Inter-kingdom relationships in Crohn’s disease explored using a multi-omics approach

References

• Segal JP, Mullish BH, Quraishi MN, Acharjee A, Williams HRT, Iqbal T, Hart AL, Marchesi JR. The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease. Therap Adv Gastroenterol. 2019;12:1–21. doi:10.1177/1756284818822250.
   Google Scholar
• Ye BD, McGovern DPB. Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility. Expert Rev Clin Immunol. 2016;12:1091–1107. doi:10.1080/1744666X.2016.1184972.
   Google Scholar
• Barreiro-de Acosta M, Alvarez Castro A, Souto R, Iglesias M, Lorenzo A, Dominguez-Muñoz JE. Emigration to western industrialized countries: a risk factor for developing inflammatory bowel disease. J Crohn’s Colitis. 2011;5:566–569. doi:10.1016/j.crohns.2011.05.009.
   Google Scholar
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505:559–563. doi:10.1038/nature12820.
   Google Scholar
• Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS. Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016;43:596–611. doi:10.1111/apt.13522.
   Google Scholar
• Miyoshi J, Sofia MA, Pierre JF. The evidence for fungus in Crohn’s disease pathogenesis. Clin J Gastroenterol. 2018;11:449–456. doi:10.1007/s12328-018-0886-9.
   Google Scholar
• Manichanh C. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–211. doi:10.1136/gut.2005.073817.
   Google Scholar
• Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15:382–392. doi:10.1016/j.chom.2014.02.005.
   Google Scholar
• Ott SJ, Kühbacher T, Musfeldt M, Rosenstiel P, Hellmig S, Rehman A, Drews O, Weichert W, Timmis KN, Schreiber S. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol. 2008;43:831–841. doi:10.1080/00365520801935434.
   Google Scholar
• Li Q, Wang C, Tang C, He Q, Li N, Li J. Dysbiosis of gut fungal microbiota is associated with mucosal inflammation in Crohn’s disease. J Clin Gastroenterol. 2014;48:513–523. doi:10.1097/MCG.0000000000000035.
   Google Scholar
• Liguori G, Lamas B, Richard ML, Brandi G, Da Costa G, Hoffmann TW, Di Simone MP, Calabrese C, Poggioli G, Langella P, et al. Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients. J Crohn’s Colitis. 2016;10:296–305. doi:10.1093/ecco-jcc/jjv209.
   Google Scholar
• Sokol H, Leducq V, Aschard H, Pham H-P, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I, et al. Fungal microbiota dysbiosis in IBD. Gut. 2016;66:1039–1048. doi:10.1136/gutjnl-2015-310746.
   Google Scholar
• Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, Neut C, Vermeire S, Clemente J, Colombel JF, et al. Bacteriome and mycobiome interactions underscore microbial dysbiosis in familial Crohn’s disease. MBio. 2016;7:e01250–16. doi:10.1128/mBio.01250-16.
   Google Scholar
• Imai T, Inoue R, Kawada Y, Morita Y, Inatomi O, Nishida A, Bamba S, Kawahara M, Andoh A. Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease. J Gastroenterol. 2018;54:149–159. doi:10.1007/s00535-018-1530-7.
   Google Scholar
• Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD. Fungal signature in the gut microbiota of pediatric patients with inflammatory bowel disease. Inflamm Bowel Dis. 2015;21:1. doi:10.1097/MIB.0000000000000454.
   Google Scholar
• Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe. 2015;18:489–500. doi:10.1016/j.chom.2015.09.008.
   Google Scholar
• Mukhopadhya I, Hansen R, Meharg C, Thomson JM, Russell RK, Berry SH, El-Omar EM, Hold GL. The fungal microbiota of de-novo paediatric inflammatory bowel disease. Microbes Infect. 2014;17:304–310. doi:10.1016/j.micinf.2014.12.001.
   Google Scholar
• Limon JJ, Tang J, Li D, Wolf AJ, Michelsen KS, Funari V, Gargus M, Nguyen C, Sharma P, Maymi VI, et al. Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. Cell Host Microbe. 2019;25(377–388.e6):377–388.e6. doi:10.1016/j.chom.2019.01.007.
