Host-mycobiome metabolic interactions in health and disease

References

• Brown GD, Denning DW, Gow NAR, Levitz SM, Netea MG, White TC. Hidden killers: human fungal infections. Sci Transl Med. 2012;4(165):165rv13–19. doi:10.1126/scitranslmed.3004404.
   PubMed Web of Science ®Google Scholar
• Brown GD, Denning DW, Levitz SM. Tackling human fungal infections. Science. 2012;336(6082):647. doi:10.1126/science.1222236.
   PubMed Web of Science ®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(1):153. doi:10.1186/s40168-017-0373-4.
   PubMedGoogle Scholar
• Seed PC. The human mycobiome. Cold Spring Harb Perspect Med. 2015;5(5):a019810–a019810. doi:10.1101/cshperspect.a019810.
   Web of Science ®Google Scholar
• Forbes JD, Bernstein CN, Tremlett H, Van Domselaar G, Knox NC. A fungal world: could the gut mycobiome be involved in neurological disease?. Front Microbiol. 2019;10:3249. doi:10.3389/fmicb.2018.03249.
   Google Scholar
• Chin VK, Yong VC, Chong PP, Amin Nordin S, Basir R, Abdullah M. Mycobiome in the gut: a multiperspective review. Mediators Inflamm. 2020;2020:1–16. doi:10.1155/2020/9560684.
   Web of Science ®Google Scholar
• Schulze J, Sonnenborn U. Yeasts in the gut: from commensals to infectious agents. Dtsch Arzteblatt Int. 2009;106:837–842.
   PubMed Web of Science ®Google Scholar
• Suhr MJ, Hallen-Adams HE. The human gut mycobiome: pitfalls and potentials-a mycologist’ s perspective the human gut mycobiome: pitfalls and potentials-a mycologist’s perspective. 2015. doi:10.3852/15-147.
   Google Scholar
• Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65. doi:10.1038/nature08821.
   PubMed Web of Science ®Google Scholar
• Huffnagle GB, Noverr MC. The emerging world of the fungal microbiome. Trends Microbiol. 2013;21(7):334–341. doi:10.1016/j.tim.2013.04.002.
   PubMed Web of Science ®Google Scholar
• Baker JL, Bor B, Agnello M, Shi W, He X. Ecology of the Oral Microbiome: beyond Bacteria. Trends Microbiol. 2017;25(5):362–374. doi:10.1016/j.tim.2016.12.012.
   PubMed Web of Science ®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(2):e00092–18. doi:10.1128/mSphere.00092-18.
   PubMed Web of Science ®Google Scholar
• Perrone G, Gallo A. Aspergillus species and their associated mycotoxins. In: Moretti A, Susca A, editors. Mycotoxigenic fungi: methods and protocols. Springer;2017. p. 33–49. doi:10.1007/978-1-4939-6707-0_3.
   Google Scholar
• Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE. 2013;8(6):e66019. doi:10.1371/journal.pone.0066019.
   PubMed Web of Science ®Google Scholar
• Strati F, Di Paola M, Stefanini I, Albanese D, Rizzetto L, Lionetti P, Calabrò A, Jousson O, Donati C, Cavalieri D, De Filippo C. Age and gender affect the composition of fungal population of the human gastrointestinal tract. Front Microbiol. 2016;7. doi:10.3389/fmicb.2016.01227
   Web of Science ®Google Scholar
• Borges FM, de Paula TO, Sarmiento MRA, de Oliveira MG, Pereira MLM, Toledo IV, Nascimento TC, Ferreira-Machado AB, Silva VL, Diniz CG. Fungal diversity of human gut microbiota among eutrophic, overweight, and obese individuals based on aerobic culture-dependent approach. Curr Microbiol. 2018;75(6):726–735. doi:10.1007/s00284-018-1438-8.
   PubMed Web of Science ®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(3):209–215. doi:10.1111/lam.12539.
   PubMed Web of Science ®Google Scholar
• Huseyin CE, Rubio RC, O’Sullivan O, Cotter PD, Scanlan PD. The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome. Front Microbiol. 2017;8. doi:10.3389/fmicb.2017.01432.
