{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T01:45:23Z","timestamp":1793324723623,"version":"4.5.0"},"reference-count":287,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T00:00:00Z","timestamp":1565136000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2019.01676","type":"journal-article","created":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T00:27:59Z","timestamp":1565137679000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":141,"title":["Infectious Threats, the Intestinal Barrier, and Its Trojan Horse: Dysbiosis"],"prefix":"10.3389","volume":"10","author":[{"given":"Simona","family":"Iacob","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana Gabriela","family":"Iacob","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2019,8,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"4453","DOI":"10.4049\/jimmunol.174.8.4453","article-title":"TLR signaling in the gut in health and disease.","volume":"174","author":"Abreu","year":"2005","journal-title":"J. Immunol."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3390\/cancers10060178","article-title":"P53 and the viral connection: back into the future \u2021.","volume":"10","author":"Aloni-Grinstein","year":"2018","journal-title":"Cancers"},{"key":"B3","doi-asserted-by":"publisher","first-page":"4843","DOI":"10.4049\/jimmunol.166.8.4843","article-title":"The role of dendritic cells, B cells, and M cells in gut-oriented immune responses.","volume":"166","author":"Alpan","year":"2001","journal-title":"J. Immunol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.00322","article-title":"The Influence of host stress on the mechanism of infection: lost microbiomes, emergent pathobiomes, and the role of interkingdom signaling.","volume":"8","author":"Alverdy","year":"2017","journal-title":"Front. Microbiol."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00707-13","article-title":"The intestinal microbiota interferes with the microRNA response upon oral Listeria infection.","volume":"4","author":"Archambaud","year":"2013","journal-title":"MBio."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1799","DOI":"10.1097\/QAD.0b013e32832ec1dc","article-title":"Expression of latent human immunodeficiency type 1 is induced by novel and selective histone deacetylase inhibitors.","volume":"23","author":"Archin","year":"2009","journal-title":"AIDS"},{"key":"B7","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1038\/nature11286","article-title":"Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy.","volume":"487","author":"Archin","year":"2012","journal-title":"Nature"},{"key":"B8","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/nature12726","article-title":"Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation.","volume":"504","author":"Arpaia","year":"2013","journal-title":"Nature"},{"key":"B9","doi-asserted-by":"publisher","first-page":"205","DOI":"10.3109\/08820139.2015.1122613","article-title":"Short-chain fatty acids regulate cytokines and Th17\/Treg cells in human peripheral blood mononuclear cells in vitro.","volume":"45","author":"Asarat","year":"2016","journal-title":"Immunol. Invest."},{"key":"B10","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota.","volume":"500","author":"Atarashi","year":"2013","journal-title":"Nature"},{"key":"B11","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1038\/cdd.2017.169","article-title":"How does p53 induce apoptosis and how does this relate to p53-mediated tumour suppression?","volume":"25","author":"Aubrey","year":"2018","journal-title":"Cell Death Differ."},{"key":"B12","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1099\/00222615-44-4-285","article-title":"Penetration of M cells and destruction of Peyer\u2019s patches by Yersinia enterocolitica: an ultrastructural and histological study.","volume":"44","author":"Autenrieth","year":"1996","journal-title":"J. Med. Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nm.2729","article-title":"Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota.","volume":"18","author":"Ayres","year":"2012","journal-title":"Nat. Med."},{"key":"B14","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1016\/j.jhep.2013.12.019","article-title":"Altered profile of human gut microbiome is associated with cirrhosis and its complications.","volume":"60","author":"Bajaj","year":"2014","journal-title":"J. Hepatol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"G675","DOI":"10.1152\/ajpgi.00152.2012","article-title":"Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation.","volume":"303","author":"Bajaj","year":"2012","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"B16","doi-asserted-by":"crossref","first-page":"42984","DOI":"10.1074\/jbc.M405410200","article-title":"In vitro and ex vivo activation of the TLR5 signaling pathway in intestinal epithelial Ccells by a commensal Escherichia coli strain.","volume":"279","author":"Bambou","year":"2004","journal-title":"J. Biol. Chem."},{"key":"B17","doi-asserted-by":"publisher","first-page":"6387","DOI":"10.1128\/JVI.00619-16","article-title":"Hepatitis C virus-induced upregulation of microRNA miR-146a-5p in hepatocytes promotes viral infection and deregulates metabolic pathways associated with liver disease pathogenesis.","volume":"90","author":"Bandiera","year":"2016","journal-title":"J. Virol."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20092241","article-title":"Immunoepigenetics combination therapies: an overview of the role of HDACs in cancer immunotherapy.","volume":"20","author":"Banik","year":"2019","journal-title":"Int. J. Mol. Sci."},{"key":"B19","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1136\/gut.2008.171546","article-title":"Nod2 regulates the host response towards microflora by modulating T cell function and epithelial permeability in mouse Peyer\u2019s patches.","volume":"59","author":"Barreau","year":"2010","journal-title":"Gut"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1002\/bies.201600200","article-title":"MicroRNAs at the epicenter of intestinal homeostasis.","volume":"39","author":"Belcheva","year":"2017","journal-title":"BioEssays"},{"key":"B21","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1038\/nm1511","article-title":"Microbial translocation is a cause of systemic immune activation in chronic HIV infection.","volume":"12","author":"Brenchley","year":"2006","journal-title":"Nat. Med."},{"key":"B22","doi-asserted-by":"publisher","first-page":"749","DOI":"10.1084\/jem.20040874","article-title":"CD4+ T cell depletion during all stages of HIV disease occurs predominantly in the gastrointestinal tract.","volume":"200","author":"Brenchley","year":"2004","journal-title":"J. Exp. Med."},{"key":"B23","doi-asserted-by":"publisher","first-page":"2326","DOI":"10.1128\/AAC.02176-12","article-title":"Meta-analysis of antibiotics and the risk of community-associated Clostridium difficile infection.","volume":"57","author":"Brown","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"B24","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1038\/nature13828","article-title":"Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.","volume":"517","author":"Buffie","year":"2015","journal-title":"Nature"},{"key":"B25","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1016\/j.crohns.2007.08.006","article-title":"NOD2 activity modulates the phenotype of LPS-stimulated dendritic cells to promote the development of T-helper type 2-like lymphocytes \u2014 Possible implications for NOD2-associated Crohn\u2019s disease.","volume":"1","author":"Butler","year":"2007","journal-title":"J. Crohn\u2019s Colitis"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00498","article-title":"Outer membrane vesicles from probiotic and commensal Escherichia coli activate NOD1-mediated immune responses in intestinal epithelial cells.","volume":"9","author":"Ca\u00f1as","year":"2018","journal-title":"Front. Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/0092-8674(78)90305-7","article-title":"Sodium butyrate inhibits histone deacetylation in cultured cells.","volume":"14","author":"Candido","year":"1978","journal-title":"Cell"},{"key":"B28","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1093\/cid\/ciu084","article-title":"Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections.","volume":"58","author":"Carl","year":"2014","journal-title":"Clin. Infect. Dis."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0196551","article-title":"Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes.","volume":"13","author":"Carrasco Pro","year":"2018","journal-title":"PLoS One"},{"key":"B30","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1086\/655229","article-title":"Persistent microbial translocation and immune activation in HIV-1\u2013infected south africans receiving combination cntiretroviral therapy.","volume":"202","author":"Cassol","year":"2010","journal-title":"J. Infect. Dis."},{"key":"B31","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1016\/j.ijantimicag.2015.07.011","article-title":"Bacteriocins and their position in the next wave of conventional antibiotics.","volume":"46","author":"Cavera","year":"2015","journal-title":"Int. J. Antimicrob. Agents"},{"key":"B32","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1016\/j.chom.2010.09.005","article-title":"miR-146a mediates protective innate immune tolerance in the neonate Intestine.","volume":"8","author":"Chassin","year":"2010","journal-title":"Cell Host Microbe."},{"key":"B33","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1097\/QAD.0b013e328344cefb","article-title":"Sigmoid Th17 populations, the HIV latent reservoir, and microbial translocation in men on long-term antiretroviral therapy.","volume":"25","author":"Chege","year":"2011","journal-title":"AIDS"},{"key":"B34","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1038\/s41430-018-0377-6","article-title":"Effects of prebiotics on sepsis, necrotizing enterocolitis, mortality, feeding intolerance, time to full enteral feeding, length of hospital stay, and stool frequency in preterm infants: a meta-analysis.","volume":"73","author":"Chi","year":"2019","journal-title":"Eur. J. Clin. Nutr."