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• W3003277102 abstract "Patients with chronic liver disease and cirrhosis demonstrate a global mucosal immune impairment, which is associated with altered gut microbiota composition and functionality. These changes progress along with the advancing degree of cirrhosis and can be linked with hepatic encephalopathy, infections and even prognostication independent of clinical biomarkers. Along with compositional changes, functional alterations to the microbiota, related to short-chain fatty acids, bioenergetics and bile acid metabolism, are also associated with cirrhosis progression and outcomes. Altering the functional and structural profile of the microbiota is partly achieved by medications used in patients with cirrhosis such as rifaximin, lactulose, proton pump inhibitors and other antibiotics. However, the role of faecal or intestinal microbiota transplantation is increasingly being recognised. Herein, we review the challenges, opportunities and road ahead for the appropriate and safe use of intestinal microbiota transplantation in liver disease. Patients with chronic liver disease and cirrhosis demonstrate a global mucosal immune impairment, which is associated with altered gut microbiota composition and functionality. These changes progress along with the advancing degree of cirrhosis and can be linked with hepatic encephalopathy, infections and even prognostication independent of clinical biomarkers. Along with compositional changes, functional alterations to the microbiota, related to short-chain fatty acids, bioenergetics and bile acid metabolism, are also associated with cirrhosis progression and outcomes. Altering the functional and structural profile of the microbiota is partly achieved by medications used in patients with cirrhosis such as rifaximin, lactulose, proton pump inhibitors and other antibiotics. However, the role of faecal or intestinal microbiota transplantation is increasingly being recognised. Herein, we review the challenges, opportunities and road ahead for the appropriate and safe use of intestinal microbiota transplantation in liver disease. Changes in the composition and functionality of intestinal microbiota contribute to the progression of chronic liver disease and make an attractive target for intervention.[1]Schnabl B. Brenner D.A. Interactions between the intestinal microbiome and liver diseases.Gastroenterology. 2014; 146: 1513-1524Abstract Full Text Full Text PDF PubMed Scopus (379) Google Scholar,[2]Wiest R. Albillos A. Trauner M. Bajaj J.S. Jalan R. Targeting the gut-liver axis in liver disease.J Hepatol. 2017; 67: 1084-1103Abstract Full Text Full Text PDF PubMed Scopus (85) Google Scholar While various intrinsic and extrinsic factors, such as ethnicity, age, diet, co-morbid conditions and medications affect the intestinal microbiota (Fig. 1),[3]Allaband C. McDonald D. Vazquez-Baeza Y. Minich J.J. Tripathi A. Brenner D.A. et al.Microbiome 101: studying, analyzing, and interpreting gut microbiome data for clinicians.Clin Gastroenterol Hepatol. 2019; 17: 218-230Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar further unique co-variates, such as alcohol, disease aetiology, stage of liver disease, and the multiple microbiota-modifying medications need to be considered in these patients.[4]Acharya C. Bajaj J.S. Altered microbiome in patients with cirrhosis and complications.Clin Gastroenterol Hepatol. 2019; 17: 307-321Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar In addition, it is important to remember that most liver diseases are lifestyle-related and therapies targeting the microbiota represent only one aspect of the multi-pronged interventional approach that is needed in these patients.4Acharya C. Bajaj J.S. Altered microbiome in patients with cirrhosis and complications.Clin Gastroenterol Hepatol. 2019; 17: 307-321Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar, 5Asrani S.K. Devarbhavi H. Eaton J. Kamath P.S. Burden of liver diseases in the world.J Hepatol. 2019; 70: 151-171Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar, 6Bajaj J.S. Alcohol, liver disease and the gut microbiota.Nat Rev Gastroenterol Hepatol. 