Maslowski KM. Metabolism at the centre of the host-microbe relationship. Clin Exp Immunol. 2019;197(2):193–204.
Article
CAS
Google Scholar
Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med. 2017;23(7):859–68.
Article
CAS
Google Scholar
Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. 2016;535(7612):376–81.
Article
CAS
Google Scholar
Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011;472(7341):57–63.
Article
CAS
Google Scholar
Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, et al. Human gut microbiota from autism spectrum disorder promote behavioral symptoms in mice. Cell. 2019;177(6):1600–1618.e17.
Article
CAS
Google Scholar
Hertel J, Harms AC, Heinken A, Baldini F, Thinnes CC, Glaab E, et al. Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in parkinson’s disease. Cell Rep. 2019;29(7):1767–1777.e8.
Article
CAS
Google Scholar
Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA. Untargeted metabolomics strategies-challenges and emerging directions. J Am Soc Mass Spectrom. 2016;27(12):1897–905.
Article
CAS
Google Scholar
Lamichhane S, Sen P, Dickens AM, Orešič M, Bertram HC. Gut metabolome meets microbiome: a methodological perspective to understand the relationship between host and microbe. Methods. 2018;149:3–12.
Article
CAS
Google Scholar
Smirnov KS, Maier TV, Walker A, et al. Challenges of metabolomics in human gut microbiota research. Int J Med Microbiol. 2016;306(5):266–79.
Article
CAS
Google Scholar
Lee-Sarwar KA, Lasky-Su J, Kelly RS, Litonjua AA, Weiss ST. Metabolome-microbiome crosstalk and human disease. Metabolites. 2020;10(5):181.
Article
CAS
Google Scholar
Stevens VL, Hoover E, Wang Y, Zanetti KA. Pre-analytical factors that affect metabolite stability in human urine, plasma, and serum: a review. Metabolites. 2019;9(8):156.
Article
CAS
Google Scholar
Lim MY, Hong S, Kim BM, Ahn Y, Kim HJ, Nam YD. Changes in microbiome and metabolomic profiles of fecal samples stored with stabilizing solution at room temperature: a pilot study. Sci Rep. 2020;10(1):1789. Published 2020 Feb 4. https://doi.org/10.1038/s41598-020-58719-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Loftfield E, Vogtmann E, Sampson JN, Moore SC, Nelson H, Knight R, et al. Comparison of collection methods for fecal samples for discovery metabolomics in epidemiologic studies. Cancer Epidemiol Biomarkers Prev. 2016;25(11):1483–90.
Article
Google Scholar
Roager HM, Licht TR. Microbial tryptophan catabolites in health and disease. Nat Commun. 2018;9(1):3294.
Article
Google Scholar
Kaur H, Bose C, Mande SS. Tryptophan metabolism by gut microbiome and gut-brain-axis: an in silico analysis. Front Neurosci. 2019;13:1365.
Article
Google Scholar
Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol. 2014;30(3):332–8.
Article
Google Scholar
Gratton J, Phetcharaburanin J, Mullish BH, Williams HR, Thursz M, Nicholson JK, et al. Optimized sample handling strategy for metabolic profiling of human feces. Anal Chem. 2016;88(9):4661–8.
Article
CAS
Google Scholar
Karu N, Deng L, Slae M, Guo AC, Sajed T, Huynh H, et al. A review on human fecal metabolomics: methods, applications and the human fecal metabolome database. Anal Chim Acta. 2018;1030:1–24. https://doi.org/10.1016/j.aca.2018.05.031.
Article
CAS
PubMed
Google Scholar
Wang Z, Zolnik CP, Qiu Y, Usyk M, Wang T, Strickler HD, et al. Comparison of fecal collection methods for microbiome and metabolomics studies. Front Cell Infect Microbiol. 2018;8:301.
Article
Google Scholar
Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, et al. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature. 2017;551(7682):648–52.
Article
CAS
Google Scholar
Torchia EC, Cheema SK, Agellon LB. Coordinate regulation of bile acid biosynthetic and recovery pathways. Biochem Biophys Res Commun. 1996;225(1):128–33.
Article
CAS
Google Scholar
Zierer J, Jackson MA, Kastenmüller G, Mangino M, Long T, Telenti A, et al. The fecal metabolome as a functional readout of the gut microbiome. Nat Genet. 2018;50(6):790–5.
Article
CAS
Google Scholar
Ford L, Kennedy AD, Goodman KD, Pappan KL, Evans AM, Miller LAD, et al. Precision of a clinical metabolomics profiling platform for use in the identification of inborn errors of metabolism. J Appl Lab Med. 2020;5(2):342–56.
Article
Google Scholar
Evans AM, Bridgewater BR, Liu Q, Mitchell MW, Robinson RJ, Dai H, et al. High resolution mass spectrometry improves data quantity and qualityas compared to unit mass resolution mass spectrometry in high throughput profiling metabolomics. Metabolomics. 2014;4(2):1000132.
Google Scholar
Evans AM, DeHaven CD, Barrett T, Mitchell M, Milgram E. Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. Anal Chem. 2009;81(16):6656–67.
Article
CAS
Google Scholar
Evans AM, Mitchell MW, Dai H, DeHaven CD. Categorizing Ion? Features in Liquid Chromatography/Mass Spectrometry Metobolomics Data Abstract. Metabolomics. ISSN: 2153–0769. https://doi.org/10.4172/2153-0769.1000110.
Dehaven CD, Evans AM, Dai H, Lawton KA. Organization of GC/MS and LC/MS metabolomics data into chemical libraries. J Cheminform. 2010;2(1):9.
Article
Google Scholar