liver

      Current knowledge about the composition and organisation of microbial communities inhabiting us vastly surpasses knowledge about the microbial molecules produced by these communities and their importance on human physiology. The gut microbial metabolome is complex as nutrient biotransformation requires community-level interactions in which different microbes and even the host have specific roles within each metabolic pathway.
      We currently have only a loose grasp of the full spectrum of the gut microbiome metabolome, even though significant efforts have been made to crack the "black-box". Biological functional mapping of metagenomic sequences, targeted and/or untargeted metabolomics, integrating pathway prediction into the metabolomics workflow and even using systems biology approaches have proven robust tools to identify physiologically relevant classes of microbial metabolites. Readers are referred to the recent article by Donia et al., which reviewed some of the major gut microbiome-derived metabolites identified to date and the methodologies used to identify those molecules.
      • Donia M.S.
      • Fischbach M.A.
      Small molecules from the human microbiota.
      Herein, we highlight the key microbial molecules that participate in gut-liver crosstalk and have proven to play a role in hepatic function. Table 1 comprehensively presents these metabolites and their identified hepatic molecular targets (additional information regarding the bacterial sources of the metabolites is included in Table S1).
      Table 1Microbial molecules from the gut and their known/predicted effects on the liver.
      ClassCompoundKnown/predicted function in liver/hepatocytesMolecular targets
      Short-chain fatty acids
      • Acetate
      • Lipogenesis
      Anti-lipogenic

      Fatty acid oxidation
      • Reduces triglyceride accumulation in bovine hepatocytes.
      • Increases AMPK phosphorylation, and downstream increases the transcriptional activity of PPARα (upregulates ACO, CPT1, CPT2, L-FABP) and decreases the transcriptional activity of SREPB-1c and ChREBP (downregulates ACCA, FASN, SCD1) in bovine hepatocytes.
        • Li X.
        • Chen H.
        • Guan Y.
        • Li X.
        • Lei L.
        • Liu J.
        • et al.
        Acetic acid activates the AMP-activated protein kinase signaling pathway to regulate lipid metabolism in bovine hepatocytes.
      • Cholesterol synthesis
      • Serves as an intermediate metabolic precursor and is converted into acetyl-CoA for de novo cholesterol synthesis in mice.
        • den Besten G.
        • Lange K.
        • Havinga R.
        • van Dijk T.H.
        • Gerding A.
        • van Eunen K.
        • et al.
        Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids.
      • Epigenetic regulator
      • Induces histone 3 acetylations (H3K9, H3K27, H3K56) at FASN and ACACA promotor regions in an ACSS1/2-dependent manner in HepG2 hepatocytes.
        • Gao X.
        • Lin S.H.
        • Ren F.
        • Li J.T.
        • Chen J.J.
        • Yao C.B.
        • et al.
        Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia.
      • Propionate
      • Gluconeogenesis
      • Anti-gluconeogenesis
      • Anti-lipogenic
      ButyrateAnti-lipogenic

      Fatty acid oxidation
      • Gluconeogenesis
      • Upregulates PEPCK, G6Pase, FOXO1, PGC-1α and HNF4α in primary mouse hepatocytes via cAMP/CREB pathway activation.
        • Ji X.
        • Zhou F.
        • Zhang Y.
        • Deng R.
        • Xu W.
        • Bai M.
        • et al.
        Butyrate stimulates hepatic gluconeogenesis in mouse primary hepatocytes.
      • Cholesterol synthesis
      • Serves as an intermediate metabolic precursor and is converted into acetyl-CoA for de novo cholesterol synthesis.
        • den Besten G.
        • Lange K.
        • Havinga R.
        • van Dijk T.H.
        • Gerding A.
        • van Eunen K.
        • et al.
        Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids.
      • Insulin sensitivity
      • Anti-inflammatory
      Mitochondrial function Antioxidant
      • Epigenetic regulator
      • Hepatic Differentiation
      Amino acid catabolites
      Tryptophan
      • Tryptamine
      • Anti-inflammatory
      • Indole
      • Anti-inflammatory
      • Modulates the NF-κB pathway and downstream downregulates murine pro-inflammatory genes (Nlrp3, Il-1β and Il-18) in ex vivo liver slices.
        • Beaumont M.
        • Neyrinck A.M.
        • Olivares M.
        • Rodriguez J.
        • de Rocca Serra A.
        • Roumain M.
        • et al.
        The gut microbiota metabolite indole alleviates liver inflammation in mice.
      • Cholesterol metabolism regulation
      • Xenobiotic metabolism
      • Indole-3-acetate/indole-3-acetic acid
      • Anti-inflammatory
      • Antioxidant
      • Decreases ROS production and increases superoxide dismutase activity in HFD mice.
        • Ji Y.
        • Gao Y.
        • Chen H.
        • Yin Y.
        • Zhang W.
        Indole-3-acetic acid alleviates nonalcoholic fatty liver disease in mice via attenuation of hepatic lipogenesis, and oxidative and inflammatory stress.
      • Anti-lipogenic
      • Xenobiotic metabolism
      • Interacts and inhibits in a dose-dependent manner drug transporters (OATP1B1 and OATP1B3).
        • Sato T.
        • Yamaguchi H.
        • Kogawa T.
        • Abe T.
        • Mano N.
        Organic anion transporting polypeptides 1B1 and 1B3 play an important role in uremic toxin handling and drug-uremic toxin interactions in the liver.
      • Indole-3-propionic acid
      • Anti-inflammatory
      • Modulates the NF-κB pathway and downstream downregulates pro-inflammatory cytokine levels (TNF-α, IL-1β and IL-16) in NAFLD mice.
        • Zhao Z.H.
        • Xin F.Z.
        • Xue Y.
        • Hu Z.
        • Han Y.
        • Ma F.
        • et al.
        Indole-3-propionic acid inhibits gut dysbiosis and endotoxin leakage to attenuate steatohepatitis in rats.
      Anti-lipogenic

      Anticholesterolemic
      • Skatole (indole-3-methyl)
      • Xenobiotic metabolism
      Phenylalanine
      • Phenylacetic acid
      • Lipogenesis
      • Promotes triglyceride accumulation in primary human hepatocytes (upregulation of lipid metabolism genes LPL and FASN) and in mice (steatosis).
        • Hoyles L.
        • Fernández-Real J.M.
        • Federici M.
        • Serino M.
        • Abbott J.
        • Charpentier J.
        • et al.
        Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.
      • Insulin resistance
      Tyrosine
      p-cresol

      (4-methylphenol)
      • Xenobiotic metabolism
      Secondary bile acids
      • Deoxycholic acid and/or lithocholic acid
      • Bile acid synthesis repression
      Lithocholic acidBile acid transport