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1104","DOI":"10.1016\/j.cell.2014.03.055","article-title":"An essential mesenchymal function for miR-143\/145 in intestinal epithelial regeneration.","volume":"157","author":"Chivukula","year":"2014","journal-title":"Cell"},{"key":"B36","doi-asserted-by":"publisher","first-page":"1475","DOI":"10.1177\/1535370217723166","article-title":"Tiny RNAs and their voyage via extracellular vesicles: secretion of bacterial small RNA and eukaryotic microRNA.","volume":"242","author":"Choi","year":"2017","journal-title":"Exp. Biol. Med."},{"key":"B37","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1016\/0923-2508(94)90031-0","article-title":"Preferential interaction of Salmonella typhimurium with mouse Peyer\u2019s patch M cells.","volume":"145","author":"Clark","year":"1994","journal-title":"Res. Microbiol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/j.micpath.2006.08.003","article-title":"An in vitro cell-culture model demonstrates internalin- and hemolysin-independent translocation of Listeria monocytogenes across M cells.","volume":"41","author":"Corr","year":"2006","journal-title":"Microb. Pathog."},{"key":"B39","doi-asserted-by":"crossref","first-page":"5549","DOI":"10.3748\/wjg.15.5549","article-title":"Short-chain fatty acids act as antiinflammatory mediators by regulating prostaglandin E(2) and cytokines.","volume":"15","author":"Cox","year":"2009","journal-title":"World J. Gastroenterol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"2109","DOI":"10.1002\/hep.27254","article-title":"Immune tolerance in liver disease.","volume":"60","author":"Crispe","year":"2014","journal-title":"Hepatology"},{"key":"B41","doi-asserted-by":"publisher","first-page":"16099","DOI":"10.1074\/jbc.M115.659318","article-title":"MicroRNA-193a-3p reduces intestinal inflammation in response to microbiota via down-regulation of colonic PepT1.","volume":"290","author":"Dai","year":"2015","journal-title":"J. Biol. Chem."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0019293","article-title":"Microbiota modulate host gene expression via microRNAs.","volume":"6","author":"Dalmasso","year":"2011","journal-title":"PLoS One"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.3390\/nu9060615","article-title":"Microbiota and probiotics in health and HIV Infection.","volume":"9","author":"D\u2019Angelo","year":"2017","journal-title":"Nutrients"},{"key":"B44","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.virol.2014.10.033","article-title":"Short chain fatty acids potently induce latent HIV-1 in T-cells by activating P-TEFb and multiple histone modifications.","volume":"474","author":"Das","year":"2015","journal-title":"Virology"},{"key":"B45","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1016\/j.immuni.2013.10.001","article-title":"Systemic effects of inflammation on health during chronic HIV infection.","volume":"39","author":"Deeks","year":"2013","journal-title":"Immunity"},{"key":"B46","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1097\/00004630-198711000-00005","article-title":"Bacterial translocation from the gut: a mechanism of infection.","volume":"8","author":"Deitch","year":"1987","journal-title":"J. Burn Care Rehabil."},{"key":"B47","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1097\/00024382-199402000-00010","article-title":"Evidence favoring the role of the gut as a cytokine-generating organ in rats subjected to hemorrhagic shock.","volume":"1","author":"Deitch","year":"1994","journal-title":"Shock"},{"key":"B48","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1016\/s0039-6060(03)00302-7","article-title":"Enterocyte apoptosis and barrier function are modulated by SIgA after exposure to bacteria and hypoxia\/reoxygenation.","volume":"134","author":"Diebel","year":"2003","journal-title":"Surgery"},{"key":"B49","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1097\/QAD.0000000000001366","article-title":"Low abundance of colonic butyrate-producing bacteria in HIV infection is associated with microbial translocation and immune activation.","volume":"31","author":"Dillon","year":"2017","journal-title":"AIDS"},{"key":"B50","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1038\/mi.2013.116","article-title":"An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia.","volume":"7","author":"Dillon","year":"2014","journal-title":"Mucosal Immunol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"885","DOI":"10.4049\/jimmunol.1200681","article-title":"HIV-1 infection of human intestinal lamina propria CD4+ T cells in vitro is enhanced by exposure to commensal Escherichia coli.","volume":"189","author":"Dillon","year":"2012","journal-title":"J. Immunol."},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-22662-6","article-title":"Trichostatin A inhibits the activation of Hepatic stellate cells by increasing C\/EBP-\u03b1 acetylation in vivo and in vitro.","volume":"8","author":"Ding","year":"2018","journal-title":"Sci. Rep."},{"key":"B53","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1164\/ajrccm.158.2.9710092","article-title":"Increased intestinal permeability is associated with the development of multiple organ dysfunction syndrome in critically Ill ICU patients.","volume":"158","author":"Doig","year":"1998","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B54","doi-asserted-by":"publisher","first-page":"3288","DOI":"10.1099\/mic.0.040139-0","article-title":"Lactobacillus rhamnosus GG attenuates interferon- and tumour necrosis factor- -induced barrier dysfunction and pro-inflammatory signalling.","volume":"156","author":"Donato","year":"2010","journal-title":"Microbiology"},{"key":"B55","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1016\/j.cmet.2011.02.018","article-title":"The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon.","volume":"13","author":"Donohoe","year":"2011","journal-title":"Cell Metab."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00441","article-title":"Common occurrence of antibacterial agents in human intestinal microbiota.","volume":"6","author":"Drissi","year":"2015","journal-title":"Front. Microbiol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"742","DOI":"10.4161\/rna.20018","article-title":"The mammalian microRNA response to bacterial infections.","volume":"9","author":"Eulalio","year":"2012","journal-title":"RNA Biol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"13477","DOI":"10.3748\/wjg.v20.i37.13477","article-title":"Complex interactions between microRNAs and hepatitis B\/C viruses.","volume":"20","author":"Fan","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.jim.2015.03.020","article-title":"Induction of Th17 cells by segmented filamentous bacteria in the murine intestine.","volume":"421","author":"Farkas","year":"2015","journal-title":"J. Immunol. Methods"},{"key":"B60","doi-asserted-by":"publisher","first-page":"2574","DOI":"10.1016\/j.bbadis.2017.03.005","article-title":"The intestinal microenvironment in sepsis.","volume":"1863","author":"Fay","year":"2017","journal-title":"Biochim. Biophys. Acta. - Mol. Basis Dis."},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00151","article-title":"Gut microbiota: an integral moderator in health and disease.","volume":"9","author":"Feng","year":"2018","journal-title":"Front. Microbiol."},{"key":"B62","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1159\/000492853","article-title":"Short-chain fatty acids manifest stimulative and protective effects on intestinal barrier function through the inhibition of NLRP3 inflammasome and autophagy.","volume":"49","author":"Feng","year":"2018","journal-title":"Cell Physiol. Biochem."},{"key":"B63","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1016\/j.yexmp.2014.04.009","article-title":"Elevated circulating miR-150 and miR-342-3p in patients with irritable bowel syndrome.","volume":"96","author":"Fourie","year":"2014","journal-title":"Exp. Mol. Pathol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1038\/nature09646","article-title":"Bifidobacteria can protect from enteropathogenic infection through production of acetate.","volume":"469","author":"Fukuda","year":"2011","journal-title":"Nature"},{"key":"B65","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0033715","article-title":"Therapeutic DNA vaccine induces broad T cell responses in the gut and sustained protection from viral rebound and AIDS in SIV-infected rhesus macaques.","volume":"7","author":"Fuller","year":"2012","journal-title":"PLoS One"},{"key":"B66","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nature12721","article-title":"Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.","volume":"504","author":"Furusawa","year":"2013","journal-title":"Nature"},{"key":"B67","doi-asserted-by":"publisher","DOI":"10.1155\/2018\/5823823","article-title":"Recent advances in the molecular mechanisms underlying pyroptosis in sepsis.","volume":"2018","author":"Gao","year":"2018","journal-title":"Mediators Inflamm."},{"key":"B68","doi-asserted-by":"publisher","first-page":"6268","DOI":"10.1128\/JVI.00097-14","article-title":"Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections.","volume":"88","author":"Gaulke","year":"2014","journal-title":"J. Virol."},{"key":"B69","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms6030075","article-title":"Akkermansia muciniphila in the human gastrointestinal tract: when, where, and how?","volume":"6","author":"Geerlings","year":"2018","journal-title":"Microorganisms"},{"key":"B70","doi-asserted-by":"publisher","first-page":"1882","DOI":"10.4049\/jimmunol.167.4.1882","article-title":"Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression.","volume":"167","author":"Gewirtz","year":"2001","journal-title":"J. Immunol."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002120","article-title":"A Salmonella small non-coding RNA facilitates bacterial invasion and intracellular replication by modulating the expression of virulence factors.","volume":"7","author":"Gong","year":"2011","journal-title":"PLoS Pathog."