References
- Koppel N, Balskus EP. Exploring and understanding the biochemical diversity of the human microbiota. Cell Chem Biol. 2016;23(1):18–30. doi:https://doi.org/10.1016/j.chembiol.2015.12.008.
- Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24(4):392–400. doi:https://doi.org/10.1038/nm.4517.
- Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341(6150):1241214. doi:https://doi.org/10.1126/science.1241214.
- Jia B, Jeon CO. Promotion and induction of liver cancer by gut microbiome-mediated modulation of bile acids. PLoS Pathog. 2019;15(9):e1007954. doi:https://doi.org/10.1371/journal.ppat.1007954.
- Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI, Banks AS, Bry L, Devlin AS. A selective gut bacterial bile salt hydrolase alters host metabolism. Elife. 2018;7. doi:https://doi.org/10.7554/eLife.37182.
- Canfora EE, Meex RCR, Venema K, Blaak EE. Gut microbial metabolites in obesity, NAFLD and T2DM. Nat Rev Endocrinol. 2019;15(5):261–273. doi:https://doi.org/10.1038/s41574-019-0156-z.
- Cho CE, Taesuwan S, Malysheva OV, Bender E, Tulchinsky NF, Yan J, Sutter JL, Caudill MA. Trimethylamine-N-oxide (TMAO) response to animal source foods varies among healthy young men and is influenced by their gut microbiota composition: A randomized controlled trial. Mol Nutr Food Res. 2017;61. doi:https://doi.org/10.1002/mnfr.201600324.
- Winston JA, Theriot CM. Diversification of host bile acids by members of the gut microbiota. Gut Microbes. 2019:1–14. doi:https://doi.org/10.1080/19490976.2019.1674124.
- Tilg H, Cani PD, Mayer EA. Gut microbiome and liver diseases. Gut. 2016;65(12):2035–2044. doi:https://doi.org/10.1136/gutjnl-2016-312729.
- Yu LX, Schwabe RF. The gut microbiome and liver cancer: mechanisms and clinical translation. Nat Rev Gastroenterol Hepatol. 2017;14(9):527–539. doi:https://doi.org/10.1038/nrgastro.2017.72.
- Shapiro H, Kolodziejczyk AA, Halstuch D, Elinav E. Bile acids in glucose metabolism in health and disease. J Exp Med. 2018;215(2):383–396. doi:https://doi.org/10.1084/jem.20171965.
- Foley MH, O’Flaherty S, Barrangou R, Theriot CM. Bile salt hydrolases: gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract. PLoS Pathog. 2019;15(3):e1007581. doi:https://doi.org/10.1371/journal.ppat.1007581.
- Jones ML, Tomaro-Duchesneau C, Martoni CJ, Prakash S. Cholesterol lowering with bile salt hydrolase-active probiotic bacteria, mechanism of action, clinical evidence, and future direction for heart health applications. Expert Opin Biol Ther. 2013;13(5):631–642. doi:https://doi.org/10.1517/14712598.2013.758706.
- Joyce SA, Shanahan F, Hill C, Gahan CGM. Bacterial bile salt hydrolase in host metabolism: potential for influencing gastrointestinal microbe-host crosstalk. Gut Microbes. 2014;5(5):669–674. doi:https://doi.org/10.4161/19490976.2014.969986.
- Dong Z, Lee BH. Bile salt hydrolases: structure and function, substrate preference, and inhibitor development. Protein Sci. 2018;27(10):1742–1754. doi:https://doi.org/10.1002/pro.3484.
- Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci USA. 2008;105(36):13580–13585. doi:https://doi.org/10.1073/pnas.0804437105.
- Song Z, Cai Y, Lao X, Wang X, Lin X, Cui Y, Kalavagunta PK, Liao J, Jin L, Shang J, et al. Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome. Microbiome. 2019;7(1):9. doi:https://doi.org/10.1186/s40168-019-0628-3.
- Pearson WR An introduction to sequence similarity (“homology”) searching. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al] 2013; Chapter 3: Unit31. doi:https://doi.org/10.1002/0471250953.bi0301s42.
- Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015;16(1):51. doi:https://doi.org/10.1186/s13059-015-0611-7.