      Repression
      • Xenobiotic metabolism
      • Deoxycholic acid and/or ursodeoxycholic acid
      • Energy metabolism
      • Activates the ERK1/2 and Akt pathways via a ROS-dependent manner in primary mouse hepatocytes; consequently, this inactivates phosphotyrosine phosphatases resulting in EGFR activation.
        • Dent P.
        • Fang Y.
        • Gupta S.
        • Studer E.
        • Mitchell G.
        • Spiegel S.
        • et al.
        Conjugated bile acids promote ERK1/2 and AKT activation via a pertussis toxin-sensitive mechanism in murine and human hepatocytes.
        - DCA
      • Taurine-conjugated DCA, glycine-conjugated DCA and taurine-conjugated UDCA activate the ERK1/2 and Akt pathways through S1P2 in primary mouse hepatocytes.
        • Studer E.
        • Zhou X.
        • Zhao R.
        • Wang Y.
        • Takabe K.
        • Nagahashi M.
        • et al.
        Conjugated bile acids activate the sphingosine-1-phosphate receptor 2 in primary rodent hepatocytes.
        - BOTH
      • Deoxycholic acid
      • Apoptosis
      • Activates in a dose-dependent manner the p53/miR-34a/SIRT1 proapoptotic pathway through downstream JNK1 phosphorylation in mice.
        • Ferreira D.M.S.
        • Afonso M.B.
        • Rodrigues P.M.
        • Simão A.L.
        • Pereira D.M.
        • Borralho P.M.
        • et al.
        c-Jun N-terminal kinase 1/c-Jun activation of the p53/MicroRNA 34a/sirtuin 1 pathway contributes to apoptosis induced by deoxycholic acid in rat liver.
      • Activated in a dose-depended manner the miR-21/PDC4 proapoptotic pathway by downstream inhibiting NF-κB transcriptional activity in mice.
        • Rodrigues P.M.
        • Afonso M.B.
        • Simão A.L.
        • Borralho P.M.
        • Rodrigues C.M.P.
        • Castro R.E.
        Inhibition of NF-κ B by deoxycholic acid induces miR-21/PDCD4-dependent hepatocelular apoptosis.
      • Inhibits in a dose-dependent manner the EGFR/Ras/MAPK pathway and potentiates FAS-mediated apoptosis in primary mouse and human hepatocytes.
        • Qiao L.
        • Studer E.
        • Leach K.
        • McKinstry R.
        • Gupta S.
        • Decker R.
        • et al.
        Deoxycholic acid (DCA) causes ligand-independent activation of epidermal growth factor receptor (EGFR) and FAS receptor in primary hepatocytes: inhibition of EGFR/mitogen-activated protein kinase-signaling module enhances DCA-induced apoptosis.
      Oxidative stress

      Lipid Peroxidation
      • Ursodeoxycholic acid
      • Cell survival
      • Antioxidant
      • Reduced the mitochondrial membrane permeability transition in mice with DCA-induced injury.
        • Rodrigues C.M.
        • Fan G.
        • Wong P.Y.
        • Kren B.T.
        • Steer C.J.
        Ursodeoxycholic acid may inhibit deoxycholic acid-induced apoptosis by modulating mitochondrial transmembrane potential and reactive oxygen species production.
      • Prevented mitochondrial release of cytochrome c and BAX accumulation in mitochondria of primary mouse hepatocytes with DCA-induced injury.
        • Rodrigues C.M.
        • Ma X.
        • Linehan-Stieers C.
        • Fan G.
        • Kren B.T.
        • Steer C.J.
        Ursodeoxycholic acid prevents cytochrome c release in apoptosis by inhibiting mitochondrial membrane depolarization and channel formation.
      • Increases GSH and metallothionein levels in primary mouse hepatocytes.
        • Mitsuyoshi H.
        • Nakashima T.
        • Sumida Y.
        • Yoh T.
        • Nakajima Y.
        • Ishikawa H.
        • et al.
        Ursodeoxycholic acid protects hepatocytes against oxidative injury via induction of antioxidants.
      • Deoxycholic acid and/or ursodeoxycholic acid
      • Liver regeneration
      • Delays early regeneration in mice after two-thirds PH, due to altered expression of cell-cycle markers cyclins A, B, D1 and D3. By day 8 regeneration is much accelerated, as shown by a 20% increase in hepatic mass relative to controls.
        • Kren B.T.
        • Rodrigues C.M.
        • Setchell K.D.R.
        • Steer C.J.
        Modulation of steady-state messenger RNA levels in the regenerating rat liver with bile acid feeding.
        - DCA
      • Promotes cholestatic hepatitis and a damage-induced hepatocyte proliferation in mice after 40% PH (SGPT and bilirubin elevations).
        • Barone M.
        • Francavilla A.
        • Polimeno L.
        • Ierardi E.
        • Romanelli D.
        • Berloco P.
        • et al.
        Modulation of rat hepatocyte proliferation by bile salts: in vitro and in vivo studies.
        - DCA
      Vitamins
      B vitamins
      • Thiamine (B1)
      • Coenzyme
      • Increases (by itself or when transformed into thiamine phosphate) the specific activity of branched chain α-ketoacid dehydrogenase in the human liver,
        • Danner D.J.
        • Davidson E.D.
        • Elsas L.J.
        Thiamine increases the specific activity of human liver branched chain α-ketoacid dehydrogenase.
        which is necessary for carbohydrate metabolism.
      • Riboflavin (B2)
      • Coenzyme
      Antioxidant

      Anti-inflammatory
      • Protects hepatocytes against ischaemia/reperfusion injury in mice.
        • Sanches S.C.
        • Ramalho L.N.Z.
        • Mendes-Braz M.
        • Terra V.A.
        • Cecchini R.
        • Augusto M.J.
        • et al.
        Riboflavin (vitamin B-2) reduces hepatocellular injury following liver ischaemia and reperfusion in mice.
      • Protects against oxidative-mediated hepatotoxicity induced by thioacetamide in rats (in combination with nicotinamide and vitamin C).
        • Bashandy S.A.E.
        • Ebaid H.
        • Abdelmottaleb Moussa S.A.
        • Alhazza I.M.
        • Hassan I.
        • Alaamer A.
        • et al.
        Potential effects of the combination of nicotinamide, vitamin B2 and vitamin C on oxidative-mediated hepatotoxicity induced by thioacetamide.
      • Provides protective effects against the risk of cirrhosis in human subjects (in combination with vitamin B12).
        • Corrao G.
        • Torchio P.
        • Zambon A.
        • D’Amicis A.
        • Lepore A.R.
        • di Orio F.
        Alcohol consumption and micronutrient intake as risk factors for liver cirrhosis: a case-control study. The Provincial Group for the study of Chronic Liver Disease.
      Niacin (B3)Antioxidant

      Anti-inflammatory
      • Anti-lipogenic
      • Pantothenic acid (B5)
      • Coenzyme
      Antioxidant

