Interactions Between the Intestinal Microbiome and Liver Diseases

The human intestine harbors a diverse community of microbes that promote metabolism and digestion in their symbiotic relationship with the host. Disturbance of its homeostasis can result in disease. We review factors that disrupt intestinal homeostasis and contribute to nonalcoholic fatty liver disease, steatohepatitis, alcoholic liver disease, and cirrhosis. Liver disease has long been associated with qualitative and quantitative (overgrowth) dysbiotic changes in the intestinal microbiota. Extrinsic factors, such as the Western diet and alcohol, contribute to these changes. Dysbiosis results in intestinal inflammation, a breakdown of the intestinal barrier, and translocation of microbial products in animal models. However, the contribution of the intestinal microbiome to liver disease goes beyond simple translocation of bacterial products that promote hepatic injury and inflammation. Microbial metabolites produced in a dysbiotic intestinal environment and host factors are equally important in the pathogenesis of liver disease. We review how the combination of liver insult and disruptions in intestinal homeostasis contribute to liver disease. The human intestine harbors a diverse community of microbes that promote metabolism and digestion in their symbiotic relationship with the host. Disturbance of its homeostasis can result in disease. We review factors that disrupt intestinal homeostasis and contribute to nonalcoholic fatty liver disease, steatohepatitis, alcoholic liver disease, and cirrhosis. Liver disease has long been associated with qualitative and quantitative (overgrowth) dysbiotic changes in the intestinal microbiota. Extrinsic factors, such as the Western diet and alcohol, contribute to these changes. Dysbiosis results in intestinal inflammation, a breakdown of the intestinal barrier, and translocation of microbial products in animal models. However, the contribution of the intestinal microbiome to liver disease goes beyond simple translocation of bacterial products that promote hepatic injury and inflammation. Microbial metabolites produced in a dysbiotic intestinal environment and host factors are equally important in the pathogenesis of liver disease. We review how the combination of liver insult and disruptions in intestinal homeostasis contribute to liver disease. David A. BrennerView Large Image Figure ViewerDownload Hi-res image Download (PPT) The intestine and its microbiota (bacteria and other microbes) have a symbiotic relationship. The microbiota contributes to digestion, synthesis of vitamins, and resistance to intestinal colonization by pathogens, but also contains potentially pathogenic bacteria. Disruption of intestinal homeostasis and alterations in the intestinal microbiome contribute to the pathogenesis of many disorders, including liver disease. How do disturbances in the intestinal microbiome (detected by analyses of its metagenome and metabolome) contribute to liver disease? We discuss how host and dietary factors, including alcohol, affect the composition of the intestinal microbiome and development of liver diseases, and, in turn, how liver disease can alter the enteric microbiome. We review alterations in the composition of the intestinal microbiome associated with several liver diseases. These studies were performed primarily in patients with disease (Tables 1 and 2). The functional consequences of the intestinal microbiome for each of these diseases, based primarily on animal models, are reviewed later.Table 1Changes in the Intestinal Microbiota Associated With NAFLD and NASH in Human BeingsDiseaseComparisonaA comparison of condition A vs condition B: ↑, increase in condition B relative to condition A; ↓, decrease in condition B relative to condition A; ns, no significant difference.Implicated microbiotabTaxonomy was updated using the National Center for Biotechnology Information (NCBI) Taxonomy Browser.MethodologyReferencecReferences focus on microbiota changes associated with liver disease rather than obesity or the metabolic syndrome.PhylumClassOrderFamilyGenusHealthy (n = 30)NAFLD (n = 30)Healthy vs NAFLDFirmicutesBacilliLactobacillalesLactobacillaceae ↑Lactobacillus ↑16S rRNA gene pyrosequencingStool sample5ClostridiaClostridialesLachnospiraceae ↑Robinsoniella ↑,Roseburia ↑, Dorea ↑ClostridiaClostridialesRuminococcaceae ↓OscillospiraceaeOscillibacter ↓Children:Healthy (n = 16)Obese (n = 25)NASH (n = 22)Healthy vs obeseBacteroidetes ↑Prevotellaceae ↑Prevotella ↑16S rRNA gene pyrosequencingStool sample7Rikenellaceae ↓Alistipes ↓Firmicutes ↓Lachnospiraceae ↓Blautia ↓, Coprococcus ↓, Roseburia ↓EubacteriaceaeEubacterium ↓Ruminococcaceae ↓Healthy vs NASHBacteroidetes ↑Prevotellaceae ↑Prevotella ↑Rikenellaceae ↓Alistipes ↓Firmicutes ↓Lachnospiraceae ↓Blautia ↓, Coprococcus ↓EubacteriaceaeEubacterium ↓Ruminococcaceae ↓Oscillospira ↓Actinobacteria ↓Bifidobacteriaceae ↓Bifidobacterium ↓Proteobacteria ↑γ-proteobacteriaEnterobacterialesEnterobacteriaceae ↑Escherichia ↑Obese vs NASHProteobacteria ↑γ-proteobacteriaEnterobacterialesEnterobacteriaceae ↑Escherichia ↑Healthy (n = 17)Steatosis (n = 11)NASH (n = 22)Healthy vs NASHBacteroidetes ↓Quantitative real-time PCRStool sample6ProteobacteriaEnterobacteriaceaeEscherichia coli nsSteatosis vs NASHBacteroidetes ↓FirmicutesLachnospiraceaeClostridium coccoides ↑ProteobacteriaEnterobacteriaceaeEscherichia coli nsa A comparison of condition A vs condition B: ↑, increase in condition B relative to condition A; ↓, decrease in condition B relative to condition A; ns, no significant difference.b Taxonomy was updated using the National Center for Biotechnology Information (NCBI) Taxonomy Browser.c References focus on microbiota changes associated with liver disease rather than obesity or the metabolic syndrome. Open table in a new tab Table 2Changes in the Intestinal Microbiota Associated With Cirrhosis in Human BeingsDiseaseComparisonaA comparison of condition A vs condition B: ↑, increase in condition B relative to condition A; ↓, decrease in condition B relative to condition A.Implicated microbiotabTaxonomy was updated using the NCBI Taxonomy Browser.MethodologyReferencesPhylumClassOrderFamilyGenusHealthy (n = 32)HBV cirrhotic patients (n = 31)Healthy vs HBV cirrhotic patientsBacteroidetesPrevotella ↓Quantitative real-time PCRStool sample27FirmicutesEnterococcus faecalis ↑Faecalibacterium prausnitzii ↓, Clostridium clusters XI ↓,Clostridium clusters XIV ↓Lactic acid bacteria ↓ (including Lactobacillus, Pediococcus, Leuconostoc, and Weissella)ActinobacteriaBifidobacterium ↓ProteobacteriaEnterobacteriaceae ↑Healthy (n = 15)HBV cirrhotic patients (n = 16)Healthy vs HBV cirrhotic patientsActinobacteriaBifidobacterium catenulatum group ↓Quantitative real-time PCRStool sample29Healthy (n = 38)HBV cirrhotic patients (n = 61)Healthy vs HBV cirrhotic patientsFirmicutesLactobacillus acidophilus ↓, Lactobacillus rhamnosus ↓, Lactobacillus reuteri ↓, Lactobacillus gasseri ↑Quantitative real-time PCRStool sample30Healthy (n = 24)HBV cirrhotic patients (n = 24)Alcoholic cirrhotic patients (n = 12)Healthy vs cirrhotic patientsBacteroidetes ↓Bacteroidia ↓Bacteroidaceae ↓16S rRNA gene pyrosequencing, quantitative real-time PCRStool sample28FirmicutesEnterococcus faecalis ↑Bacilli ↑Streptococcaceae ↑ClostridiaLachnospiraceae ↓NegativicutesVeillonellaceae ↑Clostridium clusters XI ↑Proteobacteria ↑γ-proteobacteria ↑Enterobacteriaceae ↑, Pasteurellaceae ↑Fusobacteria ↑Fusobacteriia ↑Fusobacteriaceae ↑Healthy vs alcoholic cirrhotic patientsBacteroidetesPrevotellaceae ↑HBV cirrhosis vsalcoholic cirrhotic patientsBacteroidetesPrevotellaceae ↑Healthy (n = 10)Cirrhotic patientscMixed etiology. (n = 25)Healthy vs cirrhotic patientsFirmicutesLachnospiraceae ↓, Ruminococcaceae ↓, Clostridium Incertae sedis XIV ↓, Leuconostocaceae ↑, Lactobacillaceae ↑16S rRNA gene pyrosequencingStool sample32ProteobacteriaEnterobacteriaceae ↑, Alcaligenaceae ↑FusobacteriaFusobacteriaceae ↑Healthy (n = 17)Cirrhotic patientscMixed etiology. (n = 36)Mucosal samples - healthy vs cirrhotic patientsFirmicutesClostridiaceaeClostridium ↑16S rRNA gene pyrosequencingStool sample, rectosigmoid mucosal biopsy31LachnospiraceaeDorea ↓RuminococcaceaeSubdoligranulum ↓AcidaminococcaceaeAcidaminococcus ↑EnterococcaceaeEnterococcus ↑ProteobacteriaBurkholderiaceaeBurkholderia ↑, Ralstonia ↑EnterobacteriaceaeProteus ↑Mucosal samples cirrhotic patients vs stool samples cirrhotic patientsFirmicutesVeillonellaceaeVeillonella ↑LachnospiraceaeRoseburia ↑, Blautia ↓LeuconostocaceaeLeuconostoc ↑ActinobacteriaPropionibacteriaceaePropionibacterium ↓StreptomycetaceaeStreptomyces ↓ProteobacteriaVibrionaceaeVibrio ↓HBV, hepatitis B virusa A comparison of condition A vs condition B: ↑, increase in condition B relative to condition A; ↓, decrease in condition B relative to condition A.b Taxonomy was updated using the NCBI Taxonomy Browser.c Mixed etiology. Open table in a new tab HBV, hepatitis B virus Nonalcoholic fatty liver disease (NAFLD) is the hepatic manifestation of the metabolic syndrome. NAFLD is generally a benign disease; approximately one third of the US population has hepatic steatosis.1Browning J.D. Szczepaniak L.S. Dobbins R. et al.Prevalence of hepatic steatosis in an urban population in the United States: impact of ethnicity.Hepatology. 2004; 40: 1387-1395Crossref PubMed Scopus (3008) Google Scholar The prevalence of nonalcoholic steatohepatitis (NASH) among a general medical population diagnosed with NAFLD is 30%.2Williams C.D. Stengel J. Asike M.I. et al.Prevalence of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis among a largely middle-aged population utilizing ultrasound and liver biopsy: a prospective study.Gastroenterology. 2011; 140: 124-131Abstract Full Text Full Text PDF PubMed Scopus (1673) Google Scholar NASH is characterized by the development of liver inflammation and fibrosis. Patients with NASH have a high likelihood of developing advanced fibrosis and cirrhosis; it has been estimated that approximately one third of cases of early stage NASH will progress to stage 3 or 4 fibrosis (cirrhosis) over 5–10 years.3Caldwell S. Argo C. The natural history of non-alcoholic fatty liver disease.Dig Dis. 2010; 28: 162-168Crossref PubMed Scopus (146) Google Scholar Dietary factors and changes in diet are determinants of the composition of the microbiome.4Wu G.D. Chen J. Hoffmann C. et al.Linking long-term dietary patterns with gut microbial enterotypes.Science. 2011; 334: 105-108Crossref PubMed Scopus (4431) Google Scholar Although patients with NAFLD often are obese and insulin resistant, we focus on published studies of patients with documented liver disease, rather than obesity. The fecal microbiota in NAFLD and NASH patients has been assessed using culture-independent techniques such as quantitative polymerase chain reaction (PCR) and deep sequencing of a conserved region in the bacterial 16S ribosomal RNA (rRNA) gene.5Raman M. Ahmed I. Gillevet P.M. et al.Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease.Clin Gastroenterol Hepatol. 2013; 11: 868-875.e3Abstract Full Text Full Text PDF PubMed Scopus (506) Google Scholar, 6Mouzaki M. Comelli E.M. Arendt B.M. et al.Intestinal microbiota in patients with nonalcoholic fatty liver disease.Hepatology. 2013; 58: 120-127Crossref PubMed Scopus (565) Google Scholar, 7Zhu L. Baker S.S. Gill C. et al.Characterization of the gut microbiome in non-alcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH.Hepatology. 2013; 57: 601-609Crossref PubMed Scopus (1143) Google Scholar Details about dysbiosis associated with NAFLD and NASH are summarized in Table 1. Microbiota samples from patients with NAFLD or NASH have a lower proportion of members of the Ruminococcaceae family than healthy subjects. Escherichia is the only abundant genus of bacteria in the intestinal microbiota that is significantly disproportionate between obese children and pediatric patients with NASH.7Zhu L. Baker S.S. Gill C. et al.Characterization of the gut microbiome in non-alcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH.Hepatology. 2013; 57: 601-609Crossref PubMed Scopus (1143) Google Scholar In contrast, adult patients with NASH had a significantly higher percentage of Clostridium coccoides than patients with biopsy-proven NAFLD.6Mouzaki M. Comelli E.M. Arendt B.M. et al.Intestinal microbiota in patients with nonalcoholic fatty liver disease.Hepatology. 