2019; 16: 235-246Crossref PubMed Scopus (22) Google Scholar Of late, faecal or intestinal microbiota transplantation or FMT/IMT has been increasingly used in chronic liver disease.[7]Hatton G. Shawcross D.L. Is treating the gut microbiome the key to achieving better outcomes in cirrhosis?.Expert Rev Gastroenterol Hepatol. 2019; 13: 1-2Crossref PubMed Scopus (1) Google Scholar This review will focus on microbiota changes in human patients with chronic liver disease and the current and future FMT/IMT studies in this population. We will discuss FMT/IMT from a pharmacological perspective and refer to the treatment strategy as ‘IMT’, as recently advocated to avoid the common tendency to morph it into the inaccurate ‘faecal transplant’.[8]Khoruts A. Brandt L.J. Fecal microbiota transplant: a rose by any other name.Am J Gastroenterol. 2019; 114: 1176Crossref PubMed Scopus (2) Google Scholar The focus of this review is to describe studies on the use of IMT in patients with cirrhosis. It also includes a brief overview of changes in the pre-cirrhotic and alcoholic hepatitis stages. Further reading on interpretation and evaluation of microbiota in general and specifically in alcoholic liver disease and alcoholic hepatitis are discussed in reviews by Allaband et al.[3]Allaband C. McDonald D. Vazquez-Baeza Y. Minich J.J. Tripathi A. Brenner D.A. et al.Microbiome 101: studying, analyzing, and interpreting gut microbiome data for clinicians.Clin Gastroenterol Hepatol. 2019; 17: 218-230Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar and Bajaj et al.[6]Bajaj J.S. Alcohol, liver disease and the gut microbiota.Nat Rev Gastroenterol Hepatol. 2019; 16: 235-246Crossref PubMed Scopus (22) Google Scholar Of note, most studies in cirrhosis in humans have used 16S rRNA sequencing and not the more in-depth metagenomics. Also, several studies have performed linkages between metabolomics and bacterial function and microbiota composition, while others have reported composition and/or implied functionality. Changes in microbiota are found in several liver diseases with distinct aetiologies in the pre-cirrhotic stage. Most studies have been performed in non-alcoholic fatty liver disease (NAFLD) and alcohol-related liver disease, while autoimmune hepatitis (AIH), primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) have been studied in a few instancesKey pointCirrhosis and chronic liver disease are associated with alterations in microbiota composition and function, which start in the pre-cirrhotic phase for most disease aetiologies and are affected by several cirrhosis-related and unrelated factors.. Cirrhosis and chronic liver disease are associated with alterations in microbiota composition and function, which start in the pre-cirrhotic phase for most disease aetiologies and are affected by several cirrhosis-related and unrelated factors. Alcohol and microbiota: multiple studies evaluated the stool, salivary and circulating microbiota across the spectrum of alcohol-related liver disease.[6]Bajaj J.S. Alcohol, liver disease and the gut microbiota.Nat Rev Gastroenterol Hepatol. 2019; 16: 235-246Crossref PubMed Scopus (22) Google Scholar This ranges from healthy controls who consume alcohol to patients who develop alcoholic hepatitis.[9]Szabo G. Gut-liver axis in alcoholic liver disease.Gastroenterology. 2015; 148: 30-36Abstract Full Text Full Text PDF PubMed Scopus (226) Google Scholar Most patients with alcoholic hepatitis have cirrhosis, therefore, these changes are described in the section below. These changes are commensurate with bacterial and fungal composition, as well as their products such as secondary bile acids.[10]Yang A.M. Inamine T. Hochrath K. Chen P. Wang L. Llorente C. et al.Intestinal fungi contribute to development of alcoholic liver disease.J Clin Invest. 2017; 127: 2829-2841Crossref PubMed Scopus (84) Google Scholar,[11]Mutlu E.A. Gillevet P.M. Rangwala H. Sikaroodi M. Naqvi A. Engen P.A. et al.Colonic microbiome is altered in alcoholism.Am J Physiol Gastrointest Liver Physiol. 