      Anti-inflammatory
      • Shows hepatoprotective and antioxidant effects in experimental models of CCl4-induced toxicity.
        • Eidi A.
        • Mortazavi P.
        • Tehrani M.E.
        • Rohani A.H.
        • Safi S.
        Hepatoprotective effects of pantothenic acid on carbon tetrachloride-induced toxicity in rats.
      • Anti-lipogenic
      • Decreases hepatic, perinephric, and plasma lipid accumulation in rats fed with pantothenic acid free diet and/or under ethanol regimen.
        • Shibata K.
        • Fukuwatari T.
        • Higashiyama S.
        • Sugita C.
        • Azumano I.
        • Onda M.
        Pantothenic acid refeeding diminishes the liver, perinephrical fats, and plasma fats accumulated by pantothenic acid deficiency and/or ethanol consumption.
      • Pyridoxine (B6)
      • Coenzyme
      • Antioxidant
      • Biotin (B7)
      • Coenzyme
      • Glucose metabolism
      • Improves glucose metabolism and protein expression levels of IRS-1, PPAR-γ, and NF-κB in rats (in combination with chromium histidinate).
        • Turgut M.
        • Cinar V.
        • Pala R.
        • Tuzcu M.
        • Orhan C.
        • Telceken H.
        • et al.
        Biotin and chromium histidinate improve glucose metabolism and proteins expression levels of IRS-1, PPAR-γ, and NF-ΚB in exercise-trained rats.
      • Folate (B9)
      • Coenzyme
      • Anti-glycaemic
      • Anti-lipogenic
      • Chronic folate deficiency increases serum triglyceride levels, upregulates Acc1 and Fasn, and downregulates Cd36 and ApoB mRNA levels in mice.
        • Zhao M.
        • Yuan M.M.
        • Yuan L.
        • Huang L.L.
        • Liao J.H.
        • Yu X.L.
        • et al.
        Chronic folate deficiency induces glucose and lipid metabolism disorders and subsequent cognitive dysfunction in mice.
      • Anti-apoptotic
      • Protects hyperhomocysteinemia mice from apoptosis via CFTR-activated endoplasmic reticulum stress.
        • Yang A.
        • Sun Y.
        • Mao C.
        • Yang S.
        • Huang M.
        • Deng M.
        • et al.
        Folate protects hepatocytes of hyperhomocysteinemia mice from apoptosis via cystic fibrosis transmembrane conductance regulator (CFTR)-Activated endoplasmic reticulum stress.
      • Attenuates apoptosis caused by arsenic-induced toxicity in Chang human hepatocytes.
        • Xu Y.
        • Wang H.
        • Wang Y.
        • Zheng Y.
        • Sun G.
        Effects of folate on arsenic toxicity in Chang human hepatocytes: involvement of folate antioxidant properties.
      • Folate deficiency enhances perturbations in hepatic methionine metabolism and DNA damage, besides promoting alcoholic liver injury.
        • Halsted C.H.
        • Villanueva J.A.
        • Devlin A.M.
        • Niemelä O.
        • Parkkila S.
        • Garrow T.A.
        • et al.
        Folate deficiency disturbs hepatic methionine metabolism and promotes liver injury in the ethanol-fed micropig.
      • Cobalamin (B12)
      • Storage
      • Stored in liver parenchymal cells, and from there can be transported to the bone marrow and other sites where it is involved in nuclear maturation processes
        • Joske R.A.
        The vitamin B12 content of human liver tissue obtained by aspiration biopsy.
        (serves as a co-factor for methionine synthase in the biosynthesis of purines and pyrimidines).
      Vitamin K2 (menaquinone)
      • Vitamin K2
      • Anticoagulant factor synthesis
      • Hepatic differentiation
      • Increases the expression of plasma proteins (ALB and AAT), genes associated with cell-cell communication (Cnx32 and CLDN1), urea cycle (CPS1 and OTC1), hepatic phase I (CYP3A4), II (UGT1A1, UGT1AB, UGT1A4 and UGT2B7) and III (OATP1B1 and MDR1) metabolic enzymes, and hepatic nuclear receptors (SHIP, FXR, LXRA and PPARα) in hESC-derived hepatocytes.
        • Qin J.
        • Chang M.
        • Wang S.
        • Liu Z.
        • Zhu W.
        • Wang Y.
        • et al.
        Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells.
      • Hepatic maturation
      • Increases albumin secretion, urea production, LDL uptake, triglyceride accumulation and glycogen storage in hESC-derived hepatocytes.
        • Avior Y.
        • Levy G.
        • Zimerman M.
        • Kitsberg D.
        • Schwartz R.
        • Sadeh R.
        • et al.
        Microbial-derived lithocholic acid and vitamin K2 drive the metabolic maturation of pluripotent stem cells-derived and fetal hepatocytes.
        ,
        • Qin J.
        • Chang M.
        • Wang S.
        • Liu Z.
        • Zhu W.
        • Wang Y.
        • et al.
        Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells.
      • Promotes higher expression of genes involved in PPAR signalling, xenobiotic metabolism by CYP450, pentose and glucuronate interconversions, glycine, serine and threonine metabolism, and complement and coagulating cascades in hESC-derived hepatocytes.
        • Qin J.
        • Chang M.
        • Wang S.
        • Liu Z.
        • Zhu W.
        • Wang Y.
        • et al.
        Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells.
      • Induces PXR activation and upregulation in hESC-derived and isolated foetal hepatocytes. Together with LCA, promotes inducible CYP450 activity.
        • Avior Y.
        • Levy G.
        • Zimerman M.
        • Kitsberg D.
        • Schwartz R.
        • Sadeh R.
        • et al.
        Microbial-derived lithocholic acid and vitamin K2 drive the metabolic maturation of pluripotent stem cells-derived and fetal hepatocytes.
      • Promotes formation and assembly of gap junctions enriched in Cnx32 by inhibiting the MAPK/p38 pathway in hESC-derived hepatocytes, thereby increasing gap junction intracellular communication.
        • Qin J.
        • Chang M.
        • Wang S.
        • Liu Z.
        • Zhu W.
        • Wang Y.
        • et al.
        Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells.
      Probiotic extracellular proteins and bioactive peptides
      FR-16, LR-17, peptide B7, peptide B12, serine threonine peptideUnknownUnknown
      ACAC, acetyl-CoA carboxylase; ACACA/Acc1, acetyl-CoA carboxylase 1; ACCA, acetyl-coenzyme A carboxylase carboxyl transferase subunit α; ACLY, ATP citrate lyase; ACO, 1-aminocyclopropane-1-carboxylate oxidase; ACSS1/2, acyl-CoA synthetase short-chain family member 1/2; AhR, aryl hydrocarbon receptor; AMPK/ACC, AMP-activated protein kinase/acetyl-CoA carboxylase (pathway); ApoB, apolipoprotein B; ASM, acid sphingomyelinase; BAX, Bcl-2-associated X protein; BSEP, bile salt export pump; Ca2+/CaMKKβ; calcium/calmodulin-dependent protein kinase kinase β; cAMP/CREB, cAMP- response element-binding protein (pathway); CCl4, carbon tetrachloride; CFTR, cystic fibrosis transmembrane conductance regulator; ChREBP, carbohydrate-responsive element-binding protein; Cnx32/43, connexin-32/43; CPT1/2, carnitine palmitoyltransferase I/II; CYP, cytochromes P450; DCA, deoxycholic acid; DGAT2, diacylglycerol acyltransferase 2; EGFR, epidermal growth factor receptor; ERK(1/2), extracellular signal-regulated protein kinase (1/2); FABP4, fatty acid-binding protein 4; FASN, fatty acid synthase; FFAR2, free fatty acid receptor 2; FGF21, fibroblast growth factor 21; FOXO1, forkhead box protein O1; FXR, farnesoid X receptor; G6Pase, glucose 6-phosphatase; GLP-1, glucagon-like peptide-1; GLP-1R, glucagon-like peptide-1 receptor; GLUT2, glucose transporter; GPR43, G protein-coupled receptor 43; GPR109A, hydroxycarboxylic acid receptor 2 (HCA2); GSH, reduced glutathione; GSSG, oxidized glutathione; GST, Glutathione S-transferase; HDAC2, histone deacetylase 2; HNF4α, hepatocyte nuclear factor 4α; hESC, human embryonic stem cells; HFD, high-fat diet; hiPSC, human induced pluripotent stem cells; IL-1β/8/16/18, interleukin-1β/8/16/18; INSR, insulin receptor; IRS-1, insulin receptor substrate-1; JNK(1), c-Jun N-terminal kinase (1); LCA, lithocholic acid; L-FABP, liver-type fatty acid-binding protein; LPL, lipoprotein lipase; LPS, lipopolysaccharide; LXRα, liver X receptor α; MAPK, mitogen-activated protein kinase; MCD, methionine-choline deficient (diet); MCP-1, monocyte chemoattractant protein-1; miR, micro RNA; MRP, multidrug resistance-associated protein; NAFLD, non-alcoholic fatty liver disease; Nlrp3, NOD-, LRR- and pyrin domain-containing protein 3; NQO1, NAD(P)H dehydrogenase [quinone] 1; NTCP, Na+-taurocholate cotransporting polypeptide; OATP, organo anion transporter; PDC4, programmed cell death 4; PEPCK, phosphoenolpyruvate carboxykinase; PGC1-α, peroxisome proliferator-activated receptor gamma coactivator 1-alpha; PH, partial hepatectomy; PI3K, phosphatidyl ionositol 3-kinase; PIDD, p53-induced protein with a death domain; PPARα/γ, peroxisome proliferator-activated receptor α/γ; PXR, pregnane X receptor; ROS, reactive oxygen species; S1P2, sphingosine-1-phosphate receptor 2; SCD1, stearoyl-CoA desaturase-1; SGPT, serum glutamic pyruvic transaminase; SIRT1, sirtuin 1; SREPB-1c, sterol regulatory element-binding protein-1c; SULT, sulfotransferase; TBARS, thiobarbituric acid reactive substances; TNF-α, tumour necrosis factor α; TLR2/4/9, toll-like receptor-2/4/9; UDCA, ursodeoxycholic acid; UGT, UDP-glucuronosyltransferase; VDR, vitamin D receptor.