},{"key":"B72","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/icb.2012.80","article-title":"Intestinal epithelial cells as mediators of the commensal-host immune crosstalk.","volume":"91","author":"Goto","year":"2013","journal-title":"Immunol. Cell Biol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1093\/cid\/cir632","article-title":"Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection.","volume":"53","author":"Gough","year":"2011","journal-title":"Clin. Infect. Dis."},{"key":"B74","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-02669-1","article-title":"Salmonella produce microRNA-like RNA fragment Sal-1 in the infected cells to facilitate intracellular survival.","volume":"7","author":"Gu","year":"2017","journal-title":"Sci. Rep."},{"key":"B75","doi-asserted-by":"publisher","first-page":"11708","DOI":"10.1128\/jvi.77.21.11708-11717.2003","article-title":"Severe CD4+ T-cell depletion in gut lymphoid tissue during primary human immunodeficiency virus type 1 infection and substantial delay in restoration following highly active antiretroviral therapy.","volume":"77","author":"Guadalupe","year":"2003","journal-title":"J. Virol."},{"key":"B76","doi-asserted-by":"publisher","first-page":"1362","DOI":"10.1016\/s0002-9270(03)00250-8","article-title":"Small intestinal motility disturbances and bacterial overgrowth in patients with liver cirrhosis and portal hypertension.","volume":"98","author":"Gunnarsdottir","year":"2003","journal-title":"Am. J. Gastroenterol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/S2468-1253(16)30119-4","article-title":"The role of the gut microbiota in sepsis.","volume":"2","author":"Haak","year":"2017","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"44715","DOI":"10.1074\/jbc.m202524200","article-title":"Molecular mechanisms for lipopolysaccharide-induced biphasic Aactivation of nuclear factor-\u03baB (NF-\u03baB).","volume":"277","author":"Han","year":"2002","journal-title":"J. Biol. Chem."},{"key":"B79","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1097\/00024382-200115010-00001","article-title":"Post-injury multiple organ multiple organ failure:the role of the gut: shock.","volume":"15","author":"Hassoun","year":"2001","journal-title":"Shock"},{"key":"B80","doi-asserted-by":"publisher","first-page":"2361","DOI":"10.1007\/s10620-011-1649-3","article-title":"Dramatic changes of the gut flora immediately after severe and sudden Insults.","volume":"56","author":"Hayakawa","year":"2011","journal-title":"Dig. Dis. Sci."},{"key":"B81","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1038\/35074106","article-title":"The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5.","volume":"410","author":"Hayashi","year":"2001","journal-title":"Nature"},{"key":"B82","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nature10809","article-title":"Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity.","volume":"482","author":"Henao-Mejia","year":"2012","journal-title":"Nature"},{"key":"B83","doi-asserted-by":"publisher","first-page":"4981","DOI":"10.1128\/JVI.00099-16","article-title":"Effects of fecal microbial transplantation on microbiome and immunity in simian immunodeficiency virus-infected macaques.","volume":"90","author":"Hensley-McBain","year":"2016","journal-title":"J. Virol."},{"key":"B84","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2018.00357","article-title":"Increased virulence of bloodstream over peripheral isolates of P. aeruginosa identified through post-transcriptional regulation of virulence factors.","volume":"8","author":"Hickey","year":"2018","journal-title":"Front. Cell Infect. Microbiol."},{"key":"B85","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1084\/jem.20020005","article-title":"Multidrug efflux systems play an important role in the invasiveness of Pseudomonas aeruginosa.","volume":"196","author":"Hirakata","year":"2002","journal-title":"J. Exp. Med."},{"key":"B86","doi-asserted-by":"publisher","first-page":"1359","DOI":"10.1002\/ibd.21478","article-title":"NLRP3 inflammasome plays a key role in the regulation of intestinal homeostasis.","volume":"17","author":"Hirota","year":"2011","journal-title":"Inflamm. Bowel Dis."},{"key":"B87","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1126\/science.291.5505.881","article-title":"Molecular analysis of commensal host-microbial relationships in the intestine.","volume":"291","author":"Hooper","year":"2001","journal-title":"Science"},{"key":"B88","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1097\/00003246-199907000-00002","article-title":"Apoptotic cell death in patients with sepsis, shock, and multiple organ dysfunction.","volume":"27","author":"Hotchkiss","year":"1999","journal-title":"Crit. Care Med."},{"key":"B89","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1073\/pnas.93.3.1060","article-title":"Hsp90 is required for the activity of a hepatitis B virus reverse transcriptase.","volume":"93","author":"Hu","year":"1996","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B90","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0016221","article-title":"The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer.","volume":"6","author":"Hu","year":"2011","journal-title":"PLoS One"},{"key":"B91","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/gmic.2.2.15787","article-title":"Effect of 25 weeks probiotic supplementation on immune function of HIV patients.","volume":"2","author":"Hummelen","year":"2011","journal-title":"Gut. Microbes."},{"key":"B92","doi-asserted-by":"publisher","first-page":"485","DOI":"10.3109\/08830185.2010.505310","article-title":"Altered host-microbe interaction in HIV: a target for intervention with pro- and prebiotics.","volume":"29","author":"Hummelen","year":"2010","journal-title":"Int. Rev. Immunol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"2583","DOI":"10.1007\/s00018-012-0936-2","article-title":"Reactivation of latent HIV-1 by a wide variety of butyric acid-producing bacteria.","volume":"69","author":"Imai","year":"2012","journal-title":"Cell Mol. Life Sci."},{"key":"B94","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria.","volume":"139","author":"Ivanov","year":"2009","journal-title":"Cell"},{"key":"B95","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.chom.2008.09.009","article-title":"Specific microbiota direct the differentiation of Th17 cells in the mucosa of the small intestine.","volume":"4","author":"Ivanov","year":"2008","journal-title":"Cell Host Microbe"},{"key":"B96","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1084\/jem.190.2.229","article-title":"Freshly isolated Peyer\u2019s Patch, but not spleen, dendritic cells produce interleukin 10 and induce the differentiation of T helper type 2 cells.","volume":"190","author":"Iwasaki","year":"1999","journal-title":"J. Exp. Med."},{"key":"B97","doi-asserted-by":"publisher","DOI":"10.1186\/1757-4749-3-2","article-title":"Treating critically ill patients with probiotics: beneficial or dangerous?","volume":"3","author":"Jacobi","year":"2011","journal-title":"Gut. Pathog."},{"key":"B98","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1016\/j.clnu.2003.12.002","article-title":"Influence of synbiotic containing Lactobacillus acidophilus La5, Bifidobacterium lactis Bb 12, Streptococcus thermophilus, Lactobacillus bulgaricus and oligofructose on gut barrier function and sepsis in critically ill patients: a randomised controlled trial.","volume":"23","author":"Jain","year":"2004","journal-title":"Clin. Nutr."},{"key":"B99","doi-asserted-by":"publisher","first-page":"5363","DOI":"10.1128\/iai.69.9.5363-5374.2001","article-title":"Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia.","volume":"69","author":"Johnson","year":"2001","journal-title":"Infect. Immun."},{"key":"B100","doi-asserted-by":"publisher","first-page":"835","DOI":"10.1093\/ecco-jcc\/jjy038","article-title":"Loss of microRNA-21 influences the gut microbiota, causing reduced susceptibility in a murine model of colitis.","volume":"12","author":"Johnston","year":"2018","journal-title":"J. Crohn\u2019s Colitis"},{"key":"B101","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1111\/j.1462-5822.2011.01579.x","article-title":"Recognition of bacterial pathogens and mucosal immunity.","volume":"13","author":"Jones","year":"2011","journal-title":"Cell Microbiol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1007\/s10620-009-0870-9","article-title":"Association between small intestinal bacterial overgrowth and peripheral bacterial DNA in cirrhotic patients.","volume":"55","author":"Jun","year":"2010","journal-title":"Dig. Dis. Sci."},{"key":"B103","doi-asserted-by":"publisher","first-page":"313","DOI":"10.14348\/molcells.2019.2431","article-title":"Microbial colonization at early life promotes the development of diet-induced CD8\u03b1\u03b2 intraepithelial T cells.","volume":"42","author":"Jung","year":"2019","journal-title":"Mol. Cells."},{"key":"B104","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2017.01429","article-title":"Butyrate Conditions Human Dendritic Cells to Prime Type 1 Regulatory T Cells via both Histone Deacetylase Inhibition and G Protein-Coupled Receptor 109A Signaling.","volume":"8","author":"Kaisar","year":"2017","journal-title":"Front. Immunol."},{"key":"B105","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1007\/s00284-013-0411-9","article-title":"Identification of microRNA-Size, Small RNAs in Escherichia coli.","volume":"67","author":"Kang","year":"2013","journal-title":"Curr. Microbiol."},{"key":"B106","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1016\/j.jhin.2017.04.007","article-title":"Gut microbiota and hepatitis-B-virus-induced chronic liver disease: implications for faecal microbiota transplantation therapy.","volume":"96","author":"Kang","year":"2017","journal-title":"J. Hosp. Infect."},{"key":"B107","doi-asserted-by":"publisher","first-page":"18786","DOI":"10.1073\/pnas.0905859106","article-title":"Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection.","volume":"106","author":"Kantor","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B108","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1080\/19390211.2017.1380103","article-title":"Effect of probiotic supplementation on CD4 cell count in HIV-infected patients: a systematic review and meta-analysis.","volume":"15","author":"Kazemi","year":"2018","journal-title":"J. Diet Suppl."