2012; 302: G966-G978Crossref PubMed Scopus (278) Google Scholar Continuing alcohol misuse in patients with cirrhosis and alcohol-related liver disease further worsens dysbiosis, changes bile acids and can lead to the development of alcoholic hepatitis.[12]Bajaj J.S. Kakiyama G. Zhao D. Takei H. Fagan A. Hylemon P. et al.Continued alcohol misuse in human cirrhosis is associated with an impaired gut-liver axis.Alcohol Clin Exp Res. 2017; 41: 1857-1865Crossref PubMed Scopus (27) Google Scholar Increasing severity of liver disease is associated with worsening of dysbiosis, characterised by a decrease in bacterial diversity and increases in relative abundances of Enterobacteriaceae and Enterococcaceae, which are potentially pathogenic as they are more prone to gut translocation.13Llopis M. Cassard A.M. Wrzosek L. Boschat L. Bruneau A. Ferrere G. et al.Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease.Gut. 2016; 65: 830-839Crossref PubMed Scopus (130) Google Scholar, 14Llorente C. Jepsen P. Inamine T. Wang L. Bluemel S. Wang H.J. et al.Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.Nat Commun. 2017; 8: 837Crossref PubMed Scopus (46) Google Scholar, 15Pinzone M.R. Celesia B.M. Di Rosa M. Cacopardo B. Nunnari G. Microbial translocation in chronic liver diseases.Int J Microbiol. 2012; 2012: 694629Crossref PubMed Scopus (60) Google Scholar These microbial changes and concomitant increased intestinal permeability are variably reversed after successful alcohol cessation.[16]Leclercq S. Matamoros S. Cani P.D. Neyrinck A.M. Jamar F. Starkel P. et al.Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity.Proc Natl Acad Sci U S A. 2014; 111: E4485-E4493Crossref PubMed Scopus (242) Google Scholar NAFLD and microbiota: NAFLD, which includes simple steatosis, non-alcoholic steatohepatitis (NASH) and cirrhosis, has been studied extensively from a microbiota standpoint. A special challenge when assessing changes in the microbiota in NAFLD is the overlay of diabetes, metabolic syndrome and obesity.[17]Young V.B. The role of the microbiome in human health and disease: an introduction for clinicians.BMJ. 2017; 356: j831Crossref PubMed Scopus (105) Google Scholar This often makes it difficult to differentiate between the contribution of the liver disease vs. the underlying metabolic factors that co-exist with it. Most studies have shown an increase in relative abundances of Enterobacteraceae in stool and endotoxemia as disease progresses.[18]Boursier J. Mueller O. Barret M. Machado M. Fizanne L. Araujo-Perez F. et al.The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.Hepatology. 2016; 63: 764-775Crossref PubMed Scopus (284) Google Scholar In paediatric NASH, where the concomitant impact of alcohol use is unlikely, there have been interesting reports of alcohol-producing bacteria.[19]Zhu L. Baker S.S. Gill C. Liu W. Alkhouri R. Baker R.D. et al.Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH.Hepatology. 2013; 57: 601-609Crossref PubMed Scopus (0) Google Scholar This finding was subsequently confirmed in adult studies.[20]Yuan J. Chen C. Cui J. Lu J. Yan C. Wei X. et al.Fatty liver disease caused by high-alcohol-producing Klebsiella pneumoniae.Cell Metab. 2019; 30: 675-688.e7Abstract Full Text Full Text PDF PubMed Scopus (12) Google Scholar Thus, it is possible that endogenously produced alcohol from microbiota can cause fatty liver disease. These widespread microbial changes have been described in the circulating and hepatic microbiome in recent studies,[21]Lelouvier B. Servant F. Paisse S. Brunet A.C. Benyahya S. Serino M. et al.Changes in blood microbiota profiles associated with liver fibrosis in obese patients: a pilot analysis.Hepatology. 2016; 64: 2015-2027Crossref PubMed Scopus (63) Google Scholar,[22]Sookoian S. Salatino A. Castano G.O. Landa M.S. Fijalkowky C. Garaycoechea M. et al.Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease.Gut. 2020; Crossref PubMed Scopus (1) Google Scholar although changes in the circulating microbiome have been disputed vis-à-vis contaminants.