      Short-chain fatty acids

      Various soluble dietary fibres and resistant starch that escape digestion can be fermented by gut saccharolytic microbes, which harbour a broader range of carbohydrate-degrading enzymes. Bacterial fermentation of undigestible fibres mainly produces short-chain fatty acids (SCFAs),
      • Cummings J.H.
      • Pomare E.W.
      • Branch W.J.
      • Naylor C.P.
      • Macfarlane G.T.
      Short chain fatty acids in human large intestine, portal, hepatic and venous blood.
      a subset of fatty acids with 6 or less carbon atoms in their backbone. Around 500-600 mmol of SCFAs are produced in the gut every day,
      • Bergman E.N.
      Energy contributions of volatile fatty acids from the gastrointestinal tract in various species.
      depending on dietary fibre consumption, and among these, acetate (C2), propionate (C3) and butyrate (C4) account for >95% of intestinal SCFA content.
      • Cummings J.H.
      • Pomare E.W.
      • Branch W.J.
      • Naylor C.P.
      • Macfarlane G.T.
      Short chain fatty acids in human large intestine, portal, hepatic and venous blood.
      In the gut, SCFAs maintain intestinal barrier integrity,
      • Peng L.
      • He Z.
      • Chen W.
      • Holzman I.R.
      • Lin J.
      Effects of butyrate on intestinal barrier function in a caco-2 cell monolayer model of intestinal barrier.
      and mediate mucus secretion
      • Barcelo A.
      • Claustre J.
      • Moro F.
      • Chayvialle J.A.
      • Cuber J.C.
      • Plaisancié P.
      Mucin secretion is modulated by luminal factors in the isolated vascularly perfused rat colon.
      and gut immunity.
      • Smith P.M.
      • Howitt M.R.
      • Panikov N.
      • Michaud M.
      • Gallini C.A.
      • Bohlooly-Y M.
      • et al.
      The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis.
      SCFAs also fuel colonocyte metabolism, especially butyrate, which provides up to 70% of its energy through β-oxidation.
      • Ahmad M.S.
      • Krishnan S.
      • Ramakrishna B.S.
      • Mathan M.
      • Pulimood A.B.
      • Murthy S.N.
      Butyrate and glucose metabolism by colonocytes in experimental colitis in mice.
      In fact, the colonic epithelial layer of germ-free mice is under an energy-deprived state that promotes colonocyte autophagy.
      • Donohoe D.R.
      • Garge N.
      • Zhang X.
      • Sun W.
      • O’Connell T.M.
      • Bunger M.K.
      • et al.
      The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon.
      Animal studies using 13C radiolabelling have demonstrated that absorbed SCFAs can be transported into the portal circulation,
      • Zhao S.
      • Jang C.
      • Liu J.
      • Uehara K.
      • Gilbert M.
      • Izzo L.
      • et al.
      Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate.
      from where they can reach various organs. In humans, portal blood contains on average 258 μM of acetate, 88 μM of propionate and 29 μM of butyrate, but these concentrations drop in hepatic venous circulation to 115 μM, 21 μM and 12 μM, respectively.
      • Cummings J.H.
      • Pomare E.W.
      • Branch W.J.
      • Naylor C.P.
      • Macfarlane G.T.
      Short chain fatty acids in human large intestine, portal, hepatic and venous blood.
      Peripheral blood concentration is even lower and so, compared to other tissues, the liver receives the greatest proportion of microbial SCFAs. Hepatic gene expression can be regulated by SCFAs, as they control various metabolic pathways involved in lipogenesis,
      • Zhao S.
      • Jang C.
      • Liu J.
      • Uehara K.
      • Gilbert M.
      • Izzo L.
      • et al.
      Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate.
      ,
      • Gao X.
      • Lin S.H.
      • Ren F.
      • Li J.T.
      • Chen J.J.
      • Yao C.B.
      • et al.
      Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia.
      lipolysis or fatty acid oxidation,
      • Li X.
      • Chen H.
      • Guan Y.
      • Li X.
      • Lei L.
      • Liu J.
      • et al.
      Acetic acid activates the AMP-activated protein kinase signaling pathway to regulate lipid metabolism in bovine hepatocytes.
      • Weitkunat K.
      • Schumann S.
      • Nickel D.
      • Kappo K.A.
      • Petzke K.J.
      • Kipp A.P.
      • et al.
      Importance of propionate for the repression of hepatic lipogenesis and improvement of insulin sensitivity in high-fat diet-induced obesity.
      • Zhou D.
      • Chen Y.W.
      • Zhao Z.H.
      • Yang R.X.
      • Xin F.Z.
      • Liu X.L.
      • et al.
      Sodium butyrate reduces high-fat diet-induced non-alcoholic steatohepatitis through upregulation of hepatic GLP-1R expression.
      • Mollica M.P.
      • Raso G.M.
      • Cavaliere G.
      • Trinchese G.
      • De Filippo C.
      • Aceto S.
      • et al.
      Butyrate regulates liver mitochondrial function, efficiency, and dynamics in insulin-resistant obese mice.
      • Ye J.
      • Lv L.
      • Wu W.
      • Li Y.
      • Shi D.
      • Fang D.
      • et al.
      Butyrate protects mice against methionine–choline-deficient diet-induced non-alcoholic steatohepatitis by improving gut barrier function, attenuating inflammation and reducing endotoxin levels.
      • Mattace Raso G.
      • Simeoli R.
      • Russo R.
      • Iacono A.
      • Santoro A.
      • Paciello O.
      • et al.
      Effects of sodium butyrate and its synthetic amide derivative on liver inflammation and glucose tolerance in an animal model of steatosis induced by high fat diet.
      gluconeogenesis
      • Yoshida H.
      • Ishii M.
      • Akagawa M.
      Propionate suppresses hepatic gluconeogenesis via GPR43/AMPK signaling pathway.
      ,
      • Ji X.
      • Zhou F.
      • Zhang Y.
      • Deng R.
      • Xu W.
      • Bai M.
      • et al.
      Butyrate stimulates hepatic gluconeogenesis in mouse primary hepatocytes.
      and insulin sensitivity.
      • Zhou D.
      • Chen Y.W.
      • Zhao Z.H.
      • Yang R.X.
      • Xin F.Z.
      • Liu X.L.
      • et al.
      Sodium butyrate reduces high-fat diet-induced non-alcoholic steatohepatitis through upregulation of hepatic GLP-1R expression.
      • Mollica M.P.
      • Raso G.M.
      • Cavaliere G.
      • Trinchese G.
      • De Filippo C.
      • Aceto S.
      • et al.
      Butyrate regulates liver mitochondrial function, efficiency, and dynamics in insulin-resistant obese mice.
      • Ye J.
      • Lv L.
      • Wu W.
      • Li Y.
      • Shi D.
      • Fang D.
      • et al.
      Butyrate protects mice against methionine–choline-deficient diet-induced non-alcoholic steatohepatitis by improving gut barrier function, attenuating inflammation and reducing endotoxin levels.
      SCFAs might influence hepatic metabolism via interaction with the G protein-coupled receptors GPR43/FFAR2 and GPR41/FFAR3,
      • Brown A.J.
      • Goldsworthy S.M.
      • Barnes A.A.
      • Eilert M.M.
      • Tcheang L.
      • Daniels D.
      • et al.
      The Orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids.
      but also by regulating histone deacetylases
      • Gao X.
      • Lin S.H.
      • Ren F.
      • Li J.T.
      • Chen J.J.
      • Yao C.B.
      • et al.
      Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia.
      ,
      • Zhou D.
      • Chen Y.W.
      • Zhao Z.H.
      • Yang R.X.
      • Xin F.Z.
      • Liu X.L.
      • et al.
      Sodium butyrate reduces high-fat diet-induced non-alcoholic steatohepatitis through upregulation of hepatic GLP-1R expression.
      and hormone levels.
      • Mollica M.P.
      • Raso G.M.
      • Cavaliere G.
      • Trinchese G.
      • De Filippo C.
      • Aceto S.
      • et al.
      Butyrate regulates liver mitochondrial function, efficiency, and dynamics in insulin-resistant obese mice.
      ,
      • Tirosh A.
      • Calay E.S.
      • Tuncman G.
      • Claiborn K.C.
      • Inouye K.E.
      • Eguchi K.
      • et al.
      The short-chain fatty acid propionate increases glucagon and FABP4 production, impairing insulin action in mice and humans.
      Fluxomics analyses have also revealed that SCFAs can simply serve as intermediate substrates in de novo lipid,
      • Zhao S.
      • Jang C.
      • Liu J.
      • Uehara K.
      • Gilbert M.
      • Izzo L.
      • et al.
      Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate.
      ,
      • Gao X.
      • Lin S.H.
      • Ren F.
      • Li J.T.
      • Chen J.J.
      • Yao C.B.
      • et al.
      Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia.
      cholesterol
      • den Besten G.
      • Lange K.
      • Havinga R.
      • van Dijk T.H.
      • Gerding A.
      • van Eunen K.
      • et al.
      Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids.
      and glucose
      • den Besten G.
      • Lange K.
      • Havinga R.
      • van Dijk T.H.
      • Gerding A.
      • van Eunen K.
      • et al.
      Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids.
      ,
      • Perry R.J.
      • Borders C.B.
      • Cline G.W.
      • Zhang X.M.
      • Alves T.C.
      • Petersen K.F.
      • et al.
      Propionate increases hepatic pyruvate cycling and anaplerosis and alters mitochondrial metabolism.
      synthesis in the liver.
      Besides this, SCFAs have also been reported to influence stem cell fate. It has been shown that the invaginated architecture of the intestinal epithelium, together with a natural limiting gradient imposed by diffusion, allows for the majority of butyrate to be absorbed by the surface layer of differentiated colonocytes, thus shielding stem/progenitor cells from this metabolite which would otherwise suppress their proliferative capacity.
      • Kaiko G.E.
      • Ryu S.H.
      • Koues O.I.
      • Collins P.L.
      • Solnica-Krezel L.
      • Pearce E.J.
      • et al.
      The colonic crypt protects stem cells from microbiota-derived metabolites.
      In turn, acetate is involved in goblet cell differentiation, besides increasing their mucin production and its glycosylation.
      • Wrzosek L.
      • Miquel S.
      • Noordine M.-L.
      • Bouet S.
      • Chevalier-Curt M.J.
      • Robert V.
      • et al.
      Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent.
      As the liver is a privileged site enriched in SCFA content, it is tempting to speculate that SCFAs play a role in hepatic commitment and specification, similar to what happens in the gut. In vivo data is lacking to support such an hypothesis, but in vitro butyrate is capable of promoting hepatic endoderm specification of human pluripotent stem cells (hPSCs)
      • Hay D.C.
      • Zhao D.
      • Fletcher J.
      • Hewitt Z.A.
      • McLean D.
      • Urruticoechea-Uriguen A.
      • et al.
      Efficient differentiation of hepatocytes from human embryonic stem cells exhibiting markers recapitulating liver development in vivo.
      ,
      • Du C.
      • Feng Y.
      • Qiu D.
      • Xu Y.
      • Pang M.
      • Cai N.
      • et al.
      Highly efficient and expedited hepatic differentiation from human pluripotent stem cells by pure small-molecule cocktails.
      and hepatic transdifferentiation of human fibroblasts.
      • Zhu S.
      • Wang H.
      • Ding S.
      Reprogramming fibroblasts toward cardiomyocytes, neural stem cells and hepatocytes by cell activation and signaling-directed lineage conversion.