},{"key":"B109","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1016\/j.chom.2015.03.005","article-title":"Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function.","volume":"17","author":"Kelly","year":"2015","journal-title":"Cell Host Microbe"},{"key":"B110","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1097\/ALN.0b013e318291c2fc","article-title":"Probiotic administration reduces mortality and improves intestinal epithelial homeostasis in experimental sepsis.","volume":"119","author":"Khailova","year":"2013","journal-title":"Anesthesiology"},{"key":"B111","doi-asserted-by":"publisher","first-page":"2164","DOI":"10.4049\/jimmunol.1300829","article-title":"Mucosal Th17 cell function is altered during HIV infection and is an independent predictor of systemic immune activation.","volume":"191","author":"Kim","year":"2013","journal-title":"J. Immunol."},{"key":"B112","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.1128\/iai.72.3.1487-1495.2004","article-title":"Nod1 is an essential signal transducer in intestinal epithelial cells infected with bacteria that avoid recognition by toll-like receptors.","volume":"72","author":"Kim","year":"2004","journal-title":"Infect. Immun."},{"key":"B113","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1538\/expanim.48.137","article-title":"Changes in colonic mucosal permeability in mouse colitis induced with dextran sulfate sodium.","volume":"48","author":"Kitajima","year":"1999","journal-title":"Exp. Anim."},{"key":"B114","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1007\/bf01295730","article-title":"Intestinal mucosal inflammation associated with human immunodeficiency virus infection.","volume":"38","author":"Kotler","year":"1993","journal-title":"Dig. Dis. Sci."},{"key":"B115","doi-asserted-by":"publisher","first-page":"1848","DOI":"10.1007\/s00268-005-0653-1","article-title":"Benefits of a synbiotic formula (Synbiotic 2000Forte\u00ae) in critically Ill trauma patients: early results of a randomized controlled trial.","volume":"30","author":"Kotzampassi","year":"2006","journal-title":"World J. Surg."},{"key":"B116","doi-asserted-by":"publisher","first-page":"842.e2","DOI":"10.1053\/j.gastro.2013.07.001","article-title":"MicroRNA-124 regulates STAT3 expression and is down-regulated in colon tissues of pediatric patients with ulcerative colitis.","volume":"145","author":"Koukos","year":"2013","journal-title":"Gastroenterology"},{"key":"B117","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.01491","article-title":"The epigenetic control of hepatitis B virus modulates the outcome of infection.","volume":"6","author":"Koumbi","year":"2015","journal-title":"Front. Microbiol."},{"key":"B118","doi-asserted-by":"publisher","DOI":"10.1093\/femspd\/fty082","article-title":"Listeriolysin O-dependent host surfaceome remodeling modulates Listeria monocytogenes invasion.","volume":"76","author":"K\u00fchbacher","year":"2018","journal-title":"Pathog. Dis."},{"key":"B119","doi-asserted-by":"publisher","DOI":"10.3390\/nu10060731","article-title":"Targeting histone deacetylases with natural and synthetic agents: an emerging anticancer strategy.","volume":"10","author":"Kumar","year":"2018","journal-title":"Nutrients"},{"key":"B120","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.4049\/jimmunol.1701148","article-title":"miR-130a and miR-212 disrupt the intestinal epithelial barrier through modulation of PPAR\u03b3 and occludin expression in chronic simian immunodeficiency virus-infected rhesus macaques.","volume":"200","author":"Kumar","year":"2018","journal-title":"J. Immunol."},{"key":"B121","doi-asserted-by":"publisher","first-page":"5003","DOI":"10.1128\/JVI.00189-16","article-title":"Longitudinal examination of the intestinal lamina propria cellular compartment of simian immunodeficiency virus-infected Rhesus macaques provides broader and deeper insights into the link between aberrant microRNA expression and persistent immune activati.","volume":"90","author":"Kumar","year":"2016","journal-title":"J. Virol."},{"key":"B122","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1038\/nri2936","article-title":"Emerging inflammasome effector mechanisms.","volume":"11","author":"Lamkanfi","year":"2011","journal-title":"Nat. Rev. Immunol."},{"key":"B123","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a001651","article-title":"The nuclear factor NF-kappaB pathway in inflammation.","volume":"1","author":"Lawrence","year":"2009","journal-title":"Cold Spring Harb Perspect. Biol."},{"key":"B124","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1002\/rmv.696","article-title":"Interference with p53 functions in human viral infections, a target for novel antiviral strategies?","volume":"21","author":"Lazo","year":"2011","journal-title":"Rev. Med. Virol."},{"key":"B125","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1111\/j.1462-5822.2011.01720.x","article-title":"Viral interference with innate immunity bypreventing NF-kB activity.","volume":"14","author":"Le Negrate","year":"2012","journal-title":"Cell Microbiol."},{"key":"B126","doi-asserted-by":"publisher","first-page":"25481","DOI":"10.1074\/jbc.m301403200","article-title":"Functional characterization of human receptors for short chain fatty acids and their role in polymorphonuclear cell activation.","volume":"278","author":"Le Poul","year":"2003","journal-title":"J. Biol. Chem."},{"key":"B127","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1016\/j.immuni.2014.03.009","article-title":"Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses.","volume":"40","author":"L\u00e9cuyer","year":"2014","journal-title":"Immunity"},{"key":"B128","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-32585-x","article-title":"Enrichment of gut-derived Fusobacterium is associated with suboptimal immune recovery in HIV-infected individuals.","volume":"8","author":"Lee","year":"2018","journal-title":"Sci. Rep."},{"key":"B129","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/s00281-014-0451-7","article-title":"Inflammasomes and the microbiota\u2014partners in the preservation of mucosal homeostasis.","volume":"37","author":"Levy","year":"2015","journal-title":"Semin. Immunopathol."},{"key":"B130","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.3748\/wjg.v22.i4.1487","article-title":"MicroRNA-mediated interactions between host and hepatitis C virus.","volume":"22","author":"Li","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"B131","doi-asserted-by":"publisher","DOI":"10.3389\/fphar.2018.00233","article-title":"Time and concentration dependent effects of short chain fatty acids on lipopolysaccharide- or tumor necrosis factor \u03b1-induced endothelial activation.","volume":"9","author":"Li","year":"2018","journal-title":"Front. Pharmacol."},{"key":"B132","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1002\/path.2525","article-title":"Disruption of tight junctions during polymicrobial sepsis in vivo.","volume":"218","author":"Li","year":"2009","journal-title":"J. Pathol."},{"key":"B133","doi-asserted-by":"publisher","first-page":"602","DOI":"10.1038\/modpathol.2013.152","article-title":"Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity.","volume":"27","author":"Lin","year":"2014","journal-title":"Mod. Pathol."},{"key":"B134","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/0168-8278(95)80424-2","article-title":"Endotoxemia in patients with chronic liver diseases: relationship to severity of liver diseases, presence of esophageal varices, and hyperdynamic circulation.","volume":"22","author":"Lin","year":"1995","journal-title":"J. Hepatol."},{"key":"B135","doi-asserted-by":"publisher","DOI":"10.1038\/srep30673","article-title":"Alterations in the fecal microbiota of patients with HIV-1 infection: an observational study in a chinese population.","volume":"6","author":"Ling","year":"2016","journal-title":"Sci. Rep."},{"key":"B136","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.cellimm.2012.05.011","article-title":"Butyrate interferes with the differentiation and function of human monocyte-derived dendritic cells.","volume":"277","author":"Liu","year":"2012","journal-title":"Cell Immunol."},{"key":"B137","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1016\/j.chom.2015.12.005","article-title":"The host shapes the gut microbiota via fecal microRNA.","volume":"19","author":"Liu","year":"2016","journal-title":"Cell Host Microbe"},{"key":"B138","doi-asserted-by":"publisher","first-page":"176","DOI":"10.15698\/mic2016.04.492","article-title":"Control of the gut microbiome by fecal microRNA.","volume":"3","author":"Liu","year":"2016","journal-title":"Microb. Cell."},{"key":"B139","doi-asserted-by":"publisher","first-page":"1330","DOI":"10.1161\/01.cir.100.12.1330","article-title":"Inhibition of NF-kappaB activation by pyrrolidine dithiocarbamate prevents In vivo expression of proinflammatory genes.","volume":"100","author":"Liu","year":"1999","journal-title":"Circulation"},{"key":"B140","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0200322","article-title":"Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens.","volume":"13","author":"Livanos","year":"2018","journal-title":"PLoS One."},{"key":"B141","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1053\/jhep.2003.50116","article-title":"Oral bile acids reduce bacterial overgrowth, bacterial translocation, and endotoxemia in cirrhotic rats.","volume":"37","author":"Lorenzo-Z\u00fa\u00f1iga","year":"2003","journal-title":"Hepatology"},{"key":"B142","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1128\/MMBR.00052-12","article-title":"Role of pore-forming toxins in bacterial infectious diseases.","volume":"77","author":"Los","year":"2013","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"B143","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1007\/s00248-010-9801-8","article-title":"Intestinal microbiota was assessed in cirrhotic patients with hepatitis B virus infection.","volume":"61","author":"Lu","year":"2011","journal-title":"Microb. Ecol."},{"key":"B144","doi-asserted-by":"publisher","first-page":"1186","DOI":"10.1016\/j.jnutbio.2009.10.004","article-title":"Butyrate reduced lipopolysaccharide-mediated macrophage migration by suppression of Src enhancement and focal adhesion kinase activity.","volume":"21","author":"Maa","year":"2010","journal-title":"J. Nutr. Biochem."