2013; 58: 120-127Crossref PubMed Scopus (565) Google Scholar However, studies comparing the bacterial taxonomic composition of patients with NAFLD vs those with NASH produced variable and even contradictory findings. Possible reasons for discrepant results include the small number of subjects included in the studies, differences in cohorts (age, sex, ethnicity, geographic location, medication use), insufficient documentation of liver disease, and differences in methodology. To determine whether patients with NAFLD and NASH have distinct compositions of the intestinal microbiome, studies (ideally longitudinal) are needed of larger, better-characterized cohorts. Identifying specific microbial compositions of these patients could improve our understanding of intestine–liver interactions and lead to fecal biomarkers for NAFLD and/or NASH. Small-bowel bacterial overgrowth is a disorder in which abnormally large numbers of bacteria grow in the small intestine. Patients with obesity or NAFLD have a higher prevalence of small intestinal bacterial overgrowth.8Miele L. Valenza V. La Torre G. et al.Increased intestinal permeability and tight junction alterations in nonalcoholic fatty liver disease.Hepatology. 2009; 49: 1877-1887Crossref PubMed Scopus (1074) Google Scholar, 9Sabate J.M. Jouet P. Harnois F. et al.High prevalence of small intestinal bacterial overgrowth in patients with morbid obesity: a contributor to severe hepatic steatosis.Obes Surg. 2008; 18: 371-377Crossref PubMed Scopus (196) Google Scholar Intestinal permeability and bacterial overgrowth correlate with severity of steatosis, but not fibrosis or hepatic inflammation, based on liver biopsy analysis.8Miele L. Valenza V. La Torre G. et al.Increased intestinal permeability and tight junction alterations in nonalcoholic fatty liver disease.Hepatology. 2009; 49: 1877-1887Crossref PubMed Scopus (1074) Google Scholar Small intestinal bacterial overgrowth also was present in 50% of patients with NASH, which is significantly higher than in healthy controls, matched for sex and age.10Wigg A.J. Roberts-Thomson I.C. Dymock R.B. et al.The role of small intestinal bacterial overgrowth, intestinal permeability, endotoxaemia, and tumour necrosis factor alpha in the pathogenesis of non-alcoholic steatohepatitis.Gut. 2001; 48: 206-211Crossref PubMed Scopus (727) Google Scholar In these studies, patients with small intestinal bacterial overgrowth were identified by breath tests. However, researchers have debated whether breath tests accurately detect this disorder. Total bacterial counts in the feces, based on real-time PCR, did not differ between healthy subjects and persons with NAFLD or NASH.6Mouzaki M. Comelli E.M. Arendt B.M. et al.Intestinal microbiota in patients with nonalcoholic fatty liver disease.Hepatology. 2013; 58: 120-127Crossref PubMed Scopus (565) Google Scholar Further studies are needed to determine whether fecal bacterial counts actually correlate with the amount of microbes present in the small intestine. Culture- and breath test–independent methods are needed to reassess the prevalence of intestinal bacterial overgrowth in patients with NAFLD or NASH. Alcohol abuse is one of the leading causes of chronic liver disease. Chronic alcoholic liver disease may progress from simple steatosis to steatohepatitis, liver fibrosis, and, in 15%–40% of patients, cirrhosis. Patients with only alcoholic fatty liver disease usually do not present with any clinical symptoms and their liver continues to function well.11Bode C. Bode J.C. Activation of the innate immune system and alcoholic liver disease: effects of ethanol per se or enhanced intestinal translocation of bacterial toxins induced by ethanol?.Alcohol Clin Exp Res. 2005; 29: 166S-171SCrossref PubMed Scopus (147) Google Scholar, 12Yan A.W. Schnabl B. Bacterial translocation and changes in the intestinal microbiome associated with alcoholic liver disease.World J Hepatol. 