   Google Scholar
• Nelson A, Stewart CJ, Kennedy NA, Lodge JK, Tremelling M, Probert CS, Parkes M, Mansfield JC, Smith DL, Hold GL, et al. The impact of NOD2 genetic variants on the gut mycobiota in Crohn’s disease patients in remission and individuals without gastrointestinal inflammation. J Crohn’s & Colitis. 2021;15(5):800–812. doi: 10.1093/ecco-jcc/jjaa220
   Google Scholar
• Jain U, Ver Heul AM, Xiong S, Gregory MH, Demers EG, Kern JT, Lai CW, Muegge BD, Barisas DAG, Steven Leal-Ekman J, et al. Debaryomyces is enriched in Crohn’s disease intestinal tissue and impairs healing in mice. Science. 2021;371:1154–1159. doi:10.1126/science.abd0919.
   Google Scholar
• Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M, et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science. 2012;336:1314–1317. doi:10.1126/science.1221789.
   Google Scholar
• Wang T, Pan D, Zhou Z, You Y, Jiang C, Zhao X, Lin X. Dectin-3 deficiency promotes colitis development due to impaired antifungal innate immune responses in the gut. PLoS Pathog. 2016;12:e1005662. doi:10.1371/journal.ppat.1005662.
   Google Scholar
• Qiu X, Zhang F, Yang X, Wu N, Jiang W, Li X, Li X, Liu Y. Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis. Sci Rep. 2015;5:1–12. doi:10.1038/srep10416.
   Google Scholar
• Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, Brown J, Funari VA, Wang HL, Crother TR, et al. Immunological consequences of intestinal fungal dysbiosis. Cell Host Microbe. 2016;19:865–873. doi:10.1016/j.chom.2016.05.003.
   Google Scholar
• Leonardi I, Li X, Semon A, Li D, Doron I, Putzel G, Bar A, Prieto D, Rescigno M, McGovern DPB, et al. CX3CR1+, mononuclear phagocytes control immunity to intestinal fungi. Science. 2018;359:232–236. doi:10.1126/science.aao1503.
   Google Scholar
• Sovran B, Planchais J, Jegou S, Straube M, Lamas B, Natividad JM, Agus A, Dupraz L, Glodt J, Da Costa G, et al. Enterobacteriaceae are essential for the modulation of colitis severity by fungi. Microbiome. 2018;6:1–16. doi:10.1186/s40168-018-0538-9.
   Google Scholar
• Fan D, Coughlin LA, Neubauer MM, Kim J, Kim MS, Zhan X, Simms-Waldrip TR, Xie Y, Hooper LV, Koh AY. Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candida albicans colonization. Nat Med. 2015;21:808–814. doi:10.1038/nm.3871.
   Google Scholar
• Richard ML, Sokol H. The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol. 2019;16:331–345. doi:10.1038/s41575-019-0121-2.
   Google Scholar
• Ahmed I, Greenwood R, Costello BDL, Ratcliffe NM, Probert CS. An Investigation of Fecal Volatile Organic Metabolites in Irritable Bowel Syndrome. PLoS One. 2013;8:e58204. doi:10.1371/journal.pone.0058204.
   Google Scholar
• Garner CE, Smith S, De Lacy Costello B, White P, Spencer R, Probert CSJ, Ratcliffe NM. Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007;21:1675–1688. doi:10.1096/fj.06-6927com.
   Google Scholar
• Taylor H, Serrano-Contreras JI, McDonald JAK, Epstein J, Fell JM, Seoane RC, Li JV, Marchesi JR, Hart AL. Multiomic features associated with mucosal healing and inflammation in paediatric Crohn’s disease. Aliment Pharmacol Ther. 2020;52:1491–1502. doi:10.1111/apt.16086.
   Google Scholar
• Frau A, Kenny JG, Lenzi L, Campbell BJ, Ijaz UZ, Duckworth CA, Burkitt MD, Hall N, Anson J, Darby AC, et al. DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies. Sci Rep. 2019;9:9328. doi:10.1038/s41598-019-44974-x.
   Google Scholar
• Rohart F, Gautier B, Singh A, Lê Cao K-A. mixOmics: an R package for ‘omics feature selection and multiple data integration. PLOS Comput Biol. 2017;13:e1005752. doi:10.1371/journal.pcbi.1005752.
   Google Scholar
• Tedjo DI, Smolinska A, Savelkoul PH, Masclee AA, Van Schooten FJ, Pierik MJ, Penders J, Jonkers DMAE. The fecal microbiota as a biomarker for disease activity in Crohn’s disease. Sci Rep. 2016;6:1–10. doi:10.1038/srep35216.