},{"key":"B145","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1136\/gut.45.2.223","article-title":"Gut origin of sepsis: a prospective study investigating associations between bacterial translocation, gastric microflora, and septic morbidity.","volume":"45","author":"MacFie","year":"1999","journal-title":"Gut"},{"key":"B146","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7734","article-title":"Metabolite-sensing receptors GPR43 and GPR109A facilitate dietary fibre-induced gut homeostasis through regulation of the inflammasome.","volume":"6","author":"Macia","year":"2015","journal-title":"Nat. Commun."},{"key":"B147","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1016\/j.chom.2016.10.016","article-title":"The liver at the nexus of host-microbial interactions.","volume":"20","author":"Macpherson","year":"2016","journal-title":"Cell Host Microbe"},{"key":"B148","doi-asserted-by":"publisher","first-page":"F456","DOI":"10.1136\/fetalneonatal-2011-301373","article-title":"Gut microbial colonisation in premature neonates predicts neonatal sepsis.","volume":"97","author":"Madan","year":"2012","journal-title":"Arch. Dis. Child Fetal. Neonatal. Ed."},{"key":"B149","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1016\/j.crohns.2013.06.001","article-title":"European consensus on the histopathology of inflammatory bowel disease.","volume":"7","author":"Magro","year":"2013","journal-title":"J. Crohn\u2019s Colitis"},{"key":"B150","doi-asserted-by":"publisher","first-page":"316","DOI":"10.4161\/gmic.25486","article-title":"Altered enteric microbiota ecology in interleukin 10-deficient mice during development and progression of intestinal inflammation.","volume":"4","author":"Maharshak","year":"2013","journal-title":"Gut Microbes"},{"key":"B151","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0052876","article-title":"Distortions in development of intestinal microbiota associated with late onset sepsis in preterm infants.","volume":"8","author":"Mai","year":"2013","journal-title":"PLoS One"},{"key":"B152","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1097\/00024382-199509000-00007","article-title":"The gut: a cytokine-generating organ in systemic inflammation?","volume":"4","author":"Mainous","year":"1995","journal-title":"Shock"},{"key":"B153","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1001\/archsurg.1991.01410250037005","article-title":"Studies of the route, magnitude, and time course of bacterial translocation in a model of systemic inflammation.","volume":"126","author":"Mainous","year":"1991","journal-title":"Arch. Surg."},{"key":"B154","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1186\/ar300","article-title":"NF-kappa B in rheumatoid arthritis: a pivotal regulator of inflammation, hyperplasia, and tissue destruction.","volume":"3","author":"Makarov","year":"2001","journal-title":"Arthritis Res."},{"key":"B155","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1128\/CMR.00050-12","article-title":"Microbial translocation in the pathogenesis of HIV infection and AIDS.","volume":"26","author":"Marchetti","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"B156","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-41738-5","article-title":"The potential probiotic Lactobacillus rhamnosus CNCM I-3690 strain protects the intestinal barrier by stimulating both mucus production and cytoprotective response.","volume":"9","author":"Mart\u00edn","year":"2019","journal-title":"Sci. Rep."},{"key":"B157","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-28048-y","article-title":"Butyrate produced by gut commensal bacteria activates TGF-beta1 expression through the transcription factor SP1 in human intestinal epithelial cells.","volume":"8","author":"Martin-Gallausiaux","year":"2018","journal-title":"Sci. Rep."},{"key":"B158","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1159\/000335672","article-title":"Short-chain fatty acids induce apoptosis in colon cancer cells associated with changes to intracellular redox state and glucose metabolism.","volume":"58","author":"Matthews","year":"2012","journal-title":"Chemotherapy"},{"key":"B159","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1038\/nature07008","article-title":"A microbial symbiosis factor prevents intestinal inflammatory disease.","volume":"453","author":"Mazmanian","year":"2008","journal-title":"Nature"},{"key":"B160","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00199-16","article-title":"Extreme dysbiosis of the microbiome in critical illness.","volume":"1","author":"McDonald","year":"2016","journal-title":"mSphere"},{"key":"B161","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1097\/01.qai.0000131846.12453.29","article-title":"Increased HIV-1 mucosal replication is associated with generalized mucosal cytokine activation.","volume":"37","author":"McGowan","year":"2004","journal-title":"J. Acquir. Immune. Defic. Syndr."},{"key":"B162","doi-asserted-by":"publisher","first-page":"145","DOI":"10.3851\/IMP2551","article-title":"Therapy for latent HIV-1 infection: the role of histone deacetylase inhibitors.","volume":"23","author":"McManamy","year":"2014","journal-title":"Antivir. Chem. Chemother."},{"key":"B163","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1097\/MCO.0b013e32833eebe5","article-title":"Butyrate and other short-chain fatty acids as modulators of immunity: what relevance for health?","volume":"13","author":"Meijer","year":"2010","journal-title":"Curr. Opin. Clin. Nutr. Metab. Care."},{"key":"B164","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1097\/MCC.0000000000000386","article-title":"New insights into the gut as the driver of critical illness and organ failure.","volume":"23","author":"Meng","year":"2017","journal-title":"Curr. Opin. Crit. Care."},{"key":"B165","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018580","article-title":"Evidence for polymicrobic flora translocating in peripheral blood of HIV-infected patients with poor immune response to antiretroviral therapy.","volume":"6","author":"Merlini","year":"2011","journal-title":"PLoS One"},{"key":"B166","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1016\/j.molmed.2013.08.004","article-title":"Redefining the gut as the motor of critical illness.","volume":"20","author":"Mittal","year":"2014","journal-title":"Trends Mol. Med."},{"key":"B167","doi-asserted-by":"publisher","first-page":"323.e7","DOI":"10.1053\/j.gastro.2010.03.052","article-title":"Toll-like receptor 9 promotes steatohepatitis by induction of interleukin-1beta in mice.","volume":"139","author":"Miura","year":"2010","journal-title":"Gastroenterology"},{"key":"B168","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v20.i23.7381","article-title":"Role of gut microbiota and Toll-like receptors in nonalcoholic fatty liver disease.","volume":"20","author":"Miura","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"B169","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1093\/ecco-jcc\/jjw033","article-title":"MicroRNA 429 regulates mucin gene expression and secretion in murine model of colitis.","volume":"10","author":"Mo","year":"2016","journal-title":"J. Crohn\u2019s Colitis"},{"key":"B170","doi-asserted-by":"publisher","first-page":"291","DOI":"10.4049\/jimmunol.1401447","article-title":"Dysregulated miR-34a\u2013SIRT1\u2013acetyl p65 axis is a potential mediator of immune activation in the colon during chronic simian immunodeficiency virus infection of Rhesus macaques.","volume":"194","author":"Mohan","year":"2015","journal-title":"J. Immunol."},{"key":"B171","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1159\/000479918","article-title":"Bacterial translocation from the gut to the distant organs: an overview.","volume":"71","author":"Nagpal","year":"2017","journal-title":"Ann. Nutr. Metab."},{"key":"B172","doi-asserted-by":"publisher","first-page":"1723","DOI":"10.4049\/jimmunol.1002311","article-title":"Mechanistic role of microRNA-146a in endotoxin-induced differential cross-regulation of TLR signaling.","volume":"186","author":"Nahid","year":"2011","journal-title":"J. Immunol."},{"key":"B173","doi-asserted-by":"publisher","first-page":"15426","DOI":"10.1074\/jbc.M117.788596","article-title":"Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through the small GTPase ARF4.","volume":"292","author":"Nakata","year":"2017","journal-title":"J. Biol. Chem."},{"key":"B174","doi-asserted-by":"publisher","DOI":"10.1038\/srep16148","article-title":"The effect of short-chain fatty acids on human monocyte-derived dendritic cells.","volume":"5","author":"Nastasi","year":"2015","journal-title":"Sci. Rep."},{"key":"B175","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000852","article-title":"Exposure to HIV-1 directly impairs mucosal epithelial barrier integrity allowing microbial translocation.","volume":"6","author":"Nazli","year":"2010","journal-title":"PLoS Pathog."},{"key":"B176","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1016\/j.ebiom.2018.03.024","article-title":"Fecal microbiota composition drives immune activation in HIV-infected individuals.","volume":"30","author":"Neff","year":"2018","journal-title":"EBioMedicine"},{"key":"B177","doi-asserted-by":"publisher","first-page":"5853","DOI":"10.1128\/jb.178.20.5853-5859.1996","article-title":"Multidrug Efflux Pumps of Gram-Negative Bacteria [Internet].","volume":"178","author":"Nikaido","year":"1996","journal-title":"J. Bacteriol."},{"key":"B178","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1111\/j.1365-2958.2005.04940.x","article-title":"Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium.","volume":"59","author":"Nishino","year":"2006","journal-title":"Mol. Microbiol."},{"key":"B179","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-16189-5","article-title":"Analysis of the gut microbiome and plasma short-chain fatty acid profiles in a spontaneous mouse model of metabolic syndrome.","volume":"7","author":"Nishitsuji","year":"2017","journal-title":"Sci. Rep."