Although hypothesis-driven science has immense value, it depends to a considerable degree on a framework of maps, tools, and standards whose development often does not fit meaningfully into a hypothesis-driven framework and is therefore heavily criticized in settings such as grant review panels. However, without these types of development, hypotheses more explicit than “differences in the microbiome” or “elevation or depletion of specific taxa or molecules” cannot be tested, and completely new ideas about how to read out or control the microbiome will not be developed. Extraordinary advances in data collection technologies leave us in a world where we regularly make millions of observations of organisms about which we know virtually nothing — as exemplified by the recent ‘discovery’ of the most abundant phage in the human gut via metagenome mining . The amount of information contained in these observations in principle is enough to allow us to fine-tune more labor-intensive experiments to test critical questions with great efficiency. In practice, though, much of this information remains inaccessible. In order tobring about a future of precision medicine and precision ecological remediation, where we can specify precise microbiome changes and bring them about through defined interventions, a vast amount of non-hypothesis-driven research, often dismissed as “technical work” or “fishing expeditions”, remains to be done.In the past decade, an exciting realization has been that diverse liver diseases—ranging from NASH,growing raspberries in pots alcoholic steatohepatitis and cirrhosis, to hepatocellular carcinoma—fall along a spectrum.

Work on the biology of the gut-liver axis has assisted in understanding the basic biology of both alcoholic fatty liver disease and NAFLD. Of immense importance is the advancement in understanding of the role of the microbiome, driven by high-throughput DNA sequencing and improved computational techniques that enable the complexity of the microbiome to be interrogated, together with improved experimental designs. Here, we review gut–liver communications in liver disease, explore the molecular, genetic and microbiome relationships, and discuss prospects for exploiting the microbiome to determine liver disease stage and to predict the effects of pharmaceutical, dietary and other interventions at a population and individual level. Although much work remains to be done in understanding the relationship between the microbiome and liver disease, rapid progress towards clinical applications is being made, especially in study designs that complement human intervention studies with mechanistic work in mice that have been humanized in multiple respects, including the genetic, immunological and microbiome characteristics of individual patients. These ‘avatar mice’ could be especially useful for guiding new microbiome-based or microbiome-informed therapies.The crosstalk between the gut and liver is increasingly recognized, strengthened by the parallel rise in incidence of liver diseases and gastrointestinal and immune disorders . The most common type of liver disease, NAFLD, affects >65 million Americans with a cost burden of US$103 billion annually within the USA .

To manage the socioeconomic burden of gastrointestinal-associated liver diseases by developing new therapeutic modalities, specific molecular events that facilitate interaction between the gut and the liver must be elucidated. As we begin to appreciate these links, animal models and well-designed clinical studies are already revealing key components of these interactions. The present understanding of the etiology of the spectrum of liver diseases is underpinned by proinflammatory changes in the host. Intestinal dysbiosis and increased intestinal permeability leads to translocation of microbes and microbial products including cell wall components and DNA, together referred to as microbial- associated molecular patterns . These patterns are recognized by immune receptors on liver cells and intestinal lamina propria , which initiate and maintain inflammatory cascades that ultimately lead to liver damage in the form of fibrosis . This damage can progress from cirrhosis to hepatocellular carcinoma , the most predominant form of primary liver cancer . Previously demonstrated associations between intestinal health and several different types of neoplasia suggest a potential role of the microbiota in HCC . Additionally, the liver and microbiota engage in co-metabolism of xenobiotics including carcinogens which can independently predispose the host to HCC . The missing links in the complex interaction network between host and microorganisms are being discovered piece by piece using various experimental designs . These findings encourage microbiome-oriented therapeutic modalities to treat liver-associated and other metabolic diseases. Here, we review the current understanding of the aetiology of liver diseases and highlight the open research questions to motivate focused research in this area with special attention to the role of the microbiome.