[23]Hornung B.V.H. Zwittink R.D. Ducarmon Q.R. Kuijper E.J. Response to: ‘Circulating microbiome in blood of different circulatory compartments' by Schierwagen et al.Gut. 2019; PubMed Google Scholar While the contribution of gut microbiota towards NAFLD development is being investigated, further studies disentangling NAFLD from the overlay of diseases such as diabetes are needed. In addition, microbiota composition and metabolites have been successfully used to differentiate between NASH-related cirrhosis and non-cirrhotic populations in single-centre studies, which will be reviewed in detail below.[24]Loomba R. Seguritan V. Li W. Long T. Klitgord N. Bhatt A. et al.Gut microbiome-based metagenomic signature for non-invasive detection of advanced fibrosis in human nonalcoholic fatty liver disease.Cell Metab. 2019; 30: 607Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar Autoimmune liver diseases: These diseases comprise a spectrum ranging from cholangiopathies to autoimmune liver disease. Microbial composition and functional changes have been described in patients with AIH, PBC and PSC. PBC is associated with gut microbial alterations whether or not it is being treated with ursodeoxycholic acid (UDCA).[25]Tang R. Wei Y. Li Y. Chen W. Chen H. Wang Q. et al.Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy.Gut. 2018; 67: 534-541Crossref PubMed Scopus (72) Google Scholar In patients with PBC Bacteroidetes spp., Sutterella, Oscillospira and Faecalibacterium were lower while Haemophilus, Veillonella, Clostridium, Lactobacillus, Streptococcus, Pseudomonas and Klebsiella were higher. Moreover, Haemophilus spp., Streptococcus spp. and Pseudomonas spp. decreased after UDCA treatment, while Bacteroidetes spp, Sutterella spp. and Oscillospira spp. increased. Patients with AIH have been shown to have altered microbiota even before the initiation of steroids in a large Chinese study.[26]Wei Y. Li Y. Yan L. Sun C. Miao Q. Wang Q. et al.Alterations of gut microbiome in autoimmune hepatitis.Gut. 2019; 69: 569-577Crossref PubMed Scopus (3) Google Scholar These include expansion of pathobionts such as Veillonella, especially V. dispar and reduction of obligate anaerobes. These results need to be corroborated in other cohorts as well. PSC is a prototype of altered gut-liver axis with several variables related to inflammatory bowel disease (IBD) and its activity, stage of scarring, cholangitis episodes and cholangiocarcinoma. Studies of the stool bacteria and fungi have been performed in patients with PSC, PSC + IBD and IBD without PSC.[27]Kummen M. Holm K. Anmarkrud J.A. Nygard S. Vesterhus M. Hoivik M.L. et al.The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls.Gut. 2017; 66: 611-619Crossref PubMed Scopus (106) Google Scholar,[28]Ruhlemann M.C. Heinsen F.A. Zenouzi R. Lieb W. Franke A. Schramm C. Faecal microbiota profiles as diagnostic biomarkers in primary sclerosing cholangitis.Gut. 2017; 66: 753-754Crossref PubMed Scopus (2) Google Scholar These studies show distinctive changes in PSC independent of IBD with lower diversity, higher Enterococcus, Fusobacterium and Lactobacillus.[27]Kummen M. Holm K. Anmarkrud J.A. Nygard S. Vesterhus M. Hoivik M.L. et al.The gut microbial profile in patients with primary sclerosing cholangitis is distinct from patients with ulcerative colitis without biliary disease and healthy controls.Gut. 2017; 66: 611-619Crossref PubMed Scopus (106) Google Scholar,[29]Sabino J. Vieira-Silva S. Machiels K. Joossens M. Falony G. Ballet V. et al.Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD.Gut. 2016; 65: 1681-1689Crossref PubMed Scopus (107) Google Scholar Changes have also been shown in biliary microbiota in this condition.[30]Pereira P. Aho V. Arola J. Boyd S. Jokelainen K. Paulin L. et al.Bile microbiota in primary sclerosing cholangitis: impact on disease progression and development of biliary dysplasia.PLoS One. 2017; 12: e0182924Crossref PubMed Scopus (7) Google Scholar Viral hepatitis: Hepatitis B and hepatitis C have variable impact on gut microbial composition. Studies of HCV-associated liver disease on the microbiota are not very clear with results suggesting that the microbiota changes before cirrhosis and after cirrhosis.31Inoue T. Nakayama J. Moriya K. Kawaratani H. Momoda R. Ito K. et al.Gut dysbiosis associated with hepatitis C virus infection.Clin Infect Dis. 2018; 67: 869-877Crossref PubMed Scopus (7) Google Scholar, 32Preveden T. Scarpellini E. Milic N. Luzza F. Abenavoli L. Gut microbiota changes and chronic hepatitis C virus infection.Expert Rev Gastroenterol Hepatol. 