   PubMed Web of Science ®Google Scholar
• Wisecaver JH, Slot JC, Rokas A, Stajich JE. The evolution of fungal metabolic pathways. PLOS Genet. 2014;10(12):e1004816. doi:10.1371/journal.pgen.1004816.
   PubMed Web of Science ®Google Scholar
• Richardson JP, Moyes DL. Adaptive immune responses to Candida albicans infection. Virulence. 2015;6(4):327–337. doi:10.1080/21505594.2015.1004977.
   PubMed Web of Science ®Google Scholar
• Moyes DL, Richardson JP, Naglik JR. Candida albicans- epithelial interactions and pathogenicity mechanisms: scratching the surface. Virulence. 2015;6(4):338–346. doi:10.1080/21505594.2015.1012981.
   PubMed Web of Science ®Google Scholar
• Shanahan F, Hill C. Language, numeracy and logic in microbiome science. Nat Rev Gastroenterol Hepatol. 2019;16(7):387–388. doi:10.1038/s41575-019-0163-5.
   PubMed Web of Science ®Google Scholar
• Frey-Klett P, Burlinson P, Deveau A, Barret M, Tarkka M, Sarniguet A. Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists. Microbiol Mol Biol Rev. 2011;75(4):583–609. doi:10.1128/MMBR.00020-11.
   PubMed Web of Science ®Google Scholar
• Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders: ther. Adv Gastroenterol. 2011. doi:10.1177/1756283X11428502.
   Google Scholar
• Kurrey NK, Anu-Appaiah KA, Rao RP. Probiotic yeasts inhibit virulence of non-albicans candida species lohith kunyeit,a,b,c. mBio. 2019;10.
   PubMed Web of Science ®Google Scholar
• Huseyin CE, O’Toole PW, Cotter PD, Scanlan PD. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev. 2017;41(4):479–511. doi:10.1093/femsre/fuw047.
   PubMed Web of Science ®Google Scholar
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–563. doi:10.1038/nature12820.
   PubMed Web of Science ®Google Scholar
• Sam Q, Chang M, Chai L. The fungal mycobiome and its interaction with gut bacteria in the host. Int J Mol Sci. 2017;18(2):330. doi:10.3390/ijms18020330.
   PubMed Web of Science ®Google Scholar
• Mar Rodríguez M, Marin-Garcia P, Xifra G, Vendrell J, Jové M, Pamplona R, Ricart W. Obesity changes the human gut mycobiome. Sci Rep. 2015;5(1):14600. doi:10.1038/srep14600.
   PubMedGoogle Scholar
• Gu C, Kim GB, Kim WJ, Kim HU, Lee SY. Current status and applications of genome-scale metabolic models. Genome Biol. 2019;20(1):121. doi:10.1186/s13059-019-1730-3.
   PubMed Web of Science ®Google Scholar
• Sokol H, Leducq V, Aschard H, Pham H-P, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I. Fungal microbiota dysbiosis in IBD. Gut. 2017;66(6):1039–1048. doi:10.1136/gutjnl-2015-310746.
   PubMed Web of Science ®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(7):831–841. doi:10.1080/00365520801935434.
   PubMed Web of Science ®Google Scholar
• Witherden EA, Moyes DL, Bruce KD, Ehrlich SD, Shoaie S. Using systems biology approaches to elucidate cause and effect in host–microbiome interactions. Curr Opin Syst Biol. 2017;3:141–146. doi:10.1016/j.coisb.2017.05.003.
   Google Scholar
• Kumamoto CA. Inflammation and gastrointestinal Candida colonization. Curr Opin Microbiol. 2011;14(4):386–391. doi:10.1016/j.mib.2011.07.015.
   PubMed Web of Science ®Google Scholar
• Gerard R, Sendid B, Colombel JF, Poulain D, Jouault T. An immunological link between Candida albicans colonization and Crohn’s disease. Crit Rev Microbiol. 2015;41(2):135–139. doi:10.3109/1040841X.2013.810587.
   PubMed Web of Science ®Google Scholar
• Trojanowska D, Zwolińska-Wcisło M, Tokarczyk M, Kosowski K, Mach T, Budak A. The role of Candida in inflammatory bowel disease. Estimation of transmission of C. albicans fungi in gastrointestinal tract based on genetic affinity between strains. Med Sci Monit Int Med J Exp Clin Res. 2010;16:CR451–457.