      Amino acid catabolites

      Unlike some carbohydrates, protein fermentation in the gut can be carried out by the host or the microbiome,
      • Oliphant K.
      • Allen-Vercoe E.
      Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health.
      which brings into question the role of the microbiota in protein metabolism and renders distinction of the metabolite source more difficult. Typically, proteins that escape digestion by host proteases can be taken up by colonic bacteria (to synthesise microbial proteins) or catabolised through different pathways. Bacterial metabolites from protein catabolism positively correlate with longer transit times; as carbohydrates are depleted during transit from the proximal to the distal colon, bacteria switch from carbohydrate to protein metabolism.
      • Roager H.M.
      • Hansen L.B.S.
      • Bahl M.I.
      • Frandsen H.L.
      • Carvalho V.
      • Gøbel R.J.
      • et al.
      Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut.
      Protein fermentation can yield a wider range of metabolites, including SCFAs, branched-chain fatty acids, ammonia, amines, hydrogen sulphide, phenols and indoles.
      • Oliphant K.
      • Allen-Vercoe E.
      Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health.
      The most striking way microbial protein metabolism impacts the host is via aromatic amino acid catabolism, which yields a far more diverse set of metabolites, such as indolic and phenolic compounds. The essential amino acid tryptophan is catabolised by commensal bacteria resulting in several molecules, such as tryptamine, indole, indole-3-acetic acid (IAA), indole-3-propionic acid (IPA) and skatole. Microbiota undoubtedly play a role in systemic tryptophan balance, as corroborated by the fact that germ-free mice have increased levels of circulating tryptophan.
      • Wikoff W.R.
      • Anfora A.T.
      • Liu J.
      • Schultz P.G.
      • Lesley S.A.
      • Peters E.C.
      • et al.
      Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites.
      Indole appears to be the most abundant microbial tryptophan catabolite in the gut, at an average concentration of 2.59 mM,
      • Darkoh C.
      • Chappell C.
      • Gonzales C.
      • Okhuysen P.
      A rapid and specific method for the detection of indole in complex biological samples.
      though other derivates are still present in a μM range.
      • Lamas B.
      • Richard M.L.
      • Leducq V.
      • Pham H.P.
      • Michel M.L.
      • Da Costa G.
      • et al.
      CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.
      In the gut, tryptophan catabolites induce secretion of glucagon-like peptide 1 by enteroendocrine cells,
      • Chimerel C.
      • Emery E.
      • Summers D.K.
      • Keyser U.
      • Gribble F.M.
      • Reimann F.
      Bacterial metabolite indole modulates incretin secretion from intestinal enteroendocrine L cells.
      serve as ligands of the aryl hydrocarbon receptor (AhR) to stimulate mucosal defence
      • Qiu J.
      • Heller J.J.
      • Guo X.
      • Chen Z.M.E.
      • Fish K.
      • Fu Y.X.
      • et al.
      The aryl hydrocarbon receptor regulates gut immunity through modulation of innate lymphoid cells.
      and decrease intestinal permeability via pregnane X receptor (PXR) activation.
      • Venkatesh M.
      • Mukherjee S.
      • Wang H.
      • Li H.
      • Sun K.
      • Benechet A.P.
      • et al.
      Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and toll-like receptor 4.
      Nonetheless, tryptophan-derived compounds have been detected in human serum (indole: 0.72 μM
      • Cason C.A.
      • Dolan K.T.
      • Sharma G.
      • Tao M.
      • Kulkarni R.
      • Helenowski I.B.
      • et al.
      Plasma microbiome-modulated indole- and phenyl-derived metabolites associate with advanced atherosclerosis and postoperative outcomes.
      ; IAA: 1.30 μM
      • Rosas H.D.
      • Doros G.
      • Bhasin S.
      • Thomas B.
      • Gevorkian S.
      • Malarick K.
      • et al.
      A systems-level “misunderstanding”: the plasma metabolome in Huntington’s disease.
      ; IPA: 1.01 μM
      • Rosas H.D.
      • Doros G.
      • Bhasin S.
      • Thomas B.
      • Gevorkian S.
      • Malarick K.
      • et al.
      A systems-level “misunderstanding”: the plasma metabolome in Huntington’s disease.
      ), suggesting a potential systemic effect. Particularly in the liver, these metabolites can act via AhR to reduce inflammation
      • Krishnan S.
      • Ding Y.
      • Saedi N.
      • Choi M.
      • Sridharan G.V.
      • Sherr D.H.
      • et al.
      Gut microbiota-derived tryptophan metabolites modulate inflammatory response in hepatocytes and macrophages.
      ,
      • Ji Y.
      • Gao Y.
      • Chen H.
      • Yin Y.
      • Zhang W.
      Indole-3-acetic acid alleviates nonalcoholic fatty liver disease in mice via attenuation of hepatic lipogenesis, and oxidative and inflammatory stress.
      by modulating the NF-κB pathway
      • Beaumont M.
      • Neyrinck A.M.
      • Olivares M.
      • Rodriguez J.
      • de Rocca Serra A.
      • Roumain M.
      • et al.
      The gut microbiota metabolite indole alleviates liver inflammation in mice.
      ,
      • Zhao Z.H.
      • Xin F.Z.
      • Xue Y.
      • Hu Z.
      • Han Y.
      • Ma F.
      • et al.
      Indole-3-propionic acid inhibits gut dysbiosis and endotoxin leakage to attenuate steatohepatitis in rats.
      and attenuate cytokine-mediated lipogenesis.
      • Krishnan S.
      • Ding Y.
      • Saedi N.
      • Choi M.
      • Sridharan G.V.
      • Sherr D.H.
      • et al.
      Gut microbiota-derived tryptophan metabolites modulate inflammatory response in hepatocytes and macrophages.
      ,
      • Zhao Z.H.
      • Xin F.Z.
      • Xue Y.
      • Hu Z.
      • Han Y.
      • Ma F.
      • et al.
      Indole-3-propionic acid inhibits gut dysbiosis and endotoxin leakage to attenuate steatohepatitis in rats.
      Moreover, indole,
      • Chen G.
      • Cue R.A.
      • Lundstrom K.
      • Wood J.D.
      • Doran O.
      Regulation of CYP2A6 protein expression by skatole, indole, and testicular steroids in primary cultured pig hepatocytes.
      • Diaz G.J.
      • Squires E.J.
      Metabolism of 3-methylindole by porcine liver microsomes: responsible cytochrome P450 enzymes.
      • Banoglu E.
      • Jha G.G.
      • King R.S.
      Hepatic microsomal metabolism of indole to indoxyl, a precursor of indoxyl sulfate.
      • Banoglu E.
      • King R.S.
      Sulfation of indoxyl by human and rat aryl (phenol) sulfotransferases to form indoxyl sulfate.
      IAA
      • Sato T.
      • Yamaguchi H.
      • Kogawa T.
      • Abe T.
      • Mano N.
      Organic anion transporting polypeptides 1B1 and 1B3 play an important role in uremic toxin handling and drug-uremic toxin interactions in the liver.
      and skatole
      • Chen G.
      • Cue R.A.
      • Lundstrom K.
      • Wood J.D.
      • Doran O.
      Regulation of CYP2A6 protein expression by skatole, indole, and testicular steroids in primary cultured pig hepatocytes.
      ,
      • Diaz G.J.
      • Squires E.J.
      Metabolism of 3-methylindole by porcine liver microsomes: responsible cytochrome P450 enzymes.
      ,
      • Doran E.
      • Whittington F.W.
      • Wood J.D.
      • McGivan J.D.
      Cytochrome P450IIE1 (CYP2E1) is induced by skatole and this induction is blocked by androstenone in isolated pig hepatocytes.
      ,
      • Rasmussen M.K.
      • Balaguer P.
      • Ekstrand B.
      • Daujat-Chavanieu M.
      • Gerbal-Chaloin S.
      Skatole (3-methylindole) is a partial aryl hydrocarbon receptor agonist and induces CYP1A1/2 and CYP1B1 expression in primary human hepatocytes.
      can interact with various detoxification enzymes. Besides tryptophan, bacteria can also metabolise phenylalanine and tyrosine. The systemic effects of phenylalanine catabolites on host physiology are not yet clear, even though phenylacetic acid was found to be elevated in non-diabetic obese women with hepatic steatosis.
      • Hoyles L.
      • Fernández-Real J.M.
      • Federici M.
      • Serino M.
      • Abbott J.
      • Charpentier J.
      • et al.
      Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women.
      Tyrosine catabolism mainly yields phenolic compounds, in particular p-cresol (or 4-methylphenol), a known uremic toxin elevated in chronic kidney disease.
      • Meijers B.K.I.
      • Evenepoel P.
      The gut-kidney axis: indoxyl sulfate, p-cresyl sulfate and CKD progression.
      p-cresol is metabolised in the liver, thereby interacting with various detoxification enzymes and drug transporters,
      • Sato T.
      • Yamaguchi H.
      • Kogawa T.
      • Abe T.
      • Mano N.
      Organic anion transporting polypeptides 1B1 and 1B3 play an important role in uremic toxin handling and drug-uremic toxin interactions in the liver.
      ,
      • Barnes K.J.
      • Rowland A.
      • Polasek T.M.
      • Miners J.O.
      Inhibition of human drug-metabolising cytochrome P450 and UDP-glucuronosyltransferase enzyme activities in vitro by uremic toxins.
      ,
      • Clayton T.A.
      • Baker D.
      • Lindon J.C.
      • Everett J.R.
      • Nicholson J.K.
      Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism.
      and can be traced in urine (at an average concentration of 10.54 μM).
      • Evenepoel P.
      • Bammens B.
      • Verbeke K.
      • Vanrenterghem Y.
      Acarbose treatment lowers generation and serum concentrations of the protein-bound solute p-cresol: a pilot study.