- Vazquez G, Duval S, Jacobs DR Jr., Silventoinen K. Comparison of body mass index, waist circumference, and waist/hip ratio in predicting incident diabetes: a meta-analysis. Epidemiol Rev. 2007;29(1):115–128. doi:https://doi.org/10.1093/epirev/mxm008.
- Tomkin GH, Owens D. Obesity diabetes and the role of bile acids in metabolism. J Transl Int Med. 2016;4(2):73–80. doi:https://doi.org/10.1515/jtim-2016-0018.
- Durack J, Lynch SV. The gut microbiome: relationships with disease and opportunities for therapy. J Exp Med. 2019;216(1):20–40. doi:https://doi.org/10.1084/jem.20180448.
- Zhu J, Liao M, Yao Z, Liang W, Li Q, Liu J, Yang H, Ji Y, Wei W, Tan A, et al. Breast cancer in postmenopausal women is associated with an altered gut metagenome. Microbiome. 2018;6(1):136. doi:https://doi.org/10.1186/s40168-018-0515-3.
- Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. Enzyme function initiative-enzyme similarity tool (EFI-EST): A web tool for generating protein sequence similarity networks. Biochim Biophys Acta. 2015;1854(8):1019–1037. doi:https://doi.org/10.1016/j.bbapap.2015.04.015.
- Akiva E, Copp JN, Tokuriki N, Babbitt PC. Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci USA. 2017;114(45):E9549–E58. doi:https://doi.org/10.1073/pnas.1706849114.
- Jia B, Yuan DP, Lan WJ, Xuan YH, Jeon CO. New insight into the classification and evolution of glucose transporters in the Metazoa. Faseb J. 2019;33(6):7519–7528. doi:https://doi.org/10.1096/fj.201802617R.
- Levin BJ, Huang YY, Peck SC, Wei Y, Martíez-del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-prolinetrans −4-hydroxy-l-proline. Science. 2017;355(6325):eaai8386. doi:https://doi.org/10.1126/science.aai8386.
- Ogilvie LA, Jones BV. Dysbiosis modulates capacity for bile acid modification in the gut microbiomes of patients with inflammatory bowel disease: a mechanism and marker of disease? Gut. 2012;61(11):1642–1643. doi:https://doi.org/10.1136/gutjnl-2012-302137.
- Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 2014;40(6):843–854. doi:https://doi.org/10.1016/j.immuni.2014.05.013.
- Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L. Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst. 2013;105(24):1907–1911. doi:https://doi.org/10.1093/jnci/djt300.
- Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012;22(2):292–298. doi:https://doi.org/10.1101/gr.126573.111.
- Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol. 2014;30(3):332–338. doi:https://doi.org/10.1097/MOG.0000000000000057.
- Bernstein C, Bernstein H, Garewal H, Dinning P, Jabi R, Sampliner RE, McCuskey MK, Panda M, Roe DJ, L’Heureux L, et al. A bile acid-induced apoptosis assay for colon cancer risk and associated quality control studies.. Cancer Res. 1999;59(10):2353–2357.
- Musso G, Gambino R, Cassader M. Obesity, diabetes, and gut microbiota: the hygiene hypothesis expanded? Diabetes Care. 2010;33(10):2277–2284. doi:https://doi.org/10.2337/dc10-0556.
- Joyce SA, MacSharry J, Casey PG, Kinsella M, Murphy EF, Shanahan F, Hill C, Gahan CGM. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proc Natl Acad Sci USA. 2014;111(20):7421–7426. doi:https://doi.org/10.1073/pnas.1323599111.
- Ratziu V, Marchesini G. When the journey from obesity to cirrhosis takes an early start. J Hepatol. 2016;65(2):249–251. doi:https://doi.org/10.1016/j.jhep.2016.05.021.
- Mouzaki M, Wang AY, Bandsma R, Comelli EM, Arendt BM, Zhang L, Fung S, Fischer SE, McGilvray IG, Allard JP. Bile acids and dysbiosis in non-alcoholic fatty liver disease. PLoS One. 2016;11(5):e0151829–e. doi:https://doi.org/10.1371/journal.pone.0151829.
- Kakiyama G, Pandak WM, Gillevet PM, Hylemon PB, Heuman DM, Daita K, Takei H, Muto A, Nittono H, Ridlon JM. Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J Hepatol. 2013;58(5):949–955. doi:https://doi.org/10.1016/j.jhep.2013.01.003.