   Google Scholar
• Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, Neut C, Vermeire S, Clemente J, Colombel JF. Bacteriome and mycobiome interactions underscore microbial dysbiosis in familial Crohn’s disease. mBio. 2016;7(5). doi:10.1128/mBio.01250-16.
   PubMed Web of Science ®Google Scholar
• Severance EG, Alaedini A, Yang S, Halling M, Gressitt KL, Stallings CR, Origoni AE, Vaughan C, Khushalani S, Leweke FM. Gastrointestinal inflammation and associated immune activation in schizophrenia. Schizophr Res. 2012;138(1):48–53. doi:10.1016/j.schres.2012.02.025.
   PubMed Web of Science ®Google Scholar
• Severance EG, Gressitt KL, Stallings CR, Katsafanas E, Schweinfurth LA, Savage CL, Adamos MB, Sweeney KM, Origoni AE, Khushalani S, Leweke FM. Candida albicans exposures, sex specificity and cognitive deficits in schizophrenia and bipolar disorder. Npj Schizophr. 2016;2(1):1–7. doi:10.1038/npjschz.2016.18.
   PubMedGoogle Scholar
• Enaud R, Vandenborght L-E, Coron N, Bazin T, Prevel R, Schaeverbeke T, Berger P, Fayon M, Lamireau T, Delhaes L. The mycobiome: a neglected component in the microbiota-gut-brain axis. Microorganisms. 2018;6(1):22. doi:10.3390/microorganisms6010022.
   PubMed Web of Science ®Google Scholar
• Alonso R, Pisa D, Marina AI, Morato E, Rabano A, Carrasco L. Fungal infection in patients with Alzheimer’s disease. J Alzheimers Dis JAD. 2014;41(1):301–311. doi:10.3233/JAD-132681.
   PubMed Web of Science ®Google Scholar
• Alonso R, Pisa D, Aguado B, Carrasco L. Identification of fungal species in brain tissue from alzheimer’s disease by next-generation sequencing. J Alzheimers Dis JAD. 2017;58(1):55–67. doi:10.3233/JAD-170058.
   PubMed Web of Science ®Google Scholar
• Pisa D, Alonso R, Rábano A, Rodal I, Carrasco L. Different brain regions are infected with fungi in alzheimer’s disease. Sci Rep. 2015;5(1):1–13. doi:10.1038/srep15015.
   Google Scholar
• Benito-León J, Laurence M. The role of fungi in the etiology of multiple sclerosis. Front Neurol. 2017;8:535. doi:10.3389/fneur.2017.00535.
   PubMed Web of Science ®Google Scholar
• Severance EG, Gressitt KL, Stallings CR, Katsafanas E, Schweinfurth LA, Savage CL, Adamos MB, Sweeney KM, Origoni AE, Khushalani S, Dickerson FB. Probiotic normalization of Candida albicans in schizophrenia: a randomized, placebo-controlled, longitudinal pilot study. Brain Behav Immun. 2017;62:41–45. doi:10.1016/j.bbi.2016.11.019.
   PubMed Web of Science ®Google Scholar
• Aykut B, Pushalkar S, Chen R, Li Q, Abengozar R, Kim JI, Shadaloey SA, Wu D, Preiss P, Verma N, Guo Y. The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. Nature. 2019;1–4. doi:10.1038/s41586-019-1608-2.
   Web of Science ®Google Scholar
• Mukherjee PK, Chandra J, Retuerto M, Sikaroodi M, Brown RE, Jurevic R, Salata RA, Lederman MM, Gillevet PM, Ghannoum MA. Oral mycobiome analysis of HIV-infected patients: identification of pichia as an antagonist of opportunistic fungi. PLoS Pathog. 2014;10(3):e1003996. doi:10.1371/journal.ppat.1003996.
   PubMed Web of Science ®Google Scholar
• Remmele CW, Luther CH, Balkenhol J, Dandekar T, Müller T, Dittrich MT. Integrated inference and evaluation of host-fungi interaction networks. Front Microbiol. 2015;6:764. doi:10.3389/fmicb.2015.00764.
   PubMed Web of Science ®Google Scholar
• Jiang TT, Shao T-Y, Ang WXG, Kinder JM, Turner LH, Pham G, Whitt J, Alenghat T, Way SS. Commensal fungi recapitulate the protective benefits of intestinal bacteria. Cell Host Microbe. 2017;22(6):809–816.e4. doi:10.1016/j.chom.2017.10.013.