      Secondary bile acids

      The bile acid fraction that escapes absorption (∼5%) enters the large intestine and is metabolised by gut microbes, which transform primary to secondary bile acids via reactions including deconjugation, 7α-dehydroxylation, oxidation, epimerisation, esterification and desulfation.
      • Ridlon J.M.
      • Kang D.J.
      • Hylemon P.B.
      Bile salt biotransformations by human intestinal bacteria.
      These transformations ultimately yield over 50 different secondary bile acids,
      • Setchell K.D.R.
      • Lawson A.M.
      • Tanida N.
      • Sjövall J.
      General methods for the analysis of metabolic profiles of bile acids and related compounds in feces.
      which notably increase the chemical diversity of the bile acid pool. As expected, in germ-free mice the bile acid pool is mainly composed of primary bile acids.
      • Sayin S.I.
      • Wahlström A.
      • Felin J.
      • Jäntti S.
      • Marschall H.U.
      • Bamberg K.
      • et al.
      Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist.
      Among secondary bile acids, deoxycholic acid (DCA), lithocholic acid (LCA) and ursodeoxycholic acid (UDCA), as well as their derivates, account for the majority of bile acids present in the caecum, reaching a concentration of up to 1 mM.
      • Hamilton J.P.
      • Xie G.
      • Raufman J.P.
      • Hogan S.
      • Griffin T.L.
      • Packard C.A.
      • et al.
      Human cecal bile acids: concentration and spectrum.
      They are then either absorbed by passive diffusion or excreted in faeces.
      The acquisition of hepatic maturity is a complex and undefined process that is thought to be mediated by a set of events occurring both at the environmental and cellular levels.
      Over the past decades, both primary and secondary bile acids have been recognised as signalling molecules. Bacterially modified bile acids were shown to modulate gene expression as well as cell survival and proliferation. Perhaps the most well-known example is the regulation of bile acid synthesis, which is under negative feedback control – through farnesoid X receptor (FXR) activation. Both DCA and LCA serve as agonists of hepatic FXR, resulting in inhibition of CYP7A1, the rate-limiting enzyme in bile acid synthesis, and thus the repression of overall de novo synthesis.
      • Makishima M.
      • Okamoto A.Y.
      • Repa J.J.
      • Tu H.
      • Learned R.M.
      • Luk A.
      • et al.
      Identification of a nuclear receptor for bile acids.
      Albeit to a lesser extent, DCA has also proven capable of inhibiting other enzymes involved in bile acid synthesis, such as CYP8B1
      • Zhang M.
      • Chiang J.Y.L.
      Transcriptional regulation of the human sterol 12α-hydroxylase gene (CYP8B1): roles of hepatocyte nuclear factor 4α in mediating bile acid repression.
      and CYP27A1,
      • Chen W.
      • Chiang J.Y.L.
      Regulation of human sterol 27-hydroxylase gene (CYP27A1) by bile acids and hepatocyte nuclear factor 4α (HNF4α).
      through FXR-independent mechanisms.
      • Gupta S.
      • Natarajan R.
      • Payne S.G.
      • Studer E.J.
      • Spiegel S.
      • Dent P.
      • et al.
      Deoxycholic acid activates the c-Jun N-terminal kinase pathway via FAS receptor activation in primary hepatocytes: role of acidic sphingomyelinase-mediated ceramide generation in FAS receptor activation.
      Interestingly, LCA has been reported to function mainly as a FXR antagonist, inhibiting the bile salt export pump (BSEP, encoded by ABCB11) that consequently represses bile acid transport to the bile canaliculi.
      • Yu J.
      • Lo J.L.
      • Huang L.
      • Zhao A.
      • Metzger E.
      • Adams A.
      • et al.
      Lithocholic acid decreases expression of bile salt export pump through farnesoid X receptor antagonist activity.
      Unlike its more hydrophobic counterparts, the secondary bile acid UDCA interacts poorly with FXR.
      • Wang H.
      • Chen J.
      • Hollister K.
      • Sowers L.C.
      • Forman B.M.
      Endogenous bile acids are ligands for the nuclear receptor FXR/BAR.
      However, the hydrophobicity of bile acids can be toxic to hepatocytes, so their proper clearance (either excretion or reconjugation) is of utmost importance. In particular, LCA can activate PXR
      • Staudinger J.L.
      • Goodwin B.
      • Jones S.A.
      • Hawkins-Brown D.
      • MacKenzie K.I.
      • LaTour A.
      • et al.
      The nuclear receptor PXR is a lithocholic acid sensor that protects against liver toxicity.
      • Xie W.
      • Radominska-Pandya A.
      • Shi Y.
      • Simon C.M.
      • Nelson M.C.
      • Ong E.S.
      • et al.
      An essential role for nuclear receptors SXR/PXR in detoxification of cholestatic bile acids.
      • Avior Y.
      • Levy G.
      • Zimerman M.
      • Kitsberg D.
      • Schwartz R.
      • Sadeh R.
      • et al.
      Microbial-derived lithocholic acid and vitamin K2 drive the metabolic maturation of pluripotent stem cells-derived and fetal hepatocytes.
      and vitamin D receptor,
      • Makishima M.
      • Lu T.T.
      • Xie W.
      • Whitfield G.K.
      • Domoto H.
      • Evans R.M.
      • et al.
      Vitamin D receptor as an intestinal bile acid sensor.
      which induces expression of genes involved in detoxification of xenobiotics.
      Aside from nuclear receptors, bile acids have also been reported to interact with the G-protein receptor TGR5
      • Kawamata Y.
      • Fujii R.
      • Hosoya M.
      • Harada M.
      • Yoshida H.
      • Miwa M.
      • et al.
      A G proteincoupled receptor responsive to bile acids.
      in peripheral tissues, particularly in brown adipose tissue, where TGR5 activation increases intracellular cAMP levels to promote energy expenditure.
      • Watanabe M.
      • Houten S.M.