},{"key":"B180","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1038\/sj.embor.7400731","article-title":"The gut flora as a forgotten organ.","volume":"7","author":"O\u2019Hara","year":"2006","journal-title":"EMBO Rep."},{"key":"B181","doi-asserted-by":"publisher","first-page":"1625","DOI":"10.1086\/317625","article-title":"Human immunodeficiency virus type 1 infection is associated with significant mucosal inflammation characterized by increased expression of CCR5, CXCR4, and \u03b2-chemokines.","volume":"182","author":"Olsson","year":"2000","journal-title":"J. Infect Dis."},{"key":"B182","doi-asserted-by":"publisher","first-page":"469","DOI":"10.4161\/rna.19317","article-title":"Dynamics of Salmonella small RNA expression in non-growing bacteria located inside eukaryotic cells.","volume":"9","author":"Ortega","year":"2012","journal-title":"RNA Biol."},{"key":"B183","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1038\/mi.2015.75","article-title":"IL-21 and probiotic therapy improve Th17 frequencies, microbial translocation and microbiome in ARV-treated, SIV-infected macaques.","volume":"9","author":"Ortiz","year":"2016","journal-title":"Mucosal Immunol."},{"key":"B184","doi-asserted-by":"publisher","first-page":"1913","DOI":"10.1093\/nar\/gkn050","article-title":"Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence.","volume":"36","author":"Padalon-Brauch","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"B185","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0095476","article-title":"Short-term effect of antibiotics on human gut microbiota.","volume":"9","author":"Panda","year":"2014","journal-title":"PLoS One"},{"key":"B186","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.00426","article-title":"Microbiome dependent regulation of Tregs and Th17 cells in mucosa.","volume":"10","author":"Pandiyan","year":"2019","journal-title":"Front. Immunol."},{"key":"B187","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nature23480","article-title":"A randomized synbiotic trial to prevent sepsis among infants in rural India.","volume":"548","author":"Panigrahi","year":"2017","journal-title":"Nature"},{"key":"B188","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00700-17","article-title":"Lactobacillus rhamnosus L34 attenuates gut translocation-induced bacterial sepsis in murine models of leaky gut.","volume":"86","author":"Panpetch","year":"2017","journal-title":"Infect Immun."},{"key":"B189","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1016\/j.redox.2017.03.006","article-title":"Butyrate induces ROS-mediated apoptosis by modulating miR-22\/SIRT-1 pathway in hepatic cancer cells.","volume":"12","author":"Pant","year":"2017","journal-title":"Redox Biol."},{"key":"B190","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1590\/s1516-89132007000300018","article-title":"Bacteriocins from lactic acid bacteria: purification, properties and use as biopreservatives.","volume":"50","author":"Parada","year":"2007","journal-title":"Brazilian Arch. Biol. Technol."},{"key":"B191","doi-asserted-by":"publisher","first-page":"4820","DOI":"10.1111\/bph.12590","article-title":"A new histone deacetylase inhibitor improves liver fibrosis in BDL rats through suppression of hepatic stellate cells.","volume":"171","author":"Park","year":"2014","journal-title":"Br. J. Pharmacol."},{"key":"B192","doi-asserted-by":"publisher","first-page":"15975","DOI":"10.1074\/jbc.M116.733733","article-title":"miR-30 Family Controls Proliferation and Differentiation of Intestinal Epithelial Cell Models by Directing a Broad Gene Expression Program That Includes SOX9 and the Ubiquitin Ligase Pathway.","volume":"291","author":"Peck","year":"2016","journal-title":"J. Biol. Chem."},{"key":"B193","doi-asserted-by":"publisher","first-page":"613","DOI":"10.2174\/157016211798998808","article-title":"Induction of strong anti-HIV cellular immunity by a combination of Clostridium perfringens expressing HIV gag and virus like particles.","volume":"9","author":"Pegu","year":"2011","journal-title":"Curr. HIV Res."},{"key":"B194","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1046\/j.1365-2958.1997.3741745.x","article-title":"Non-invasive Salmonella typhimurium mutants are avirulent because of an inability to enter and destroy M cells of ileal Peyer\u2019s patches.","volume":"24","author":"Penheiter","year":"1997","journal-title":"Mol. Microbiol."},{"key":"B195","doi-asserted-by":"publisher","first-page":"1591","DOI":"10.1136\/gutjnl-2012-303184","article-title":"Gut microbiota disturbance during antibiotic therapy: a multi-omic approach.","volume":"62","author":"P\u00e9rez-Cobas","year":"2013","journal-title":"Gut"},{"key":"B196","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1136\/gut.47.3.377","article-title":"Enterohaemorrhagic Escherichia coli O157:H7 target Peyer\u2019s patches in humans and cause attaching\/effacing lesions in both human and bovine intestine.","volume":"47","author":"Phillips","year":"2000","journal-title":"Gut"},{"key":"B197","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1097\/COH.0000000000000428","article-title":"Impact of antiretroviral drugs on the microbiome: unknown answers to important questions.","volume":"13","author":"Pinto-Cardoso","year":"2018","journal-title":"Curr. Opin. HIV AIDS"},{"key":"B198","doi-asserted-by":"publisher","DOI":"10.1038\/srep43741","article-title":"Fecal bacterial communities in treated HIV infected individuals on two antiretroviral regimens.","volume":"7","author":"Pinto-Cardoso","year":"2017","journal-title":"Sci. Rep."},{"key":"B199","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1053\/j.gastro.2006.01.001","article-title":"Hepatitis B virus replication is regulated by the acetylation status of hepatitis B virus cccDNA-bound H3 and H4 histones.","volume":"130","author":"Pollicino","year":"2006","journal-title":"Gastroenterology"},{"key":"B200","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v21.i43.12322","article-title":"Effect of rifaximin on gut microbiota composition in advanced liver disease and its complications.","volume":"21","author":"Ponziani","year":"2015","journal-title":"World J. Gastroenterol."},{"key":"B201","doi-asserted-by":"publisher","first-page":"5067","DOI":"10.4049\/jimmunol.167.9.5067","article-title":"Lipopolysaccharides from distinct pathogens induce different classes of immune responses in vivo.","volume":"167","author":"Pulendran","year":"2001","journal-title":"J. Immunol."},{"key":"B202","doi-asserted-by":"publisher","first-page":"2125","DOI":"10.1111\/j.1462-2920.2007.01369.x","article-title":"Diversity of the human gastrointestinal tract microbiota revisited.","volume":"9","author":"Rajili\u0107-Stojanovi\u0107","year":"2007","journal-title":"Environ. Microbiol."},{"key":"B203","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.idc.2014.11.009","article-title":"Fecal microbiota transplantation for the management of Clostridium difficile infection.","volume":"29","author":"Rao","year":"2015","journal-title":"Infect Dis. Clin. North Am."},{"key":"B204","doi-asserted-by":"publisher","first-page":"9352","DOI":"10.1073\/pnas.0913554107","article-title":"Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile.","volume":"107","author":"Rea","year":"2010","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B205","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2019.00564","article-title":"Effect of Bacillus subtilis strains on intestinal barrier function and inflammatory response.","volume":"10","author":"Rhayat","year":"2019","journal-title":"Front. Immunol."},{"key":"B206","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.immuni.2012.09.017","article-title":"Pathogen-specific inflammatory milieux tune the antigen sensitivity of CD8+ T cells by enhancing T cell receptor signaling.","volume":"38","author":"Richer","year":"2013","journal-title":"Immunity"},{"key":"B207","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1097\/mog.0000000000000057","article-title":"Bile acids and the gut microbiome.","volume":"30","author":"Ridlon","year":"2014","journal-title":"Curr. Opin. Gastroenterol."},{"key":"B208","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/mi.2015.121","article-title":"Antigen sampling by intestinal M cells is the principal pathway initiating mucosal IgA production to commensal enteric bacteria.","volume":"9","author":"Rios","year":"2016","journal-title":"Mucosal Immunol."},{"key":"B209","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1126\/science.1139253","article-title":"Requirement of bic\/microRNA-155 for normal immune function.","volume":"316","author":"Rodriguez","year":"2007","journal-title":"Science"},{"key":"B210","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1136\/gut.21.9.793","article-title":"Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man.","volume":"21","author":"Roediger","year":"1980","journal-title":"Gut"},{"key":"B211","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2015.0504","article-title":"When pathogenic bacteria meet the intestinal microbiota.","volume":"371","author":"Rolhion","year":"2016","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"B212","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1002\/hep4.1325","article-title":"Effect of a multistrain probiotic on cognitive function and risk of falls in patients with cirrhosis: a randomized trial.","volume":"3","author":"Rom\u00e1n","year":"2019","journal-title":"Hepatol. Commun."},{"key":"B213","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1126\/science.1206095","article-title":"The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota.","volume":"332","author":"Round","year":"2011","journal-title":"Science"},{"key":"B214","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1001\/archsurg.2009.51","article-title":"Fulminant Clostridium difficile colitis.","volume":"144","author":"Sailhamer","year":"2009","journal-title":"Arch. Surg."},{"key":"B215","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1128\/jvi.01449-07","article-title":"Rapid onset of intestinal epithelial barrier dysfunction in primary human immunodeficiency virus infection is driven by an imbalance between immune response and mucosal repair and regeneration.","volume":"82","author":"Sankaran","year":"2008","journal-title":"J. Virol."