   Google Scholar
• Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P,  McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, et al. Vegan: community ecology package. 2020.
   Google Scholar
• Clarke KR, Warwick R. An approach to statistical analysis and interpretation. Chang Mar Communities. 1994;2:117–143.
   Google Scholar
• Ijaz UZ, Sivaloganathan L, McKenna A, Richmond A, Kelly C, Linton M, Stratakos AC, Lavery U, Elmi A, Wren BW, et al. Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for campylobacter. Front Microbiol. 2018;9:2452. doi:10.3389/fmicb.2018.02452.
   Google Scholar
• Metabocard for 3,7-Dimethyl-1,6-octadien-3-ol (HMDB0036100) [Internet]. [cited 2020 May 5]; Available from: https://hmdb.ca/metabolites/HMDB0036100
   Google Scholar
• Drawert F, Barton H. Biosynthesis of flavor compounds by microorganisms. 3. production of monoterpenes by the yeast Kluyveromyces lactis. J Agric Food Chem. 1978;26:765–766. doi:10.1021/jf60217a029.
   Google Scholar
• Korpi A, Järnberg J, Pasanen A-L. Microbial volatile organic compounds. Crit Rev Toxicol. 2009;39:139–193. doi:10.1080/10408440802291497.
   Google Scholar
• D’Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics. 2016;17:1–20. doi:10.1186/s12864-015-2194-9.
   Google Scholar
• Reade S, Mayor A, Aggio R, Khalid T, Pritchard D, Ewer A, Probert C. Optimisation of sample preparation for direct SPME-GC-MS analysis of murine and human faecal volatile organic compounds for metabolomic studies. J Anal Bioanal Tech. 2014;5:2.
   Google Scholar
• Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, Stewart CJ, Metcalf GA, Muzny DM, Gibbs RA, et al. The gut mycobiome of the human microbiome project healthy cohort. Microbiome. 2017;5:153. doi:10.1186/s40168-017-0373-4.
   Google Scholar
• Auchtung TA, Fofanova TY, Stewart CJ, Nash AK, Wong MC, Gesell JR, Auchtung JM, Ajami NJ, Petrosino JF. Investigating colonization of the healthy adult gastrointestinal tract by fungi. mSphere. 2018;3:1–16. doi:10.1128/mSphere.00092-18.
   Google Scholar
• Chiaro TR, Soto R, Zac Stephens W, Kubinak JL, Petersen C, Gogokhia L, Bell R, Delgado JC, Cox J, Voth W, et al. A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Sci Transl Med. 2017;9:9. doi:10.1126/scitranslmed.aaf9044.
   Google Scholar
• Sendid B, Jawhara S, Sarter H, Maboudou P, Thierny C, Gower-Rousseau C, Colombel JF, Poulain D. Uric acid levels are independent of anti-saccharomyces cerevisiae antibodies (ASCA) in crohn’s disease: a reappraisal of the role of S cerevisiae in this setting. Virulence. 2018;9:1224–1229.
   Google Scholar
• Charlet R, Bortolus C, Sendid B, Jawhara S. Bacteroides thetaiotaomicron and Lactobacillus johnsonii modulate intestinal inflammation and eliminate fungi via enzymatic hydrolysis of the fungal cell wall. Sci Rep. 2020;10:1–13. doi:10.1038/s41598-020-68214-9.
   Google Scholar
• Bajaj JS, Liu EJ, Kheradman R, Fagan A, Heuman DM, White M, Gavis EA, Hylemon P, Sikaroodi M, Gillevet PM. Fungal dysbiosis in cirrhosis. Gut. 2017;67:1146–1154. doi:10.1136/gutjnl-2016-313170.
   Google Scholar
• Suhr MJ, Banjara N, Hallen-Adams HE. Sequence-based methods for detecting and evaluating the human gut mycobiome. Lett Appl Microbiol. 2016;62:209–215. doi:10.1111/lam.12539.
   Google Scholar
• Suhr MJ, Hallen-Adams HE. The human gut mycobiome: pitfalls and potentials–a mycologists perspective. Mycologia. 2015;107:1057–1073. doi:10.3852/15-147.
   Google Scholar
• Dave M, Purohit T, Razonable R, Loftus EV. Opportunistic infections due to inflammatory bowel disease therapy. Inflamm Bowel Dis. 2014;20:196–212. doi:10.1097/MIB.0b013e3182a827d2.
