Albillos, A., de Gottardi, A.,Rescigno, M., 2020. The gut-liver axis in liver disease:Pathophysiological basis for therapy. Journal of hepatology 72, 558-577
|
Bar, N., Korem, T., Weissbrod, O., Zeevi, D., Rothschild, D., Leviatan, S., Kosower, N., Lotan-Pompan, M., Weinberger, A., Le Roy, C.I., et al., 2020. A reference map of potential determinants for the human serum metabolome. Nature 588, 135-140
|
Beloborodova, N., Bairamov, I., Olenin, A., Shubina, V., Teplova, V.,Fedotcheva, N., 2012. Effect of phenolic acids of microbial origin on production of reactive oxygen species in mitochondria and neutrophils. Journal of biomedical science 19, 89
|
Beloborodova, N.V., Khodakova, A.S., Bairamov, I.T.,Olenin, A.Y., 2009. Microbial origin of phenylcarboxylic acids in the human body. Biochemistry Biokhimiia 74, 1350-1355
|
Berg, R.D., 1999. Bacterial translocation from the gastrointestinal tract. Advances in experimental medicine and biology 473, 11-30
|
Bolger, A.M., Lohse, M.,Usadel, B., 2014. Trimmomatic:a flexible trimmer for Illumina sequence data. Bioinformatics (Oxford, England) 30, 2114-2120
|
Cani, P.D., Amar, J., Iglesias, M.A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A.M., Fava, F., Tuohy, K.M., Chabo, C., et al., 2007. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56, 1761-1772
|
Cao, E., Watt, M.J., Nowell, C.J., Quach, T., Simpson, J.S., De Melo Ferreira, V., Agarwal, S., Chu, H., Srivastava, A., Anderson, D., et al., 2021. Mesenteric lymphatic dysfunction promotes insulin resistance and represents a potential treatment target in obesity. Nature metabolism 3, 1175-1188
|
Chen, S., Zhou, Y., Chen, Y.,Gu, J., 2018. fastp:an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England) 34, i884-i890
|
Cifarelli, V.,Eichmann, A., 2019. The Intestinal Lymphatic System:Functions and Metabolic Implications. Cellular and molecular gastroenterology and hepatology 7, 503-513
|
de Jong, P.R., Gonzalez-Navajas, J.M.,Jansen, N.J., 2016. The digestive tract as the origin of systemic inflammation. Critical care (London, England) 20, 279
|
Dehghan, P., Farhangi, M.A., Nikniaz, L., Nikniaz, Z.,Asghari-Jafarabadi, M., 2020. Gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) potentially increases the risk of obesity in adults:An exploratory systematic review and dose-response meta- analysis. Obesity reviews:an official journal of the International Association for the Study of Obesity 21, e12993
|
Dodd, D., Spitzer, M.H., Van Treuren, W., Merrill, B.D., Hryckowian, A.J., Higginbottom, S.K., Le, A., Cowan, T.M., Nolan, G.P., Fischbach, M.A., et al., 2017. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551, 648-652
|
Dunn, W.B., Broadhurst, D., Begley, P., Zelena, E., Francis-McIntyre, S., Anderson, N., Brown, M., Knowles, J.D., Halsall, A., Haselden, J.N., et al., 2011. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nature protocols 6, 1060-1083
|
Franzosa, E.A., McIver, L.J., Rahnavard, G., Thompson, L.R., Schirmer, M., Weingart, G., Lipson, K.S., Knight, R., Caporaso, J.G., Segata, N., et al., 2018. Species-level functional profiling of metagenomes and metatranscriptomes. Nature methods 15, 962-968
|
Fu, B.C., Hullar, M.A.J., Randolph, T.W., Franke, A.A., Monroe, K.R., Cheng, I., Wilkens, L.R., Shepherd, J.A., Madeleine, M.M., Le Marchand, L., et al., 2020. Associations of plasma trimethylamine N-oxide, choline, carnitine, and betaine with inflammatory and cardiometabolic risk biomarkers and the fecal microbiome in the Multiethnic Cohort Adiposity Phenotype Study. The American journal of clinical nutrition 111, 1226-1234
|
Harris, H.C., Morrison, D.J.,Edwards, C.A., 2020. Impact of the source of fermentable carbohydrate on SCFA production by human gut microbiota in vitro-a systematic scoping review and secondary analysis. Critical reviews in food science and nutrition, 1-12
|
Henao-Mejia, J., Elinav, E., Jin, C., Hao, L., Mehal, W.Z., Strowig, T., Thaiss, C.A., Kau, A.L., Eisenbarth, S.C., Jurczak, M.J., et al., 2012. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature 482, 179-185