},{"key":"B216","doi-asserted-by":"publisher","first-page":"9860","DOI":"10.1073\/pnas.0503463102","article-title":"Gut mucosal T cell responses and gene expression correlate with protection against disease in long-term HIV-1-infected nonprogressors.","volume":"102","author":"Sankaran","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B217","doi-asserted-by":"publisher","first-page":"2552","DOI":"10.1093\/emboj\/cdg267","article-title":"NF-kappaB and virus infection: who controls whom.","volume":"22","author":"Santoro","year":"2003","journal-title":"EMBO J."},{"key":"B218","doi-asserted-by":"publisher","first-page":"4081","DOI":"10.4049\/jimmunol.1403169","article-title":"No vacancy: How beneficial microbes cooperate with immunity to provide colonization resistance to pathogens.","volume":"194","author":"Sassone-Corsi","year":"2015","journal-title":"J. Immunol."},{"key":"B219","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1002\/rmv.1738","article-title":"Genome guardian p53 and viral infections.","volume":"23","author":"Sato","year":"2013","journal-title":"Rev. Med. Virol."},{"key":"B220","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1097\/mog.0b013e32835ff948","article-title":"Linking intestinal homeostasis and liver disease.","volume":"29","author":"Schnabl","year":"2013","journal-title":"Curr. Opin. Gastroenterol."},{"key":"B221","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1053\/j.gastro.2014.01.020","article-title":"Interactions between the intestinal microbiome and liver diseases.","volume":"146","author":"Schnabl","year":"2014","journal-title":"Gastroenterology"},{"key":"B222","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/j.mib.2017.03.004","article-title":"Segmented filamentous bacteria, Th17 inducers and helpers in a hostile world.","volume":"35","author":"Schnupf","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"B223","doi-asserted-by":"publisher","first-page":"1324","DOI":"10.1038\/nm1663","article-title":"TLR4 enhances TGF-\u03b2 signaling and hepatic fibrosis.","volume":"13","author":"Seki","year":"2007","journal-title":"Nat. Med."},{"key":"B224","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1113\/jphysiol.2011.219691","article-title":"Role of innate immunity and the microbiota in liver fibrosis: crosstalk between the liver and gut.","volume":"590","author":"Seki","year":"2012","journal-title":"J. Physiol."},{"key":"B225","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/916202","article-title":"The functional polymorphisms of miR-146a are associated with susceptibility to severe sepsis in the Chinese population.","volume":"2014","author":"Shao","year":"2014","journal-title":"Mediators Inflamm."},{"key":"B226","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1097\/01.ta.0000197374.99755.fe","article-title":"Altered gut flora and environment in patients with severe SIRS.","volume":"60","author":"Shimizu","year":"2006","journal-title":"J. Trauma"},{"key":"B227","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1007\/s10620-010-1418-8","article-title":"Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome.","volume":"56","author":"Shimizu","year":"2011","journal-title":"Dig. Dis. Sci."},{"key":"B228","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1023\/b:joci.0000018062.01980.ba","article-title":"Lipopolysaccharide induces CD25-Positive, IL-10-producing lymphocytes without secretion of proinflammatory cytokines in the human colon: low MD-2 mRNA expression in colonic macrophages.","volume":"24","author":"Shirai","year":"2004","journal-title":"J. Clin. Immunol."},{"key":"B229","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/j.tim.2013.02.005","article-title":"Reactivation of latent HIV by histone deacetylase inhibitors.","volume":"21","author":"Shirakawa","year":"2013","journal-title":"Trends Microbiol."},{"key":"B230","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1001\/jama.2016.0287","article-title":"The third international consensus definitions for sepsis and septic shock (sepsis-3).","volume":"315","author":"Singer","year":"2016","journal-title":"JAMA"},{"key":"B231","doi-asserted-by":"publisher","first-page":"171","DOI":"10.7150\/ijbs.8.171","article-title":"The murine caecal microRNA signature depends on the presence of the endogenous microbiota.","volume":"8","author":"Singh","year":"2012","journal-title":"Int. J. Biol. Sci."},{"key":"B232","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1093\/femsre\/fuz004","article-title":"Inner sensors of endotoxin \u2013 implications for sepsis research and therapy.","volume":"43","author":"Skirecki","year":"2019","journal-title":"FEMS Microbiol. Rev."},{"key":"B233","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061250","article-title":"Genetic polymorphisms of miR-146a and miR-27a, H. pylori infection, and risk of gastric lesions in a chinese population.","volume":"8","author":"Song","year":"2013","journal-title":"PLoS One"},{"key":"B234","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/608456","article-title":"Role of pore-forming toxins in neonatal sepsis.","volume":"2013","author":"Sonnen","year":"2013","journal-title":"Clin. Dev. Immunol."},{"key":"B235","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41385-018-0053-0","article-title":"Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them.","volume":"12","author":"Sorbara","year":"2018","journal-title":"Mucosal Immunol."},{"key":"B236","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41385-018-0053-0","article-title":"Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them.","volume":"12","author":"Sorbara","year":"2019","journal-title":"Mucosal Immunol."},{"key":"B237","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.02667","article-title":"Commensal bacteria-specific CD4+ T cell responses in health and disease.","volume":"9","author":"Sorini","year":"2018","journal-title":"Front. Immunol."},{"key":"B238","doi-asserted-by":"publisher","first-page":"4137","DOI":"10.4049\/jimmunol.173.6.4137","article-title":"The essential role of the intestinal microbiota in facilitating acute inflammatory responses.","volume":"173","author":"Souza","year":"2004","journal-title":"J. Immunol."},{"key":"B239","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1016\/j.clnu.2013.05.009","article-title":"Prebiotic supplementation in preterm neonates: updated systematic review and meta-analysis of randomised controlled trials.","volume":"32","author":"Srinivasjois","year":"2013","journal-title":"Clin. Nutr."},{"key":"B240","doi-asserted-by":"publisher","first-page":"1496","DOI":"10.1111\/cmi.12159","article-title":"MicroRNAs and bacterial infection.","volume":"15","author":"Staedel","year":"2013","journal-title":"Cell Microbiol."},{"key":"B241","doi-asserted-by":"publisher","first-page":"1522","DOI":"10.1136\/gut.52.10.1522","article-title":"The dendritic cell: its role in intestinal inflammation and relationship with gut bacteria.","volume":"52","author":"Stagg","year":"2003","journal-title":"Gut"},{"key":"B242","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0097171","article-title":"Contribution of intestinal barrier damage, microbial translocation and HIV-1 infection status to an inflammaging signature.","volume":"9","author":"Steele","year":"2014","journal-title":"PLoS One"},{"key":"B243","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.jevs.2017.02.009","article-title":"Alterations in intestinal permeability: the role of the \u201cLeaky Gut\u201d in health and disease.","volume":"52","author":"Stewart","year":"2017","journal-title":"J. Equine Vet. Sci."},{"key":"B244","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0295-1","article-title":"Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls.","volume":"5","author":"Stewart","year":"2017","journal-title":"Microbiome"},{"key":"B245","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1053\/he.2000.5634","article-title":"Kupffer cell activation by lipopolysaccharide in rats: role for lipopolysaccharide binding protein and toll-like receptor 4.","volume":"31","author":"Su","year":"2000","journal-title":"Hepatology"},{"key":"B246","doi-asserted-by":"publisher","first-page":"7633","DOI":"10.1021\/acs.jafc.8b01189","article-title":"Sodium butyrate ameliorates high-fat-diet-induced non-alcoholic fatty liver disease through peroxisome proliferator-activated receptor \u03b1-mediated activation of \u03b2 oxidation and suppression of inflammation.","volume":"66","author":"Sun","year":"2018","journal-title":"J. Agric. Food Chem."},{"key":"B247","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0130604","article-title":"Center variation in intestinal microbiota prior to late-onset sepsis in preterm infants.","volume":"10","author":"Taft","year":"2015","journal-title":"PLoS One"},{"key":"B248","doi-asserted-by":"publisher","first-page":"12481","DOI":"10.1073\/pnas.0605298103","article-title":"NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses.","volume":"103","author":"Taganov","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"key":"B249","doi-asserted-by":"publisher","first-page":"10427","DOI":"10.1128\/JVI.01035-09","article-title":"Cochaperone activity of human butyrate-induced transcript 1 facilitates hepatitis C virus replication through an Hsp90-dependent pathway.","volume":"83","author":"Taguwa","year":"2009","journal-title":"J. Virol."},{"key":"B250","doi-asserted-by":"publisher","first-page":"2631","DOI":"10.1128\/jvi.02153-07","article-title":"Human butyrate-induced transcript 1 interacts with hepatitis C virus NS5A and regulates viral replication.","volume":"82","author":"Taguwa","year":"2008","journal-title":"J. Virol."