2017; 11: 813-819Crossref PubMed Scopus (6) Google Scholar, 33Heidrich B. Vital M. Plumeier I. Doscher N. Kahl S. Kirschner J. et al.Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls.Liver Int. 2018; 38: 50-58Crossref PubMed Scopus (15) Google Scholar Microbiota composition is variably affected by the eradication of the virus.[34]Bajaj J.S. Sterling R.K. Betrapally N.S. Nixon D.E. Fuchs M. Daita K. et al.HCV eradication does not impact gut dysbiosis or systemic inflammation in cirrhotic patients.Aliment Pharmacol Ther. 2016; 44: 638-643Crossref PubMed Scopus (16) Google Scholar There is an increasing body of literature on HBV before the development of cirrhosis. However, most of the changes that occur with HBV progression are largely similar to those seen with advancing fibrosis in other liver diseases.[35]Lu H. Wu Z. Xu W. Yang J. Chen Y. Li L. Intestinal microbiota was assessed in cirrhotic patients with hepatitis B virus infection. Intestinal microbiota of HBV cirrhotic patients.Microb Ecol. 2011; 61: 693-703Crossref PubMed Scopus (87) Google Scholar In addition, few studies have directly compared HBV to other liver disease aetiologies. In some of the studies of pre-cirrhotic patients, the ratio of Bacteroidetes to Firmicutes was evaluated as a measure of bacterial dysbiosis.[36]Wei X. Yan X. Zou D. Yang Z. Wang X. Liu W. et al.Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach.BMC Gastroenterol. 2013; 13: 175Crossref PubMed Scopus (41) Google ScholarKey pointChanges in microbiota composition and function are the lynchpin in the altered gut-liver-axis in cirrhosis and these have been shown in the stool, intestinal mucosa, ascites fluid, portal blood and liver parenchyma. Changes in microbiota composition and function are the lynchpin in the altered gut-liver-axis in cirrhosis and these have been shown in the stool, intestinal mucosa, ascites fluid, portal blood and liver parenchyma. Cirrhosis, the end-stage of liver disease, is associated with several complications that are directly or indirectly linked with the gut microbiota.[7]Hatton G. Shawcross D.L. Is treating the gut microbiome the key to achieving better outcomes in cirrhosis?.Expert Rev Gastroenterol Hepatol. 2019; 13: 1-2Crossref PubMed Scopus (1) Google Scholar,[37]Bajaj J.S. Gut microbiota as biosensors in patients with cirrhosis.Cell Mol Gastroenterol Hepatol. 2019; 8: 231-233Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar Decompensation of cirrhosis, characterised by variceal bleeding, hepatic encephalopathy (HE), ascites, spontaneous bacterial peritonitis (SBP) or jaundice, is the more advanced stage of cirrhosis, while patients who have not developed any of these complications are considered compensated.[38]D'Amico G. Garcia-Tsao G. Pagliaro L. Natural history and prognostic indicators of survival in cirrhosis: a systematic review of 118 studies.J Hepatol. 2006; 44: 217-231Abstract Full Text Full Text PDF PubMed Scopus (1341) Google Scholar,[39]Arvaniti V. D'Amico G. Fede G. Manousou P. Tsochatzis E. Pleguezuelo M. et al.Infections in patients with cirrhosis increase mortality four-fold and should be used in determining prognosis.Gastroenterology. 2010; 139 (1256.e1-5): 1246-1256Abstract Full Text Full Text PDF PubMed Scopus (525) Google Scholar These complications form a major burden from a medical and psycho-social perspective and strategies to improve their prognosis have largely depended on gut microbial modulation.[7]Hatton G. Shawcross D.L. Is treating the gut microbiome the key to achieving better outcomes in cirrhosis?.Expert Rev Gastroenterol Hepatol. 