2012; 4: 110-118Crossref PubMed Scopus (88) Google Scholar Research into the role of the microbiome in alcoholic liver disease unfortunately is not as advanced as that for obesity or fatty liver disease. The mucosa-associated bacterial taxonomy was evaluated in patients with alcoholic cirrhosis and in alcoholic patients without liver disease using 16S rRNA gene sequencing. The proportion of Bacteroidaceae was lower in samples from alcoholic patients than from nonalcoholic individuals.13Mutlu E.A. Gillevet P.M. Rangwala H. et al.Colonic microbiome is altered in alcoholism.Am J Physiol Gastrointest Liver Physiol. 2012; 302: G966-G978Crossref PubMed Scopus (566) Google Scholar Although microbiome studies in human beings are important to associate distinct compositions of the intestinal microbiome with different disease states, studies in animal models, under carefully controlled conditions, offer some advantages. Preclinical studies allowed researchers to control for age, sex, environment, diet, and genetic background. Littermates can be compared in mouse studies. Pups typically are colonized with the microbes they first encounter, typically from their mothers,14Schnabl B. Linking intestinal homeostasis and liver disease.Curr Opin Gastroenterol. 2013; 29: 264-270Crossref PubMed Scopus (62) Google Scholar so littermates usually have the same microbiota composition. Changes in the microbiota can be monitored in response to different environmental factors, and compared among mice that had the same initial microbial composition. For example, in the Tsukamoto–French model of alcoholic liver disease, mice are placed on specific liquid diets and given intragastric infusions of ethanol, whereas control littermates are placed on the same diet but instead given an isocaloric amount of dextrose. By using this system, researchers have been able to detect quantitative and qualitative changes in the microbiome associated with ethanol intake. Bacterial overgrowth was observed along almost the entire gastrointestinal tract; the dysbiosis was characterized by significant reductions in proportions of probiotic bacteria such as Lactobacillus, Pediococcus, Leuconostoc, and Lactococcus.15Yan A.W. Fouts D.E. Brandl J. et al.Enteric dysbiosis associated with a mouse model of alcoholic liver disease.Hepatology. 2011; 53: 96-105Crossref PubMed Scopus (586) Google Scholar An alcohol-associated decrease in the number of intestinal Lactobacillus, confirmed by quantitative real-time PCR,16Hartmann P. Chen P. Wang H.J. et al.Deficiency of intestinal mucin-2 ameliorates experimental alcoholic liver disease in mice.Hepatology. 2013; 58: 108-119Crossref PubMed Scopus (177) Google Scholar also was observed in the Lieber DeCarli diet model of alcohol feeding for 8 weeks (unpublished data). Alternatively, several studies have reported that administration of probiotic Lactobacillus reduces features of alcoholic liver disease in animal models.17Nanji A.A. Khettry U. Sadrzadeh S.M. Lactobacillus feeding reduces endotoxemia and severity of experimental alcoholic liver (disease).Proc Soc Exp Biol Med. 1994; 205: 243-247Crossref PubMed Scopus (384) Google Scholar, 18Forsyth C.B. Farhadi A. Jakate S.M. et al.Lactobacillus GG treatment ameliorates alcohol-induced intestinal oxidative stress, gut leakiness, and liver injury in a rat model of alcoholic steatohepatitis.Alcohol. 2009; 43: 163-172Abstract Full Text Full Text PDF PubMed Scopus (330) Google Scholar, 19Wang Y. Liu Y. Sidhu A. et al.Lactobacillus rhamnosus GG culture supernatant ameliorates acute alcohol-induced intestinal permeability and liver injury.Am J Physiol Gastrointest Liver Physiol. 2012; 303: G32-G41Crossref PubMed Scopus (187) Google Scholar A small clinical trial also showed improvement in alcohol-induced liver injury in patients taking probiotics.20Kirpich I.A. Solovieva N.V. Leikhter S.N. et al.Probiotics restore bowel flora and improve liver enzymes in human alcohol-induced liver injury: a pilot study.Alcohol. 2008; 42: 675-682Abstract Full Text Full Text PDF PubMed Scopus (374) Google Scholar Similar to observations made in animal models, aerobic and anaerobic bacterial cultures of jejunal aspirates from patients who chronically abuse alcohol were found to have bacterial overgrowth.21Bode J.C. Bode C. Heidelbach R. et al.Jejunal microflora in patients with chronic alcohol abuse.Hepatogastroenterology. 