- Ridlon JM, Alves JM, Hylemon PB, Bajaj JS. Cirrhosis, bile acids and gut microbiota. Gut Microbes. 2013;4(5):382–387. doi:https://doi.org/10.4161/gmic.25723.
- Pereira-Fantini PM, Lapthorne S, Joyce SA, Dellios NL, Wilson G, Fouhy F, Thomas SL, Scurr M, Hill C, Gahan CGM. Altered FXR signalling is associated with bile acid dysmetabolism in short bowel syndrome-associated liver disease. J Hepatol. 2014;61(5):1115–1125. doi:https://doi.org/10.1016/j.jhep.2014.06.025.
- Zhang L, Xie C, Nichols RG, Chan SHJ, Jiang C, Hao R, Smith PB, Cai J, Simons MN, Hatzakis E. Farnesoid X receptor signaling shapes the gut microbiota and controls hepatic lipid metabolism. mSystems. 2016;1(5):e00070–16. doi:https://doi.org/10.1128/mSystems.00070-16.
- Armstrong LE, Guo GL. Role of FXR in liver inflammation during nonalcoholic steatohepatitis. Curr Pharmacol Rep. 2017;3(2):92–100. doi:https://doi.org/10.1007/s40495-017-0085-2.
- Jones ML, Tomaro-Duchesneau C, Martoni CJ, Prakash S. Cholesterol lowering with bile salt hydrolase-active probiotic bacteria, mechanism of action, clinical evidence, and future direction for heart health applications. Expert Opin Biol Ther. 2013;13(5):631–642. doi:https://doi.org/10.1517/14712598.2013.758706.
- Khurana S, Raufman JP, Pallone TL. Bile acids regulate cardiovascular function. Clin Transl Res. 2011;4:210–218. doi:https://doi.org/10.1111/j.1752-8062.2011.00272.x.
- McMillin M, DeMorrow S. Effects of bile acids on neurological function and disease. Faseb J. 2016;30(11):3658–3668. doi:https://doi.org/10.1096/fj.201600275R.
- Schmidt TSB, Raes J, Bork P. The human gut microbiome: from association to modulation. Cell. 2018;172(6):1198–1215. doi:https://doi.org/10.1016/j.cell.2018.02.044.
- Zallot R, Oberg N, Gerlt JA. The EFI web resource for genomic enzymology tools: leveraging protein, genome, and metagenome databases to discover novel enzymes and metabolic pathways. Biochemistry. 2019;58(41):4169–4182. doi:https://doi.org/10.1021/acs.biochem.9b00735.
- Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett. 2017:364. doi:https://doi.org/10.1093/femsle/fnx211.
- Panek M, Cipcic Paljetak H, Baresic A, Peric M, Matijasic M, Lojkic I, Vranešić Bender D, Krznarić Ž, Verbanac D. Methodology challenges in studying human gut microbiota - effects of collection, storage, DNA extraction and next generation sequencing technologies. Sci Rep. 2018;8(1):5143. doi:https://doi.org/10.1038/s41598-018-23296-4.
- Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Prieme A, Aarestrup FM, Pamp SJ. Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition. mSystems. 2016;1. doi:https://doi.org/10.1128/mSystems.00095-16.
- Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat Med. 2019;25:667–678. doi:https://doi.org/10.1038/s41591-019-0405-7.
- Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med. 2019;25:679–689. doi:https://doi.org/10.1038/s41591-019-0406-6.
- Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:https://doi.org/10.1101/gr.1239303.
- Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, et al. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 2019. doi:https://doi.org/10.1093/nar/gkz268.
- Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35(6):1547–1549. doi:https://doi.org/10.1093/molbev/msy096.
- Almagro Armenteros JJ, Tsirigos KD, Søderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotech. 2019;37:420–423. doi:https://doi.org/10.1038/s41587-019-0036-z.
- Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput Biol. 2015;11(12):e1004557. doi:https://doi.org/10.1371/journal.pcbi.1004557.
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760. doi:https://doi.org/10.1093/bioinformatics/btp324.
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi:https://doi.org/10.1093/bioinformatics/btp352.