   Google Scholar
• Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, Martinez X, Varela E, Sarrabayrouse G, Machiels K, et al. A microbial signature for Crohn’s disease. Gut. 2017;66:813–822. doi:10.1136/gutjnl-2016-313235.
   Google Scholar
• Nishino K, Nishida A, Inoue R, Kawada Y, Ohno M, Sakai S, Inatomi O, Bamba S, Sugimoto M, Kawahara M, et al. Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease. J Gastroenterol. 2018;53:95–106. doi:10.1007/s00535-017-1384-4.
   Google Scholar
• Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, et al. Population-level analysis of gut microbiome variation. Science. 2016;352:560–564. doi:10.1126/science.aad3503.
   Google Scholar
• Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555:623–628. doi:10.1038/nature25979.
   Google Scholar
• Dahl J-U, Gray MJ, Bazopoulou D, Beaufay F, Lempart J, Koenigsknecht MJ, Wang Y, Baker JR, Hasler WL, Young VB, et al. The anti-inflammatory drug mesalamine targets bacterial polyphosphate accumulation. Nat Microbiol. 2017;2:16267. doi:10.1038/nmicrobiol.2016.267.
   Google Scholar
• Raymond F, Ouameur AA, Déraspe M, Iqbal N, Gingras H, Dridi B, Leprohon P, Plante PL, Giroux R, Bérubé È, et al. The initial state of the human gut microbiome determines its reshaping by antibiotics. ISME J. 2016;10:707–720. doi:10.1038/ismej.2015.148.
   Google Scholar
• Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500:541–546. doi:10.1038/nature12506.
   Google Scholar
• Hoffmann TW, Pham HP, Bridonneau C, Aubry C, Lamas B, Martin-Gallausiaux C, Moroldo M, Rainteau D, Lapaque N, Six A, et al. Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice. ISME J. 2016;10:460–477. doi:10.1038/ismej.2015.127.
   Google Scholar
• Wrzosek L, Miquel S, Noordine M-L, Bouet S, Chevalier-Curt MJ, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol. 2013;11:1–13. doi:10.1186/1741-7007-11-61.
   Google Scholar
• Edwards LA, Lucas M, Edwards EA, Torrente F, Heuschkel RB, Klein NJ, Murch SH, Bajaj-Elliott M, Phillips AD. Aberrant response to commensal Bacteroides thetaiotaomicron in Crohn’s disease: an ex vivo human organ culture study. Inflamm Bowel Dis. 2011;17:1201–1208. doi:10.1002/ibd.21501.
   Google Scholar
• Hansen JJ, Huang Y, Peterson DA, Goeser L, Fan TJ, Chang EB, Sartor RB. The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen. PLoS One. 2012;7:1–10. doi:10.1371/journal.pone.0042645.
   Google Scholar
• Bloom SM, Bijanki VN, Nava GM, Sun L, Malvin NP, Donermeyer DL, Dunne WM, Allen PM, Stappenbeck TS. Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host Microbe. 2011;9:390–403. doi:10.1016/j.chom.2011.04.009.
   Google Scholar
• Rigottier-gois L. Dysbiosis in inflammatory bowel diseases : the oxygen hypothesis. ISME J. 2013;7:1256–1261. doi:10.1038/ismej.2013.80.
   Google Scholar
• Henson MA, Phalak P. Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis. BMC Syst Biol. 2017;11:1–15. doi:10.1186/s12918-017-0522-1.
   Google Scholar
• Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, et al. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe. 2015;17:662–671. doi:10.1016/j.chom.2015.03.005.
   Google Scholar
• Ramanan D, Tang MS, Bowcutt R, Loke P, Cadwell K. Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus. Immunity. 2014;41:311–324. doi:10.1016/j.immuni.2014.06.015.
   Google Scholar
• Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3:337–346. doi:10.1038/s41564-017-0089-z.
   Google Scholar
• Quince C, Ijaz UZ, Loman N, Eren AM, Saulnier D, Russell J, Haig SJ, Calus ST, Quick J, Barclay A, et al. Extensive modulation of the fecal metagenome in children with Crohn’s disease during exclusive enteral nutrition. Am J Gastroenterol. 2015;110:1718–1729. doi:10.1038/ajg.2015.357.
   Google Scholar
• Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, et al. HMDB: the human metabolome database. Nucleic Acids Res. 2007;35:D521–6. doi:10.1093/nar/gkl923.