      • Mataki C.
      • Christoffolete M.A.
      • Kim B.W.
      • Sato H.
      • et al.
      Bile acids induce energy expenditure by promoting intracellular thyroid hormone activation.
      Even though TGR5 is solely expressed in hepatic non-parenchymal cells,
      • Keitel V.
      • Reinehr R.
      • Gatsios P.
      • Rupprecht C.
      • Görg B.
      • Selbach O.
      • et al.
      The G-protein coupled bile salt receptor TGR5 is expressed in liver sinusoidal endothelial cells.
      secondary bile acids can serve as ligands in mitogen-activated protein kinase pathways
      • Dent P.
      • Fang Y.
      • Gupta S.
      • Studer E.
      • Mitchell G.
      • Spiegel S.
      • et al.
      Conjugated bile acids promote ERK1/2 and AKT activation via a pertussis toxin-sensitive mechanism in murine and human hepatocytes.
      ,
      • Studer E.
      • Zhou X.
      • Zhao R.
      • Wang Y.
      • Takabe K.
      • Nagahashi M.
      • et al.
      Conjugated bile acids activate the sphingosine-1-phosphate receptor 2 in primary rodent hepatocytes.
      and still be able to regulate hepatic energy metabolism.
      Dysregulated gut-liver crosstalk – mediated by secondary bile acids – may be detrimental to hepatocytes, ultimately compromising cell viability and liver function. DCA elevations induce apoptosis
      • Ferreira D.M.S.
      • Afonso M.B.
      • Rodrigues P.M.
      • Simão A.L.
      • Pereira D.M.
      • Borralho P.M.
      • et al.
      c-Jun N-terminal kinase 1/c-Jun activation of the p53/MicroRNA 34a/sirtuin 1 pathway contributes to apoptosis induced by deoxycholic acid in rat liver.
      • Rodrigues P.M.
      • Afonso M.B.
      • Simão A.L.
      • Borralho P.M.
      • Rodrigues C.M.P.
      • Castro R.E.
      Inhibition of NF-κ B by deoxycholic acid induces miR-21/PDCD4-dependent hepatocelular apoptosis.
      • Qiao L.
      • Studer E.
      • Leach K.
      • McKinstry R.
      • Gupta S.
      • Decker R.
      • et al.
      Deoxycholic acid (DCA) causes ligand-independent activation of epidermal growth factor receptor (EGFR) and FAS receptor in primary hepatocytes: inhibition of EGFR/mitogen-activated protein kinase-signaling module enhances DCA-induced apoptosis.
      and oxidative stress
      • Rodrigues P.M.
      • Afonso M.B.
      • Simão A.L.
      • Borralho P.M.
      • Rodrigues C.M.P.
      • Castro R.E.
      Inhibition of NF-κ B by deoxycholic acid induces miR-21/PDCD4-dependent hepatocelular apoptosis.
      ,
      • Rodrigues C.M.
      • Ma X.
      • Linehan-Stieers C.
      • Fan G.
      • Kren B.T.
      • Steer C.J.
      Ursodeoxycholic acid prevents cytochrome c release in apoptosis by inhibiting mitochondrial membrane depolarization and channel formation.
      ,
      • Hino A.
      • Morita M.
      • Une M.
      • Fujimura K.
      • Kuramoto T.
      Effects of deoxycholic acid and its epimers on lipid peroxidation in isolated rat hepatocytes.
      in hepatocytes, while UDCA is hepatoprotective during liver injury as it promotes cell survival
      • Castro R.E.
      • Ferreira D.M.S.
      • Afonso M.B.
      • Borralho P.M.
      • Machado M.V.
      • Cortez-Pinto H.
      • et al.
      miR-34a/SIRT1/p53 is suppressed by ursodeoxycholic acid in the rat liver and activated by disease severity in human non-alcoholic fatty liver disease.
      • Azzaroli F.
      • Mehal W.
      • Soroka C.J.
      • Wang L.
      • Lee J.
      • Crispe N.
      • et al.
      Ursodeoxycholic acid diminishes Fas-ligand-induced apoptosis in mouse hepatocytes.
      • Schoemaker M.H.
      • Conde de la Rosa L.
      • Buist-Homan M.
      • Vrenken T.E.
      • Havinga R.
      • Poelstra K.
      • et al.
      Tauroursodeoxycholic acid protects rat hepatocytes from bile acid-induced apoptosis via activation of survival pathways.
      • Tanaka M.
      • Nakura H.
      • Tateishi T.
      • Watanabe M.
      • Nakaya S.
      • Kumai T.
      • et al.
      Ursodeoxycholic acid prevents hepatic cytochrome P450 isozyme reduction in rats with deoxycholic acid-induced liver injury.
      and acts as an antioxidant agent.
      • Rodrigues C.M.
      • Ma X.
      • Linehan-Stieers C.
      • Fan G.
      • Kren B.T.
      • Steer C.J.
      Ursodeoxycholic acid prevents cytochrome c release in apoptosis by inhibiting mitochondrial membrane depolarization and channel formation.
      ,
      • Rodrigues C.M.
      • Fan G.
      • Wong P.Y.
      • Kren B.T.
      • Steer C.J.
      Ursodeoxycholic acid may inhibit deoxycholic acid-induced apoptosis by modulating mitochondrial transmembrane potential and reactive oxygen species production.
      ,
      • Mitsuyoshi H.
      • Nakashima T.
      • Sumida Y.
      • Yoh T.
      • Nakajima Y.
      • Ishikawa H.
      • et al.
      Ursodeoxycholic acid protects hepatocytes against oxidative injury via induction of antioxidants.
      Nonetheless, the coordinated action of bile acids is critical during tissue- and even organ-level responses to hepatic injuries, as shown by reduced liver regrowth following partial hepatectomy in Fxr-/- mice.
      • Huang W.
      • Ma K.
      • Zhang J.
      • Qatanani M.
      • Cuvillier J.
      • Liu J.
      • et al.
      Nuclear receptor-dependent bile acid signaling is required for normal liver regeneration.
      This effect is particularly evident for secondary bile acids.
      • Kren B.T.
      • Rodrigues C.M.
      • Setchell K.D.R.
      • Steer C.J.
      Modulation of steady-state messenger RNA levels in the regenerating rat liver with bile acid feeding.
      ,
      • Barone M.
      • Francavilla A.
      • Polimeno L.
      • Ierardi E.
      • Romanelli D.
      • Berloco P.
      • et al.
      Modulation of rat hepatocyte proliferation by bile salts: in vitro and in vivo studies.