   PubMed Web of Science ®Google Scholar
• Brown GD. Innate antifungal immunity: the key role of phagocyteS. Annu Rev Immunol. 2011;29(1):1–21. doi:10.1146/annurev-immunol-030409-101229.
   PubMedGoogle Scholar
• Richardson JP, Moyes DL, Ho J, Naglik JR. Candida innate immunity at the mucosa. Semin Cell Dev Biol. 2019;89:58–70. doi:10.1016/j.semcdb.2018.02.026.
   PubMed Web of Science ®Google Scholar
• Tucey TM, Verma J, Harrison PF, Snelgrove SL, Lo TL, Scherer AK, Barugahare AA, Powell DR, Wheeler RT, Hickey MJ. Glucose homeostasis is important for immune cell viability during candida challenge and host survival of systemic fungal infection. Cell Metab. 2018;27(5):988–1006.e7. doi:10.1016/j.cmet.2018.03.019.
   PubMed Web of Science ®Google Scholar
• Chai LYA, Netea MG, Vonk AG, Kullberg B-J. Fungal strategies for overcoming host innate immune response. Med Mycol. 2009;47(3):227–236. doi:10.1080/13693780802209082.
   PubMed Web of Science ®Google Scholar
• Netea MG, Brown GD, Kullberg BJ, Gow NAR. An integrated model of the recognition of Candida albicans by the innate immune system. Nat Rev Microbiol. 2008;6(1):67–78. doi:10.1038/nrmicro1815.
   PubMed Web of Science ®Google Scholar
• Mogilnicka I, Ufnal M. Gut mycobiota and fungal metabolites in human homeostasis. Curr Drug Targets. 2019;20(2):232–240. doi:10.2174/1389450119666180724125020.
   PubMed Web of Science ®Google Scholar
• Huć T, Nowinski A, Drapala A, Konopelski P, Ufnal M. Indole and indoxyl sulfate, gut bacteria metabolites of tryptophan, change arterial blood pressure via peripheral and central mechanisms in rats. Pharmacol Res. 2018;130:172–179. doi:10.1016/j.phrs.2017.12.025.
   PubMed Web of Science ®Google Scholar
• Huc T, Konop M, Onyszkiewicz M, Podsadni P, Szczepańska A, Turło J, Ufnal M. Colonic indole, gut bacteria metabolite of tryptophan, increases portal blood pressure in rats. Am J Physiol Regul Integr Comp Physiol. 2018;315(4):R646–R655. doi:10.1152/ajpregu.00111.2018.
   PubMed Web of Science ®Google Scholar
• Tremaroli V, Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489(7415):242–249. doi:10.1038/nature11552.
   PubMed Web of Science ®Google Scholar
• Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris HMB, Coakley M, Lakshminarayanan B, O’Sullivan O. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488(7410):178–184. doi:10.1038/nature11319.
   PubMed Web of Science ®Google Scholar
• Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell. 2016;165(6):1332–1345. doi:10.1016/j.cell.2016.05.041.
   PubMed Web of Science ®Google Scholar
• Raffa N, Keller NP, Sheppard DC. A call to arms: mustering secondary metabolites for success and survival of an opportunistic pathogen. PLoS Pathog. 2019;15(4):e1007606. doi:10.1371/journal.ppat.1007606.
   PubMed Web of Science ®Google Scholar
• Dietl A-M, Meir Z, Shadkchan Y, Osherov N, Haas H. Riboflavin and pantothenic acid biosynthesis are crucial for iron homeostasis and virulence in the pathogenic mold Aspergillus fumigatus. Virulence. 2018;9(1):1036–1049. doi:10.1080/21505594.2018.1482181.
   PubMed Web of Science ®Google Scholar
• Meir Z, Osherov N. Vitamin biosynthesis as an antifungal target. J Fungi. 2018;4(72):72. doi:10.3390/jof4020072.
   Google Scholar
• Björn LO, Wang T. Vitamin D in an ecological context. Int J Circumpolar Health. 2000;59:26–32.