2019; 13: 1-2Crossref PubMed Scopus (1) Google Scholar Patients with cirrhosis have liver synthetic failure and a decrease in bile acid secretion, accompanied by impaired local and systemic immune responses and intestinal barrier dysfunction that lead to systemic and neuro-inflammation. A summary of compositional and simultaneous functional studies in human cirrhosis that have used stool and other tissues in outpatients are listed in Table 1, while those focused on inpatients and acute-on-chronic liver failure (ACLF) are listed in Table 2. Specific changes in alcoholic hepatitis-associated microbiota are an important aspect of this disease spectrum.[13]Llopis M. Cassard A.M. Wrzosek L. Boschat L. Bruneau A. Ferrere G. et al.Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease.Gut. 2016; 65: 830-839Crossref PubMed Scopus (130) Google Scholar These changes are characterised by alterations in structure and function of the gut and serum microbiota.[13]Llopis M. Cassard A.M. Wrzosek L. Boschat L. Bruneau A. Ferrere G. et al.Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease.Gut. 2016; 65: 830-839Crossref PubMed Scopus (130) Google Scholar,[40]Puri P. Liangpunsakul S. Christensen J.E. Shah V.H. Kamath P.S. Gores G.J. et al.The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis.Hepatology. 2018; 67: 1284-1302Crossref PubMed Scopus (28) Google Scholar,[41]Grander C. Adolph T.E. Wieser V. Lowe P. Wrzosek L. Gyongyosi B. et al.Recovery of ethanol-induced Akkermansia muciniphila depletion ameliorates alcoholic liver disease.Gut. 2018; 67: 891-901Crossref PubMed Scopus (87) Google Scholar Specifically increases in gram-negative rods, and specific species of Enterococcus predominate with advancing disease states.[13]Llopis M. Cassard A.M. Wrzosek L. Boschat L. Bruneau A. Ferrere G. et al.Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease.Gut. 2016; 65: 830-839Crossref PubMed Scopus (130) Google Scholar,[14]Llorente C. Jepsen P. Inamine T. Wang L. Bluemel S. Wang H.J. et al.Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.Nat Commun. 2017; 8: 837Crossref PubMed Scopus (46) Google Scholar,[42]Duan Y. Llorente C. Lang S. Brandl K. Chu H. Jiang L. et al.Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease.Nature. 2019; 575: 505-511Crossref PubMed Scopus (18) Google Scholar These changes are also associated with specific interactions with immune cells and bile acids.[13]Llopis M. Cassard A.M. Wrzosek L. Boschat L. Bruneau A. Ferrere G. et al.Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease.Gut. 2016; 65: 830-839Crossref PubMed Scopus (130) Google Scholar,[14]Llorente C. Jepsen P. Inamine T. Wang L. Bluemel S. Wang H.J. et al.Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.Nat Commun. 2017; 8: 837Crossref PubMed Scopus (46) Google Scholar,[43]Ciocan D. Voican C.S. Wrzosek L. Hugot C. Rainteau D. Humbert L. et al.Bile acid homeostasis and intestinal dysbiosis in alcoholic hepatitis.Aliment Pharmacol Ther. 2018; 48: 961-974Crossref PubMed Scopus (7) Google Scholar These changes in alcoholic hepatitis make IMT a promising option for this population. This global mucosal immune impairment in cirrhosis leads to microbiome alterations in components of the gut-liver axis but also in the skin, the serum, liver, portal blood and the saliva. Microbial changes have been most prominently described in the stool and intestinal mucosa with relatively higher abundances of gram-negative taxa and species of oral origin. These are most often components of Enterobacteriaceae, which are the major causative organisms in the pathogenesis of SBP and express a potently immunostimulatory endotoxin.[44]Tandon P. Garcia-Tsao G. Bacterial infections, sepsis, and multiorgan failure in cirrhosis.Semin Liver Dis. 2008; 28: 26-42Crossref PubMed Scopus (338) Google Scholar,[45]Di Lorenzo F. De Castro C. Silipo A. Molinaro A. Lipopolysaccharide structures of Gram-negative populations in the gut microbiota and effects on host interactions.FEMS Microbiol Rev. 2019; 43: 257-272Crossref PubMed Scopus (5) Google Scholar Taxa of oral origin, especially those belonging to Streptococcaceae and Porphyromonadaceae, increase in relative abundance with advancing cirrhosis and can be modulated by oral health and the use of proton pump inhibitors (PPIs).46Qin N. Yang F. Li A. Prifti E. Chen Y. Shao L. et al.Alterations of the human gut microbiome in liver cirrhosis.Nature. 