|
Kim, D., Langmead, B.,Salzberg, S.L., 2015. HISAT:a fast spliced aligner with low memory requirements. Nature methods 12, 357-360
|
Kimura, I., Ozawa, K., Inoue, D., Imamura, T., Kimura, K., Maeda, T., Terasawa, K., Kashihara, D., Hirano, K., Tani, T., et al., 2013. The gut microbiota suppresses insulin-mediated fat accumulation via the short-chain fatty acid receptor GPR43. Nature communications 4, 1829
|
Konturek, P.C., Harsch, I.A., Konturek, K., Schink, M., Konturek, T., Neurath, M.F., Zopf, Y., 2018. Gut-liver axis:How do gut bacteria influence the liver? Med. Sci. 6, 79
|
Kuan, E.L., Ivanov, S., Bridenbaugh, E.A., Victora, G., Wang, W., Childs, E.W., Platt, A.M., Jakubzick, C.V., Mason, R.J., Gashev, A.A., et al., 2015. Collecting lymphatic vessel permeability facilitates adipose tissue inflammation and distribution of antigen to lymph node-homing adipose tissue dendritic cells. Journal of immunology (Baltimore, Md:1950) 194, 5200-5210
|
Li, J., Li, E., Czepielewski, R.S., Chi, J., Guo, X., Han, Y.H., Wang, D., Wang, L., Hu, B., Dawes, B., et al., 2021. Neurotensin is an anti-thermogenic peptide produced by lymphatic endothelial cells. Cell Metab 33, 1449-1465 e1446
|
Liu, R., Hong, J., Xu, X., Feng, Q., Zhang, D., Gu, Y., Shi, J., Zhao, S., Liu, W., Wang, X., et al., 2017. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med 23, 859-868
|
Love, M.I., Huber, W.,Anders, S., 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15, 550
|
Luo, P., Yin, P., Hua, R., Tan, Y., Li, Z., Qiu, G., Yin, Z., Xie, X., Wang, X., Chen, W., et al., 2018. A Large-scale, multicenter serum metabolite biomarker identification study for the early detection of hepatocellular carcinoma. Hepatology (Baltimore, Md) 67, 662-675
|
Martin-Mateos, R.,Albillos, A., 2021. The Role of the Gut-Liver Axis in Metabolic Dysfunction-Associated Fatty Liver Disease. Frontiers in immunology 12, 660179
|
Martinez-del Campo, A., Bodea, S., Hamer, H.A., Marks, J.A., Haiser, H.J., Turnbaugh, P.J.,Balskus, E.P., 2015. Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria. mBio 6
|
Miller, H.R.,Pemberton, A.D., 2002. Tissue-specific expression of mast cell granule serine proteinases and their role in inflammation in the lung and gut. Immunology 105, 375-390
|
Milosevic, I., Vujovic, A., Barac, A., Djelic, M., Korac, M., Radovanovic Spurnic, A., Gmizic, I., Stevanovic, O., Djordjevic, V., Lekic, N., et al., 2019. Gut-Liver Axis, Gut Microbiota, and Its Modulation in the Management of Liver Diseases:A Review of the Literature. International journal of molecular sciences 20
|
Miura, S., Sekizuka, E., Nagata, H., Oshio, C., Minamitani, H., Suematsu, M., Suzuki, M., Hamada, Y., Kobayashi, K., Asakura, H., et al., 1987. Increased lymphocyte transport by lipid absorption in rat mesenteric lymphatics. The American journal of physiology 253, G596-600
|
Morrison, D.J.,Preston, T., 2016. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut microbes 7, 189-200
|
Mukherjee, A., Hooks, J.,Dixon, J.B. 2018. Physiology:Lymph Flow, in:Lee, B.-B., Rockson, S.G., Bergan, J. (Eds.), Lymphedema:A Concise Compendium of Theory and Practice. Springer International Publishing, Cham, pp. 91-111
|
O'Boyle, C.J., MacFie, J., Mitchell, C.J., Johnstone, D., Sagar, P.M.,Sedman, P.C., 1998. Microbiology of bacterial translocation in humans. Gut 42, 29-35
|
Prin, M., Bakker, J.,Wagener, G., 2015. Hepatosplanchnic circulation in cirrhosis and sepsis. World journal of gastroenterology 21, 2582-2592
|
Randolph, G.J., Ivanov, S., Zinselmeyer, B.H.,Scallan, J.P., 2017. The Lymphatic System:Integral Roles in Immunity. Annual review of immunology 35, 31-52
|
Ringseis, R., Gessner, D.K.,Eder, K., 2020. The Gut-Liver Axis in the Control of Energy Metabolism and Food Intake in Animals. Annual review of animal biosciences 8, 295-319
|