Bile acids are amphipathic molecules synthesized from cholesterol in the pericentral hepatocytes. On reaching the small intestine through theduodenum, BAs, together with other biliary components, facilitate emulsification and absorption of dietary fats, cholesterol and fat-soluble vitamins. About 95% of the BAs are actively reabsorbed in the terminal ileum and transported back to the liver . The remaining 5% are deconjugated, dehydrogenated and dehydroxylated by the colonic microbiota to form secondary bile acids, which reach the liver via passive absorption into the portal circulation . The liver recycles BAs and secretes them back to the biliary tract completing the so-called enterohepatic circulation, that is, a system of exchange between the gut and the liver. A carrier-mediated process transports hydrophilic primary BAs across cell membranes for uptake into intestinal epithelial cells. Regulatory effects of BAs have been best studied with respect to farnesoid X receptor and takeda G-protein-coupled receptor 5 . BAs bind to FXR in the enterocytes and induce transcription of an enterokine, fibroblast growth factor 19 . FGF19 reaches the liver through the portal vein and downregulates de novo bile acid synthesis by inhibiting CYP7A1 in hepatocytes, forming a feedback system for modulating BA production . FXR activation is known to affect glucose and lipid metabolism . Additionally, BAs bind to TGR5 on the plasma membrane and act on tissues beyond enterohepatic circulation. This binding mediates host energy expenditure , glucose homeostasis and anti-inflammatory immune responses . BAs and the gut microbiota closely interact and modulate each other; BAs exert direct control on the intestinal microbiota. By binding to FXR, they induce production of antimicrobial peptides such as angogenin1 and RNAse family member 4, which are directly involved in inhibiting gut microbial overgrowth and subsequent gut barrier dysfunction . Intestinal dysbiosis shifts the balance between primary and secondary bile acids and their subsequent enterohepatic cycling, the metabolic effects of which are not comprehensively understood. However, because of differences in the affinity of these two classes of BAs for FXR, these shifts have been associated with changes in hepatic bile acid synthesis and metabolic stress . An imbalance in BAs and gut bacteria elicits a cascade of host immune responses relevant to the progression of liver diseases.The central components of the intestinal barrier are enterocytes that are tightly bound to adjacent cells by apical junctional proteins that include claudins, occludins, E-cadherins, desmosomes, and junctional adhesion molecules . This barrier restricts movement of microbes and molecules from the gut lumen, while allowing permselective, active transport of nutrients across the tight junctions. The intestinal barrier is further strengthened by several additional lines of defense. Mucins form a physical barrier between luminal bacteria and the underlying epithelial layer , and antibacterial lectins, such as regenerating islet-derived protein III-gamma ,plant pot with drainage which are produced by intestinal Paneth cells to target bacteria associated with mucosal lining . Moreover, immunoglobulins produced by plasma cells and transported into the lumen through the intestinal epithelial cells neutralize microbial pathogens by blockading epithelial receptors . Finally, commensal bacteria are closely associated with the gut mucosa, and reinforce barrier integrity by stimulating cell-mediated immunity via Toll-like receptor mediated signaling or by producing metabolites that directly strengthen tight junctions  and inhibit other microbes . Breakdown of one or more of these barrier components compromises gut-barrier integrity. The major drivers of increased permeability include gut inflammation and dysbiosis , which have been linked to consumption of a high-fat Western diet , chronic alcohol consumption , prolonged antibiotic usage and immune-mediated inflammatorydiseases such as IBD . An important association between the gut microbiota, inflammation and gut-barrier integrity is provided by Akkermansia muciniphila, a Gram-negative anaerobe that colonizes the intestinal mucus layer. Reduced abundance of A. muciniphila has been associated with thinning of mucus layer and increased inflammation, which promotes both, alcoholic and nonalcoholic liver damage . When the gut barrier is compromised, microbes and microbederived molecules can translocate to the liver through the portal system, causing inflammation and hepatic injury .