   PubMedGoogle Scholar
• Yamamoto EA, Jørgensen TN. Relationships between vitamin D, gut microbiome, and systemic autoimmunity. Front Immunol. 2020;10. doi:10.3389/fimmu.2019.03141.
   Web of Science ®Google Scholar
• Klassert TE, Bräuer J, Hölzer M, Stock M, Riege K, Zubiría-Barrera C, Müller MM, Rummler S, Skerka C, Marz M. Differential effects of vitamins A and D on the transcriptional landscape of human monocytes during infection. Sci Rep. 2017;7(1):40599. doi:10.1038/srep40599.
   PubMedGoogle Scholar
• Weerasinghe H, Traven A. Immunometabolism in fungal infections: the need to eat to compete. Curr Opin Microbiol. 2020;58:32–40. doi:10.1016/j.mib.2020.07.001.
   PubMed Web of Science ®Google Scholar
• Domínguez-Andrés J, Arts RJW, ter Horst R, Gresnigt MS, Smeekens SP, Ratter JM, Lachmandas E, Boutens L, van de Veerdonk FL, Joosten LAB. Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis. PLOS Pathog. 2017;13(9):e1006632. doi:10.1371/journal.ppat.1006632.
   PubMed Web of Science ®Google Scholar
• Lachmandas E, Beigier-Bompadre M, Cheng S-C, Kumar V, van Laarhoven A, Wang X, Ammerdorffer A, Boutens L, de Jong D, Kanneganti T-D. Rewiring cellular metabolism via the AKT/mTOR pathway contributes to host defence against Mycobacterium tuberculosis in human and murine cells. Eur J Immunol. 2016;46(11):2574–2586. doi:10.1002/eji.201546259.
   PubMed Web of Science ®Google Scholar
• Gonçalves SM, Duarte-Oliveira C, Campos CF, Aimanianda V, ter Horst R, Leite L, Mercier T, Pereira P, Fernández-García M, Antunes D. Phagosomal removal of fungal melanin reprograms macrophage metabolism to promote antifungal immunity. Nat Commun. 2020;11(1):2282. doi:10.1038/s41467-020-16120-z.
   PubMed Web of Science ®Google Scholar
• Stappers MHT, Clark AE, Aimanianda V, Bidula S, Reid DM, Asamaphan P, Hardison SE, Dambuza IM, Valsecchi I, Kerscher B. Recognition of DHN-melanin by a C-type lectin receptor is required for immunity to aspergillus. Nature. 2018;555(7696):382–386. doi:10.1038/nature25974.
   PubMed Web of Science ®Google Scholar
• Nagpal R, Neth BJ, Wang S, Mishra SP, Craft S, Yadav H. Gut mycobiome and its interaction with diet, gut bacteria and alzheimer’s disease markers in subjects with mild cognitive impairment: a pilot study. EBioMedicine. 2020;59:102950. doi:10.1016/j.ebiom.2020.102950.
   PubMed Web of Science ®Google Scholar
• Lai GC, Tan TG, Pavelka N. The mammalian mycobiome: a complex system in a dynamic relationship with the host. Wiley Interdiscip Rev Syst Biol Med. 2018;11.
   PubMed Web of Science ®Google Scholar
• Witherden EA, Shoaie S, Hall RA, Moyes DL. The human mucosal mycobiome and fungal community interactions. J Fungi. 2017;3(4):56. doi:10.3390/jof3040056.
   Web of Science ®Google Scholar
• Calvo AM, Wilson RA, Bok JW, Keller NP. Relationship between secondary metabolism and fungal development. Microbiol Mol Biol Rev MMBR. 2002 table of contents;66(3):447–459. doi:10.1128/MMBR.66.3.447-459.2002.
   PubMed Web of Science ®Google Scholar
• Keller NP. Fungal secondary metabolism: regulation, function and drug discovery. Nat Rev Microbiol. 2019;17(3):167–180. doi:10.1038/s41579-018-0121-1.
   PubMed Web of Science ®Google Scholar
• Guinan J, Wang S, Hazbun TR, Yadav H, Thangamani S. Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans. Sci Rep. 2019;9(1):8872. doi:10.1038/s41598-019-45467-7.