2014; 513: 59-64Crossref PubMed Scopus (625) Google Scholar, 47Bajaj J.S. Acharya C. Fagan A. White M.B. Gavis E. Heuman D.M. et al.Proton pump inhibitor initiation and withdrawal affects gut microbiota and readmission risk in cirrhosis.Am J Gastroenterol. 2018; 113: 1177-1186Crossref PubMed Scopus (0) Google Scholar, 48Bajaj J.S. Betrapally N.S. Gillevet P.M. Decompensated cirrhosis and microbiome interpretation.Nature. 2015; 525: E1-E2Crossref PubMed Scopus (39) Google Scholar Bacterial taxa that are usually lacking in cirrhosis belong to Firmicutes, specifically Lachnospiraceae and Ruminococcaceae families.49Chen Y. Ji F. Guo J. Shi D. Fang D. Li L. Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology.Sci Rep. 2016; 6: 34055Crossref PubMed Scopus (49) Google Scholar, 50Chen Y. Yang F. Lu H. Wang B. Chen Y. Lei D. et al.Characterization of fecal microbial communities in patients with liver cirrhosis.Hepatology. 2011; 54: 562-572Crossref PubMed Scopus (383) Google Scholar, 51Bajaj J.S. Hylemon P.B. Ridlon J.M. Heuman D.M. Daita K. White M.B. et al.Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation.Am J Physiol Gastrointest Liver Physiol. 2012; 303: G675-685Crossref PubMed Scopus (227) Google Scholar These changes are found in the stool, serum and intestinal mucosa of patients with cirrhosis and worsen with the advancing or decompensation of cirrhosis. In the skin, especially in those who have pruritus, there is a higher relative abundance of Gammaproteobacteria, the order that includes Enterobacteriaceae.[52]Bajaj J.S. Fagan A. Sikaroodi M. Kakiyama G. Takei H. Degefu Y. et al.Alterations in skin microbiomes of patients with cirrhosis.Clin Gastroenterol Hepatol. 2019; 17: 2581-2591.e15Abstract Full Text Full Text PDF PubMed Google ScholarTable 1Studies of the gut microbiome in human cirrhosis in outpatients.StudySamples/ Groups comparedFindingsSignificancePotential limitationsStudies analysing only stool microbiotaChen et al. 2011 Hepatology[50]Chen Y. Yang F. Lu H. Wang B. Chen Y. Lei D. et al.Characterization of fecal microbial communities in patients with liver cirrhosis.Hepatology. 2011; 54: 562-572Crossref PubMed Scopus (383) Google ScholarStool/cirrhosis (36) vs. controls (24)Bacteroidetes reduced whereas Proteobacteria increased in cirrhosis.Streptococcaceae correlated positively with Child-Pugh while Lachnospiraceae correlated negativelyFirst major study to show widespread dysbiosis in cirrhosis. First to show reduction in autochthonous taxa and increase in pathogenic onesRelatively small sample size with unclear dietary history.No functional analysesBajaj et al. 2012 Am J Physiol[162]Bajaj J.S. Ridlon J.M. Hylemon P.B. Thacker L.R. Heuman D.M. Smith S. et al.Linkage of gut microbiome with cognition in hepatic encephalopathy.Am J Physiol Gastrointest Liver Physiol. 2012; 302: G168-G175Crossref PubMed Scopus (233) Google Scholar†Stool/cirrhosis (25) with 17 with OHE vs. controls (10)Increased Bacteroidetes and reduced autochthonous taxa in cirrhosis.Increased Veillonellaceae in OHE compared to no-OHE as only significant difference.Enterobacteriaceae positively correlated with MELD and Ruminococcocaceae negatively.Porphyromonadaceae correlated with poor cognition.Enterobacteriaceae and Veillonellaceae associated positively with inflammation and endotoxemia where as Ruminococcocaceae correlated negativelyFirst major study to assess the correlation between dysbiosis, systemic inflammation, endotoxemia and OHE in cirrhosis.Showed that certain families predominated during decompensation and associated with inflammation and poor cognition.Stool microbiome between OHE and no-OHE was not very differentRelatively small sample size with correlation networks.Endotoxemia and inflammation as potential bacterial functional readouts.OHE patients already on therapy as clinically indicatedZhang et al. Am J Gastro 2013[58]Zhang Z. Zhai H. Geng J. Y" @default.
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• W3003277102 title "Microbiota changes and intestinal microbiota transplantation in liver diseases and cirrhosis" @default.
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