1984; 31: 30-34PubMed Google Scholar Excessive alcohol intake therefore is accompanied by dysbiosis and an increased intestinal bacterial load, based on clinical and preclinical studies. Multiple factors are likely to contribute to changes in the intestinal microbiome during the development of alcoholic liver disease. These might include small intestinal dysmotility,22Wegener M. Schaffstein J. Dilger U. et al.Gastrointestinal transit of solid-liquid meal in chronic alcoholics.Dig Dis Sci. 1991; 36: 917-923Crossref PubMed Scopus (70) Google Scholar changes in gastric acid secretion,23Bode C. Bode J.C. Alcohol's role in gastrointestinal tract disorders.Alcohol Health Res World. 1997; 21: 76-83PubMed Google Scholar and alterations to the intestinal innate immune response. Antimicrobial molecules, which are part of the innate immune response, are secreted from enterocytes or intestinal Paneth cells. In particular, the antimicrobial molecules regenerating islet-derived (Reg)3b and Reg3g are reduced in the small intestines of mice after 3 weeks of intragastric ethanol feeding.15Yan A.W. Fouts D.E. Brandl J. et al.Enteric dysbiosis associated with a mouse model of alcoholic liver disease.Hepatology. 2011; 53: 96-105Crossref PubMed Scopus (586) Google Scholar Further studies are needed to determine if and to what extent an impaired innate immune response contributes to disease progression. The commensal microbiota not only produces ethanol, but also metabolizes it.24Salaspuro V. Nyfors S. Heine R. et al.Ethanol oxidation and acetaldehyde production in vitro by human intestinal strains of Escherichia coli under aerobic, microaerobic, and anaerobic conditions.Scand J Gastroenterol. 1999; 34: 967-973Crossref PubMed Scopus (46) Google Scholar It is not clear whether ethanol, as a dietary component or as an energy source for certain bacterial strains, directly alters the microbiota. Liver fibrosis may result in end-stage liver disease or cirrhosis, which eventually disrupts the metabolic functions of the liver. Although patients with hepatic fibrosis often are asymptomatic, the development of cirrhosis in these patients is the major determinant of morbidity and mortality.25Poynard T. Ratziu V. Benhamou Y. et al.Natural history of HCV infection.Baillieres Best Pract Res Clin Gastroenterol. 2000; 14: 211-228Abstract Full Text PDF PubMed Scopus (90) Google Scholar Major clinical complications are infections, ascites, renal failure, variceal hemorrhage, and hepatic encephalopathy. Patients with these complications have a poor prognosis and liver transplantation often is indicated.26Gines P. Cardenas A. Arroyo V. et al.Management of cirrhosis and ascites.N Engl J Med. 2004; 350: 1646-1654Crossref PubMed Scopus (671) Google Scholar Several studies have assessed the taxonomic composition of the intestinal microbiota in patients with cirrhosis27Lu H. Wu Z. Xu W. et al.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 (178) Google Scholar, 28Chen Y. Yang F. Lu H. et al.Characterization of fecal microbial communities in patients with liver cirrhosis.Hepatology. 2011; 54: 562-572Crossref PubMed Scopus (743) Google Scholar, 29Xu M. Wang B. Fu Y. et al.Changes of fecal Bifidobacterium species in adult patients with hepatitis B virus-induced chronic liver disease.Microb Ecol. 2012; 63: 304-313Crossref PubMed Scopus (85) Google Scholar, 30Wu Z.W. Lu H.F. Wu J. et al.Assessment of the fecal Lactobacilli population in patients with hepatitis B virus-related decompensated cirrhosis and hepatitis B cirrhosis treated with liver transplant.Microb Ecol. 2012; 63: 929-937Crossref PubMed Scopus (32) Google Scholar, 31Bajaj J.S. Hylemon P.B. Ridlon J.M. 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-G685Crossref PubMed Scopus (415) Google Scholar, 32Bajaj J.S. Ridlon J.M. Hylemon P.B. et al.Linkage of gut microbiome with cognition in hepatic encephalopathy.Am J Physiol Gastrointest Liver Physiol. 