   PubMedGoogle Scholar
• Kennedy MJ, Volz PA. Ecology of Candida albicans gut colonization: inhibition of Candida adhesion, colonization, and dissemination from the gastrointestinal tract by bacterial antagonism. Infect Immun. 1985;49(3):654–663. doi:10.1128/iai.49.3.654-663.1985.
   PubMed Web of Science ®Google Scholar
• Kaur J, Pethani BP, Kumar S, Kim M, Sunna A, Kautto L, Penesyan A, Paulsen IT, Nevalainen H. Pseudomonas aeruginosa inhibits the growth of Scedosporium aurantiacum, an opportunistic fungal pathogen isolated from the lungs of cystic fibrosis patients. Front Microbiol. 2015;6:866. doi:10.3389/fmicb.2015.00866.
   PubMed Web of Science ®Google Scholar
• Briard B, Heddergott C, Latgé JP. Volatile compounds emitted by pseudomonas aeruginosa stimulate growth of the fungal pathogen aspergillus fumigatus. mBio. 2016;7(2). doi:10.1128/mBio.00219-16.
   PubMed Web of Science ®Google Scholar
• Hogan DA, Kolter R. Pseudomonas - candida interactions: an ecological role for virulence factors. Science. 2002;296(5576):2229–2232. doi:10.1126/science.1070784.
   PubMed Web of Science ®Google Scholar
• Klotz SA, Chasin BS, Powell B, Gaur NK, Lipke PN. Polymicrobial bloodstream infections involving Candida species: analysis of patients and review of the literature. Diagn Microbiol Infect Dis. 2007;59(4):401–406. doi:10.1016/j.diagmicrobio.2007.07.001.
   PubMed Web of Science ®Google Scholar
• Gupta N, Haque A, Mukhopadhyay G, Narayan RP, Prasad R. Interactions between bacteria and Candida in the burn wound. Burns J Int Soc Burn Inj. 2005;31(3):375–378. doi:10.1016/j.burns.2004.11.012.
   PubMed Web of Science ®Google Scholar
• Harriott MM, Noverr MC. Candida albicans and Staphylococcus aureus form polymicrobial biofilms: effects on antimicrobial resistance. Antimicrob Agents Chemother. 2009;53(9):3914–3922. doi:10.1128/AAC.00657-09.
   PubMed Web of Science ®Google Scholar
• Allison DL, Scheres N, Willems HME, Bode CS, Krom BP, Shirtliff ME. The host immune system facilitates disseminated Staphylococcus aureus disease due to phagocytic attraction to candida albicans during coinfection: a case of bait and switch. Infect Immun. 2019;87(11):e00137–19. doi:10.1128/IAI.00137-19.
   PubMed Web of Science ®Google Scholar
• Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJ, Faber KN, Hermoso MA. Short Chain Fatty Acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019;10.
   Web of Science ®Google Scholar
• Bhaskaran N, Quigley C, Paw C, Butala S, Schneider E, Pandiyan P. Role of short chain fatty acids in controlling tregs and immunopathology during mucosal infection. Front Microbiol. 2018;9:1995. doi:10.3389/fmicb.2018.01995.
   PubMed Web of Science ®Google Scholar
• Ciarlo E, Heinonen T, Herderschee J, Fenwick C, Mombelli M, Le Roy D, Roger T. Impact of the microbial derived short chain fatty acid propionate on host susceptibility to bacterial and fungal infections in vivo. Sci Rep. 2016;6(1):37944. doi:10.1038/srep37944.
   PubMedGoogle Scholar
• Liu P, Wang Y, Yang G, Zhang Q, Meng L, Xin Y, Jiang X. The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and colonic carcinogenesis. Pharmacol Res. 2021;165:105420. doi:10.1016/j.phrs.2021.105420.
   PubMed Web of Science ®Google Scholar
• Yoo JY, Groer M, Dutra SVO, Sarkar A, McSkimming DI. Gut microbiota and immune system interactions. Microorganisms. 2020;8(10):1587. doi:10.3390/microorganisms8101587.
   PubMed Web of Science ®Google Scholar
• Fellows R, Varga-Weisz P. Chromatin dynamics and histone modifications in intestinal microbiota-host crosstalk. Mol Metab. 2020;38:100925. doi:10.1016/j.molmet.2019.12.005.