},{"key":"B251","doi-asserted-by":"publisher","first-page":"1420","DOI":"10.1126\/science.1213214","article-title":"Interconversion between intestinal stem cell populations in distinct niches.","volume":"334","author":"Takeda","year":"2011","journal-title":"Science"},{"key":"B252","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1002\/ijc.25638","article-title":"G-protein-coupled receptor for short-chain fatty acids suppresses colon cancer.","volume":"128","author":"Tang","year":"2011","journal-title":"Int. J. Cancer"},{"key":"B253","doi-asserted-by":"publisher","first-page":"351","DOI":"10.3920\/BM2013.0030","article-title":"In vitro study of beneficial properties and safety of lactic acid bacteria isolated from Portuguese fermented meat products.","volume":"5","author":"Todorov","year":"2014","journal-title":"Benef. Microbes"},{"key":"B254","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2012.00111","article-title":"Short-chain free fatty acid receptors FFA2\/GPR43 and FFA3\/GPR41 as new potential therapeutic targets.","volume":"3","author":"Ulven","year":"2012","journal-title":"Front. Endocrinol."},{"key":"B255","doi-asserted-by":"publisher","first-page":"20858","DOI":"10.1073\/pnas.0808723105","article-title":"Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface.","volume":"105","author":"Vaishnava","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B256","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-25308-9","article-title":"Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.","volume":"8","author":"Vdovikova","year":"2018","journal-title":"Sci. Rep."},{"key":"B257","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1126\/science.280.5362.427","article-title":"Gastrointestinal tract as a major site of CD4+ T cell depletion and viral replication in SIV infection.","volume":"280","author":"Veazey","year":"1998","journal-title":"Science"},{"key":"B258","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1038\/onc.2009.334","article-title":"Histone deacetylases and the immunological network: implications in cancer and inflammation.","volume":"29","author":"Villagra","year":"2010","journal-title":"Oncogene"},{"key":"B259","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-1-18","article-title":"Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection.","volume":"1","author":"Vincent","year":"2013","journal-title":"Microbiome"},{"key":"B260","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1016\/j.jnutbio.2010.07.009","article-title":"Suppressive effect of short-chain fatty acids on production of proinflammatory mediators by neutrophils.","volume":"22","author":"Vinolo","year":"2011","journal-title":"J. Nutr. Biochem."},{"key":"B261","doi-asserted-by":"publisher","first-page":"5398","DOI":"10.4049\/jimmunol.173.9.5398","article-title":"Beta-defensin-2 expression is regulated by TLR signaling in intestinal epithelial cells.","volume":"173","author":"Vora","year":"2004","journal-title":"J. Immunol."},{"key":"B262","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1080\/19490976.2017.1334034","article-title":"Limited engraftment of donor microbiome via one-time fecal microbial transplantation in treated HIV-infected individuals.","volume":"8","author":"Vujkovic-Cvijin","year":"2017","journal-title":"Gut Microbes"},{"key":"B263","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/s0092-8674(00)81564-0","article-title":"E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy.","volume":"100","author":"Wallace","year":"2000","journal-title":"Cell"},{"key":"B264","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1111\/sji.12515","article-title":"The inflammation induced by lipopolysaccharide can be mitigated by short-chain fatty acid, butyrate, through upregulation of IL-10 in septic shock.","volume":"85","author":"Wang","year":"2017","journal-title":"Scand. J. Immunol."},{"key":"B265","doi-asserted-by":"publisher","first-page":"3126","DOI":"10.1007\/s10620-012-2259-4","article-title":"Butyrate enhances intestinal epithelial barrier function via up-regulation of tight junction protein claudin-1 transcription.","volume":"57","author":"Wang","year":"2012","journal-title":"Dig. Dis. Sci."},{"key":"B266","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.vetimm.2006.04.006","article-title":"Butyrate differentially regulates cytokines and proliferation in porcine peripheral blood mononuclear cells.","volume":"113","author":"Weber","year":"2006","journal-title":"Vet. Immunol. Immunopathol."},{"key":"B267","doi-asserted-by":"crossref","DOI":"10.1186\/s13054-016-1491-2","article-title":"Successful treatment with fecal microbiota transplantation in patients with multiple organ dysfunction syndrome and diarrhea following severe sepsis.","volume":"20","author":"Wei","year":"2016","journal-title":"Crit. Care"},{"key":"B268","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1016\/j.jhep.2017.05.007","article-title":"Targeting the gut-liver axis in liver disease.","volume":"67","author":"Wiest","year":"2017","journal-title":"J. Hepatol."},{"key":"B269","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2017.01896","article-title":"MicroRNAs-Based Inter-Domain Communication between the Host and Members of the Gut Microbiome.","volume":"8","author":"Williams","year":"2017","journal-title":"Front. Microbiol."},{"key":"B270","doi-asserted-by":"publisher","first-page":"1729","DOI":"10.1002\/ibd.21267","article-title":"Identification of microRNAs associated with ileal and colonic Crohn\u2019s disease.","volume":"16","author":"Wu","year":"2010","journal-title":"Inflamm. Bowel Dis."},{"key":"B271","first-page":"929","author":"Wu","year":"2012","journal-title":"Assessment of the fecal lactobacilli population in patients with hepatitis B virus-related decompensated cirrhosis and hepatitis B cirrhosis treated with liver transplant, Microbial Ecology."},{"key":"B272","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1002\/eji.201343717","article-title":"Downregulation of microRNA-107 in intestinal CD11c + myeloid cells in response to microbiota and proinflammatory cytokines increases IL-23p19 expression.","volume":"44","author":"Xue","year":"2014","journal-title":"Eur. J. Immunol."},{"key":"B273","doi-asserted-by":"publisher","first-page":"5879","DOI":"10.4049\/jimmunol.1100535","article-title":"Microbiota downregulates dendritic cell expression of miR-10a, which targets IL-12\/IL-23p40.","volume":"187","author":"Xue","year":"2011","journal-title":"J. Immunol."},{"key":"B274","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2012.00138","article-title":"Toll-like receptors in liver fibrosis: cellular crosstalk and mechanisms.","volume":"3","author":"Yang","year":"2012","journal-title":"Front. Physiol."},{"key":"B275","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1053\/j.gastro.2011.07.005","article-title":"MicroRNA regulation of intestinal epithelial tight junction permeability.","volume":"141","author":"Ye","year":"2011","journal-title":"Gastroenterology"},{"key":"B276","article-title":"Bacterial short chain fatty acids push all the buttons needed to reactivate latent viruses.","volume":"2","author":"Ye","year":"2015","journal-title":"Stem Cell Epigenet."},{"key":"B277","doi-asserted-by":"publisher","first-page":"44641","DOI":"10.1074\/jbc.m105170200","article-title":"Butyrate suppression of colonocyte NF-kappa B activation and cellular proteasome activity.","volume":"276","author":"Yin","year":"2001","journal-title":"J. Biol. Chem."},{"key":"B278","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1097\/SHK.0000000000000565","article-title":"Mechanisms of intestinal barrier dysfunction in sepsis.","volume":"46","author":"Yoseph","year":"2016","journal-title":"Shock"},{"key":"B279","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00205-17","article-title":"Interaction between host microRNAs and the gut microbiota in colorectal cancer.","volume":"3","author":"Yuan","year":"2018","journal-title":"mSystems"},{"key":"B280","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0030035","article-title":"Dynorphin activates quorum sensing quinolone signaling in Pseudomonas aeruginosa.","volume":"3","author":"Zaborina","year":"2007","journal-title":"PLoS Pathog."},{"key":"B281","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1111\/j.1749-6632.1998.tb11118.x","article-title":"HIV\/SIV enteropathy.","volume":"859","author":"Zeitz","year":"1998","journal-title":"Ann. N.Y. Acad. Sci."},{"key":"B282","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1002\/cbf.3109","article-title":"MicroRNA-21 regulates intestinal epithelial tight junction permeability.","volume":"33","author":"Zhang","year":"2015","journal-title":"Cell Biochem. Funct."},{"key":"B283","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-17205-4","article-title":"Salmonella small RNA fragment Sal-1 facilitates bacterial survival in infected cells via suppressing iNOS induction in a microRNA manner.","volume":"7","author":"Zhao","year":"2017","journal-title":"Sci. Rep."},{"key":"B284","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-01751-y","article-title":"Total fecal microbiota transplantation alleviates high-fat diet-induced steatohepatitis in mice via beneficial regulation of gut microbiota.","volume":"7","author":"Zhou","year":"","journal-title":"Sci. Rep."},{"key":"B285","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v23.i1.60","article-title":"Sodium butyrate attenuates high-fat diet-induced steatohepatitis in mice by improving gut microbiota and gastrointestinal barrier.","volume":"23","author":"Zhou","year":"","journal-title":"World J. Gastroenterol."},{"key":"B286","doi-asserted-by":"crossref","first-page":"158.e","DOI":"10.1053\/j.gastro.2014.09.037","article-title":"MicroRNA 29 targets nuclear Factor-\u03baB\u2013repressing factor and claudin 1 to increase intestinal permeability.","volume":"148","author":"Zhou","year":"2015","journal-title":"Gastroenterology"},{"key":"B287","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1136\/gut.2009.181834","article-title":"MicroRNA-29a regulates intestinal membrane permeability in patients with irritable bowel syndrome.","volume":"59","author":"Zhou","year":"2010","journal-title":"Gut"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2019.01676\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T00:28:05Z","timestamp":1565137685000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2019.01676\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,7]]},"references-count":287,"alternative-id":["10.3389\/fmicb.2019.01676"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2019.01676","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,7]]},"article-number":"1676"}}