Rom, O., Liu, Y., Liu, Z., Zhao, Y., Wu, J., Ghrayeb, A., Villacorta, L., Fan, Y., Chang, L., Wang, L., et al., 2020. Glycine-based treatment ameliorates NAFLD by modulating fatty acid oxidation, glutathione synthesis, and the gut microbiome. Science translational medicine 12
|
Rutkowski, J.M., 2021. Fixing lymphatics improves glucose metabolism. Nature metabolism 3, 1139-1141
|
Sato, H., Zhang, L.S., Martinez, K., Chang, E.B., Yang, Q., Wang, F., Howles, P.N., Hokari, R., Miura, S.,Tso, P., 2016. Antibiotics Suppress Activation of Intestinal Mucosal Mast Cells and Reduce Dietary Lipid Absorption in Sprague-Dawley Rats. Gastroenterology 151, 923-932
|
Schroeder, B.O.,Backhed, F., 2016. Signals from the gut microbiota to distant organs in physiology and disease. Nat Med 22, 1079-1089
|
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B.,Ideker, T., 2003. Cytoscape:a software environment for integrated models of biomolecular interaction networks. Genome research 13, 2498-2504
|
Shibuya, M., 2015. VEGF-VEGFR System as a Target for Suppressing Inflammation and other Diseases. Endocrine, metabolic & immune disorders drug targets 15, 135-144
|
Son, G., Kremer, M.,Hines, I.N., 2010. Contribution of gut bacteria to liver pathobiology. Gastroenterology research and practice 2010
|
Sun, L., Xie, C., Wang, G., Wu, Y., Wu, Q., Wang, X., Liu, J., Deng, Y., Xia, J., Chen, B., et al., 2018. Gut microbiota and intestinal FXR mediate the clinical benefits of metformin. Nat Med 24, 1919-1929
|
Tajiri, K.,Shimizu, Y., 2013. Branched-chain amino acids in liver diseases. World journal of gastroenterology 19, 7620-7629
|
Thingholm, L.B., Ruhlemann, M.C., Koch, M., Fuqua, B., Laucke, G., Boehm, R., Bang, C., Franzosa, E.A., Hubenthal, M., Rahnavard, A., et al., 2019. Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. Cell Host Microbe 26, 252-264 e210
|
Tripathi, A., Debelius, J., Brenner, D.A., Karin, M., Loomba, R., Schnabl, B.,Knight, R., 2018. The gut-liver axis and the intersection with the microbiome. Nature reviews Gastroenterology & hepatology 15, 397-411
|
Truong, D.T., Franzosa, E.A., Tickle, T.L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C.,Segata, N., 2015. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nature methods 12, 902-903
|
Wan, Y., Wang, F., Yuan, J., Li, J., Jiang, D., Zhang, J., Li, H., Wang, R., Tang, J., Huang, T., et al., 2019. Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors:a 6-month randomised controlled-feeding trial. Gut 68, 1417-1429
|
Wang, R., Tang, R., Li, B., Ma, X., Schnabl, B.,Tilg, H., 2021. Gut microbiome, liver immunology, and liver diseases. Cellular & molecular immunology 18, 4-17
|
Wang, T.Y., Liu, M., Portincasa, P.,Wang, D.Q., 2013. New insights into the molecular mechanism of intestinal fatty acid absorption. European journal of clinical investigation 43, 1203-1223
|
Wei, W., Jiang, W., Tian, Z., Wu, H., Ning, H., Yan, G., Zhang, Z., Li, Z., Dong, F., Sun, Y., et al., 2021. Fecal g. Streptococcus and g. Eubacterium_coprostanoligenes_group combined with sphingosine to modulate the serum dyslipidemia in high-fat diet mice. Clinical nutrition (Edinburgh, Scotland) 40, 4234-4245
|
Yu, D., Zhou, L., Xuan, Q., Wang, L., Zhao, X., Lu, X.,Xu, G., 2018. Strategy for Comprehensive Identification of Acylcarnitines Based on Liquid Chromatography-High-Resolution Mass Spectrometry. Analytical chemistry 90, 5712-5718
|
Yu, G., Wang, L.G., Han, Y.,He, Q.Y., 2012. clusterProfiler:an R package for comparing biological themes among gene clusters. Omics:a journal of integrative biology 16, 284-287
|
Yuan, M., Breitkopf, S.B., Yang, X.,Asara, J.M., 2012. A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nature protocols 7, 872-881
|
Zheng, X., Chen, T., Jiang, R., Zhao, A., Wu, Q., Kuang, J., Sun, D., Ren, Z., Li, M., Zhao, M., et al., 2021. Hyocholic acid species improve glucose homeostasis through a distinct TGR5 and FXR signaling mechanism. Cell Metab 33, 791-803 e797
|
Zhou, A., Qu, J., Liu, M.,Tso, P., 2020. The Role of Interstitial Matrix and the Lymphatic System in Gastrointestinal Lipid and Lipoprotein Metabolism. Frontiers in physiology 11, 4
|