Some translocated intestinal products might also directly interact with host factors and contribute to exacerbation of liver disease .Bacteria and MAMPs: Intestinal permeability is characterized by compromised tight junctions between enterocytes, and is consistently seen across the spectrum of liver diseases . Liver damage is associated with small intestinal bacterial overgrowth and dysbiosis of the lower gastrointestinal tract . Together, these processes lead to increased translocation of MAMPs into the portal circulation. On reaching the liver, MAMPs induce localized inflammation through pattern-recognition receptors on Kupffer cells and hepatic stellate cells . Endotoxin-mediated activation of Toll-like receptor 4 along with TLR9 and TLR2 are the primary drivers of immune response in liver disease. TLR signaling in Kupffer cells activates a downstream proinflammatory cascade, leading to MyD88-mediated activation of NF-kB . Additionally, TLR4 signaling also promotes fibrosis by downregulating Bambi in hepatic stellate cells . These steps lead to expression of inflammatory cytokines, oxidative and endoplasmic reticulum stress, and subsequent liver damage .Choline is a macro-nutrient that is important for liver function, brain development, nerve function, muscle movement and maintaining a healthy metabolism ; notably, rodents fed a choline-deficient diet have been used to model human NASH . Choline is processed into phosphatidylcholine by the host, which assists in excretion of very-low-density lipoproteins particles from the liver. This process prevents hepatic accumulation of triglycerides . Additionally, choline can also be converted to trimethylamine by intestinal bacteria; TMA can translocate to the liver through the portal circulation where it is converted to trimethylamine N-oxide . The significance of methylamines is increasingly being recognized with respect to liver, cardiometabolic and more recently, neurological disorders . Increased systemic circulation of TMAO is concomitant with reduced levels of host-produced phosphatidylcholine, an imbalance characteristic of intestinal dysbiosis. TMAO has been linked with liver damage due to increased triglyceride accumulation and, consequently, NAFLD . Free fatty acids include SCFAs and long-chain fatty acids . Butyrate, propionate and acetate are the dominant SCFAs in the large intestine. Butyrate is an energy source for the enterocytes and facilitates maintenance of the intestinal barrier . Alcohol-induced liver injury is suggested to be marked by reduced levels of butyrate and propionate and increased levels of acetate . Increased levels of acetaldehyde can weaken gut barrier 86 and induce hepatic stress on translocation of intestinal antigens to the liver . Butyrate supplementation in the form of a glycerol ester, tributyrin, reduced ethanol induced intestinal permeability and subsequent liver injury in mice on a short-term alcohol diet . However, how tributyrin mechanistically protects the intestinal barrier remains to be established. Luminal species of LCFAs include pentadecanoic acid , palmitic acid , heptadecanoic acid , and stearic acid . In mice fed alcohol chronically, C15:0 and C17:0, which are only produced by bacterial fermentation, are markedly reduced when compared with control mice on isocaloric diet . There is also an overall reduction in total saturated LCFA levels which is associated with decreased luminal abundance of lactobacilli . To our knowledge, restoring Lactobacillus spp. by LCFA supplementation has not been experimentally demonstrated. However, dietary supplementation of Lactobacillus rhamnosus has been shown to increase luminal LCFA levels , suggesting that Lactobacillus-induced increase in intestinal FFAs contribute to its probiotic effects .The mucosa of the gastrointestinal tract absorbs ethanol by simple diffusion. Within the gastrointestinal tract, the majority of ethanol from food and beverages is absorbed by the stomach and small intestine . Although, microbial fermentation contributes to luminal ethanol concentration, the biggest share of alcohol in the large intestine comes from the systemic circulation . Gut microbiota and enterocytes express alcohol-metabolizing enzymes such as alcohol dehydrogenase, which co-metabolizes ethanol into acetaldehyde and, to a lesser-studied extent, acetate. The liver also responds to circulating levels of ethanol by upregulating its ethanol metabolism pathway .