2012; 302: G168-G175Crossref PubMed Scopus (409) Google Scholar (Table 2). A common feature of cirrhosis is an increase of potentially pathogenic bacteria, accompanied by reduced proportions of beneficial bacteria. Fecal microbial communities are similar among patients with cirrhosis of different etiologies. Therefore, features of end-stage liver disease, such as reduced bile flow, might determine the shape of the intestinal microbiome. However, fecal microbial communities from patients with alcoholic cirrhosis have significant increases in the Prevotellaceae family compared with patients with hepatitis B–related cirrhosis or healthy individuals, based on sequencing of the common 16S rRNA gene region of bacteria.28Chen Y. Yang F. Lu H. et al.Characterization of fecal microbial communities in patients with liver cirrhosis.Hepatology. 2011; 54: 562-572Crossref PubMed Scopus (743) Google Scholar Etiology (particularly an alcohol association) therefore appears to contribute to the composition of the intestinal microbiome in patients with end-stage liver disease. Most patients with cirrhosis have intestinal bacterial overgrowth, shown by quantitative analyses of bacterial cultures from jejunal aspirates.33Bauer T.M. Schwacha H. Steinbruckner B. et al.Small intestinal bacterial overgrowth in human cirrhosis is associated with systemic endotoxemia.Am J Gastroenterol. 2002; 97: 2364-2370Crossref PubMed Scopus (177) Google Scholar, 34Bauer T.M. Steinbruckner B. Brinkmann F.E. et al.Small intestinal bacterial overgrowth in patients with cirrhosis: prevalence and relation with spontaneous bacterial peritonitis.Am J Gastroenterol. 2001; 96: 2962-2967Crossref PubMed Google Scholar Therefore, they not only have taxonomic differences in microbial communities, compared with people without cirrhosis, but also an increased intestinal burden of bacteria. Several factors contribute to intestinal bacterial overgrowth in patients with cirrhosis. These include impaired motility of the small intestine,35Chang C.S. Chen G.H. Lien H.C. et al.Small intestine dysmotility and bacterial overgrowth in cirrhotic patients with spontaneous bacterial peritonitis.Hepatology. 1998; 28: 1187-1190Crossref PubMed Scopus (224) Google Scholar reduced bile flow,27Lu H. Wu Z. Xu W. et al.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 (178) Google Scholar and altered secretion of immunoglobulin A27Lu H. Wu Z. Xu W. et al.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 (178) Google Scholar and antimicrobial molecules.36Teltschik Z. Wiest R. Beisner J. et al.Intestinal bacterial translocation in rats with cirrhosis is related to compromised Paneth cell antimicrobial host defense.Hepatology. 2012; 55: 1154-1163Crossref PubMed Scopus (145) Google Scholar In rats with cirrhosis, ascites, and translocation of viable bacteria to mesenteric lymph nodes, Paneth cells produce lower levels of defensins and Reg3 molecules, compared with those without bacterial translocation. This reduction is accompanied by reduced antimicrobial activity against Enterobacteriaceae.36Teltschik Z. Wiest R. Beisner J. et al.Intestinal bacterial translocation in rats with cirrhosis is related to compromised Paneth cell antimicrobial host defense.Hepatology. 2012; 55: 1154-1163Crossref PubMed Scopus (145) Google Scholar Little is known about how Paneth cell function is impaired during the development of cirrhosis. Compromised intestinal host defense therefore might contribute to qualitative and quantitative changes in the enteric microbiome associated with end-stage liver disease. New sequencing techniques to analyze the microbiome should help determine the contribution of these factors to compositional changes in the microbiota. Most patients with NAFLD are obese and diabetic. Obesity and insulin resistance are risk factors for fatty liver disease and are associated with changes in the intestinal microbiome.37Turnbaugh P.J. Ley R.E. Mahowald M.A. et al.An obesity-associated gut microbiome with increased capacity for energy harvest.Nature. 2006; 444: 1027-1031Crossref PubMed Scopus (8793) Google Scholar, 38Ley R.E. Backhed F. Turnbaugh P. et al.Obesity alters gut microbial ecology.Proc Natl Acad Sci U S A. 2005; 102: 11070-11075Crossref PubMed Scopus (4615) Goo