   PubMed Web of Science ®Google Scholar
• Baltierra-Trejo E, Sánchez-Yáñez JM, Buenrostro-Delgado O, Márquez-Benavides L. Production of short-chain fatty acids from the biodegradation of wheat straw lignin by aspergillus fumigatus. Bioresour Technol. 2015;196:418–425. doi:10.1016/j.biortech.2015.07.105.
   PubMed Web of Science ®Google Scholar
• Cottier F, Tan ASM, Yurieva M, Liao W, Lum J, Poidinger M, Zolezzi F, Pavelka N. The transcriptional response of candida albicans to weak organic acids, carbon source, and MIG1 inactivation unveils a role for HGT16 in mediating the fungistatic effect of acetic acid. G3 Bethesda Md. 2017;7(11):3597–3604. doi:10.1534/g3.117.300238.
   PubMedGoogle Scholar
• Noverr MC, Huffnagle GB. Regulation of candida albicans morphogenesis by fatty acid metabolites. Infect Immun. 2004;72(11):6206–6210. doi:10.1128/IAI.72.11.6206-6210.2004.
   PubMed Web of Science ®Google Scholar
• García C, Tebbji F, Daigneault M, Liu -N-N, Köhler JR, Allen-Vercoe E, Sellam A. The human gut microbial metabolome modulates fungal growth via the TOR signaling pathway. mSphere. 2017;2(6):e00555–17. doi:10.1128/mSphere.00555-17.
   PubMed Web of Science ®Google Scholar
• Nguyen LN, Lopes LCL, Cordero RJB, Nosanchuk JD. Sodium butyrate inhibits pathogenic yeast growth and enhances the functions of macrophages. J Antimicrob Chemother. 2011;66(11):2573–2580. doi:10.1093/jac/dkr358.
   PubMed Web of Science ®Google Scholar
• Goyal S, Ramawat KG, Mérillon J-M. Different shades of fungal metabolites: an overview. In: Fungal metabolites. Springer International Publishing; 2017. 1–29. doi:10.1007/978-3-319-25001-4_34.
   Google Scholar
• Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, et al. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev. 2018;42(3):335–352. doi:10.1093/femsre/fuy008.
   PubMed Web of Science ®Google Scholar
• Keller NP, Turner G, Bennett JW. Fungal secondary metabolism — from biochemistry to genomics. Nat Rev Microbiol. 2005;3(12):937–947. doi:10.1038/nrmicro1286.
   PubMed Web of Science ®Google Scholar
• Fox EM, Howlett BJ. Secondary metabolism: regulation and role in fungal biology. Curr Opin Microbiol. 2008;11(6):481–487. doi:10.1016/j.mib.2008.10.007.
   PubMed Web of Science ®Google Scholar
• Pusztahelyi T, Holb IJ, Pãcsi I. Secondary metabolites in fungus-plant interactions. Front Plant Sci. 2015;6:573. doi:10.3389/fpls.2015.00573.
   PubMed Web of Science ®Google Scholar
• Thirumurugan D, Cholarajan A, Raja SSS, Vijayakumar R. An introductory chapter: secondary metabolites. In: Secondary metabolites - sources and applications. InTech; 2018. doi:10.5772/intechopen.79766
   Google Scholar
• Zhang Y-Q, Brock M, Keller NP. Connection of propionyl-CoA metabolism to polyketide biosynthesis in Aspergillus nidulans. Genetics. 2004;168(2):785–794. doi:10.1534/genetics.104.027540.
   PubMed Web of Science ®Google Scholar
• Oide S, Moeder W, Krasnoff S, Gibson D, Haas H, Yoshioka K, Turgeon BG. NPS6, encoding a nonribosomal peptide synthetase involved in siderophore-mediated iron metabolism, is a conserved virulence determinant of plant pathogenic ascomycetes. Plant Cell. 2006;18(10):2836–2853. doi:10.1105/tpc.106.045633.
   PubMed Web of Science ®Google Scholar
• Schmidt-Dannert C. Biosynthesis of terpenoid natural products in fungi. Cham: Springer; 2014. 19–61. doi:10.1007/10_2014_283.
   Google Scholar
• Metzger U, Schall C, Zocher G, Unsöld I, Stec E, Li S-M, Heide L, Stehle T. The structure of dimethylallyl tryptophan synthase reveals a common architecture of aromatic prenyltransferases in fungi and bacteria. Proc Natl Acad Sci U S A. 2009;106(34):14309–14314. doi:10.1073/pnas.0904897106.