   Google Scholar
• Reade S, Williams JM, Aggio R, Duckworth CA, Mahalhal A, Hough R, Pritchard DM, Probert CS. Potential role of fecal volatile organic compounds as biomarkers of chemically induced intestinal inflammation in mice. FASEB J. 2019;33:3129–3136. doi:10.1096/fj.201800076RR.
   Google Scholar
• Fritz KS, Petersen DR. An overview of the chemistry and biology of reactive aldehydes. Free Radic Biol Med. 2013;59:85–91. doi:10.1016/j.freeradbiomed.2012.06.025.
   Google Scholar
• Walton C, Fowler DP, Turner C, Jia W, Whitehead RN, Griffiths L, Dawson C, Waring RH, Ramsden DB, Cole JA, et al. Analysis of volatile organic compounds of bacterial origin in chronic gastrointestinal diseases. Inflamm Bowel Dis. 2013;19:2069–2078. doi:10.1097/MIB.0b013e31829a91f6.
   Google Scholar
• Walton C, Montoya MPB, Fowler DP, Turner C, Jia W, Whitehead RN, Grif L, Waring RH, Ramsden DB, Cole JA, et al. Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study. Eur J Clin Nutr. 2016;70:1052–1056. doi:10.1038/ejcn.2016.74.
   Google Scholar
• Smith EA, Macfarlane GT. Formation of phenolic and indolic compounds by anaerobic bacteria in the human large intestine. Microb Ecol. 1997;33:180–188. doi:10.1007/s002489900020.
   Google Scholar
• Smith EA, Macfarlane GT. Dissimilatory amino acid metabolism in human colonic bacteria. Anaerobe. 1997;3:327–337. doi:10.1006/anae.1997.0121.
   Google Scholar
• Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007;6:546–551. doi:10.1021/pr060470d.
   Google Scholar
• Hazelwood LA, Daran JM, Van Maris AJA, Pronk JT, Dickinson JR. The ehrlich pathway for fusel alcohol production: a century of research on Saccharomyces cerevisiae metabolism. Appl Environ Microbiol. 2008;74:2259–2266. doi:10.1128/AEM.02625-07.
   Google Scholar
• Heddergott C, Calvo AM, Latgé JP. The volatome of Aspergillus fumigatus. Eukaryot Cell. 2014;13:1014–1025. doi:10.1128/EC.00074-14.
   Google Scholar
• Bhandari S, Chambers S, Pearson J, Syhre M, Epton M, Scott-Thomas A. Determining the limits and confounders for the 2-pentyl furan breath test by gas chromatography/mass spectrometry. J Chromatogr B. 2011;879:2815–2820. doi:10.1016/j.jchromb.2011.08.010.
   Google Scholar
• Sørensen LM, Gori K, Petersen MA, Jespersen L, Arneborg N. Flavour compound production by Yarrowia lipolytica, Saccharomyces cerevisiae and Debaryomyces hansenii in a cheese-surface model. Int Dairy J. 2011;21:970–978. doi:10.1016/j.idairyj.2011.06.005.
   Google Scholar
• Raimondi S, Amaretti A, Gozzoli C, Simone M, Righini L, Candeliere F, Brun P, Ardizzoni A, Colombari B, Paulone S, et al. Longitudinal survey of fungi in the human gut: ITS profiling, phenotyping, and colonization. Front Microbiol. 2019;10:1575. doi:10.3389/fmicb.2019.01575.
   Google Scholar
• Imhann F, Bonder MJ, Vila AV, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJM, et al. Proton pump inhibitors affect the gut microbiome. Gut. 2016;65:740–748. doi:10.1136/gutjnl-2015-310376.
   Google Scholar
• Wilson ID, Nicholson JK. Gut microbiome interactions with drug metabolism, efficacy, and toxicity. Transl Res. 2017;179:204–222. doi:10.1016/j.trsl.2016.08.002.
   Google Scholar
• Van Den Heuvel TR, Jonkers DM, Jeuring SF, Romberg-Camps MJ, Oostenbrug LE, Zeegers MP, Masclee AA, Pierik MJ. Cohort profile: the inflammatory bowel disease south limburg cohort (IBDSL). Int J Epidemiol. 2015;46:e7–e7. doi:10.1093/ije/dyv088.
   Google Scholar
• Xia J, Sinelnikov IV, Han B, Wishart DS. MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Res. 2015;43:W251–7. doi:10.1093/nar/gkv380.
   Google Scholar