      Vitamins

      Vitamins participate in vital biochemical reactions in almost every cell of the human body. Human cells are unable to synthesise them in sufficient quantities to meet their needs, so vitamin acquisition is heavily reliant upon diet. Surprisingly, gut bacteria regulate both biosynthesis and metabolism of several essential vitamins. Following the establishment of the first germ-free animals, the role of gut microbes as a source of vitamins has become evident, since these animals require dietary vitamin supplementation,
      • Wostmann B.S.
      The germfree animal in nutritional studies.
      especially B and K vitamins, which is not needed by their conventional eubiotic counterparts.
      Despite B vitamins mainly being absorbed across the small intestine, B vitamins (mainly of bacterial origin) are also absorbed along the colon. A comprehensive study analysed genome annotations of 256 common gut bacteria and revealed an intricate cooperation between bacteria across distinct B vitamin biosynthetic pathways.
      • Magnúsdóttir S.
      • Ravcheev D.
      • de Crécy-Lagard V.
      • Thiele I.
      Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes.
      It also became clear that gut-resident bacteria cannot provide the host with the daily recommended intake of B vitamins, and even those that are produced in higher amounts (e.g., pyridoxine, folate and niacin) are possibly taken up by host-competing microbes in order to ensure cooperative ecosystem survival. Nonetheless, microbial B vitamins likely impact host health, as illustrated by the fact that infantile malnutrition has been associated with underrepresentation of bacteria involved in niacin/NADP biosynthesis in the gut microbiome.
      • Gehrig J.L.
      • Venkatesh S.
      • Chang H.W.
      • Hibberd M.C.
      • Kung V.L.
      • Cheng J.
      • et al.
      Effects of microbiota-directed foods in gnotobiotic animals and undernourished children.
      In fact, B vitamins shape the gut environment in numerous ways. For instance, thiamine is needed for B cell immunometabolism,
      • Kunisawa J.
      • Sugiura Y.
      • Wake T.
      • Nagatake T.
      • Suzuki H.
      • Nagasawa R.
      • et al.
      Mode of bioenergetic metabolism during B cell differentiation in the intestine determines the distinct requirement for vitamin B1.
      pyridoxine/folate participate in host-microbiome drug co-metabolism
      • Scott T.A.
      • Quintaneiro L.M.
      • Norvaisas P.
      • Lui P.P.
      • Wilson M.P.
      • Leung K.Y.
      • et al.
      Host-microbe Co-metabolism dictates cancer drug efficacy in C. elegans.
      and cobalamin influences microbe fitness.
      • Goodman A.L.
      • McNulty N.P.
      • Zhao Y.
      • Leip D.
      • Mitra R.D.
      • Lozupone C.A.
      • et al.
      Identifying genetic determinants needed to establish a human gut symbiont in its habitat.
      Notwithstanding, microbial B vitamins can enter systemic circulation and reach peripheral tissues. At a cellular level, B vitamins can function as coenzymes in a myriad of biological processes, namely those related to carbohydrate,
      • Danner D.J.
      • Davidson E.D.
      • Elsas L.J.
      Thiamine increases the specific activity of human liver branched chain α-ketoacid dehydrogenase.
      ,
      • Knowles J.R.
      The mechanism of biotin-dependent enzymes.
      fatty acid,
      • Knowles J.R.
      The mechanism of biotin-dependent enzymes.
      • Barile M.
      • Brizio C.
      • Valenti D.
      • De Virgilio C.
      • Passarella S.
      The riboflavin/FAD cycle in rat liver mitochondria.
      • Rucker R.B.
      Pantothenic acid.
      glucose,
      • Barile M.
      • Brizio C.
      • Valenti D.
      • De Virgilio C.
      • Passarella S.
      The riboflavin/FAD cycle in rat liver mitochondria.