   PubMed Web of Science ®Google Scholar
• Steffan N, Unsöld IA, Li SM. Chemoenzymatic synthesis of prenylated indole derivatives by using a 4-dimethylallyltryptophan synthase from aspergillus fumigatus. ChemBioChem. 2007;8(11):1298–1307. doi:10.1002/cbic.200700107.
   PubMed Web of Science ®Google Scholar
• de Groot AN, van Dongen PW, Vree TB, Hekster YA, van Roosmalen JEA. Current status and review of clinical pharmacology and therapeutic use compared with other oxytocics in obstetrics and gynaecology. Drugs. 1998;56(4):523–535. doi:10.2165/00003495-199856040-00002.
   PubMed Web of Science ®Google Scholar
• Wong CGT, Bottiglieri T, Iii OCS. Neurological disease. Ann Neurol. 2003;65(S6):3–12. doi:10.1002/ana.10696.
   Google Scholar
• Jo S, Yarishkin O, Hwang YJ, Chun YE, Park M, Woo DH, Bae JY, Kim T, Lee J, Chun H, et al. GABA from reactive astrocytes impairs memory in mouse models of alzheimer’s disease. Nat Med. 2014;20(8):886–896. doi:10.1038/nm.3639.
   PubMed Web of Science ®Google Scholar
• Flajs D, Peraica M. Toxicological properties of citrinin. doi:10.2478/10004-1254-60-2009-1992.
   Google Scholar
• Kumar A, Asthana M, Gupta A, Nigam D, Mahajan S. Secondary metabolism and antimicrobial metabolites of penicillium. In: New and future developments in microbial biotechnology and bioengineering. Elsevier; 2018. 47–68. doi:10.1016/b978-0-444-63501-3.00003-x.
   Google Scholar
• Tammer B, Lehmann I, Nieber K, Altenburger R. Combined effects of mycotoxin mixtures on human T cell function. Toxicol Lett. 2007;170(2):124–133. doi:10.1016/j.toxlet.2007.02.012.
   PubMed Web of Science ®Google Scholar
• Chen CC, Chan WH. Inhibition of citrinin-induced apoptotic biochemical signaling in human hepatoma G2 cells by resveratrol. Int J Mol Sci. 2009;10(8):3338–3357. doi:10.3390/ijms10083338.
   PubMed Web of Science ®Google Scholar
• Ostry V, Malir F, Ruprich J. Producers and important dietary sources of ochratoxin A and citrinin. Toxins. 2013;5(9):1574–1586. doi:10.3390/toxins5091574.
   PubMed Web of Science ®Google Scholar
• Groopman JD, Cain LG, Kensler TW, Harris CC. CRC critical reviews in toxicology aflatoxin exposure in human populations: measurements and relationship to cancer. 2008. doi:10.3109/10408448809014902.
   Google Scholar
• Deger GE. Aflatoxin: human colon carcinogenesis?. Ann Intern Med. 1976;85(2):204–205. doi:10.7326/0003-4819-85-2-204.
   PubMed Web of Science ®Google Scholar
• Aguilar F, Hussain SP, Cerutti P. Aflatoxin B1 induces the transversion of G-->T in codon 249 of the p53 tumor suppressor gene in human hepatocytes. Proc Natl Acad Sci U S A. 1993;90(18):8586–8590. doi:10.1073/pnas.90.18.8586.
   PubMed Web of Science ®Google Scholar
• Buening MK, Chang RL, Huang MT, Fortner JG, Wood AW, Conney AH. Activation and inhibition of benzo(a)pyrene and aflatoxin B1 metabolism in human liver microsomes by naturally occurring flavonoids. Cancer Res. 1981;41:67–72.
   PubMed Web of Science ®Google Scholar
• Samson RA, Noonim P, Meijer M, Houbraken J, Frisvad JC, Varga J. Diagnostic tools to identify black aspergilli. Stud Mycol. 2007;59:129–145. doi:10.3114/sim.2007.59.13.
   PubMed Web of Science ®Google Scholar
• Siddiqui MS, Thodey K, Trenchard I, Smolke CD. Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools. FEMS Yeast Res. 2012;12(2):144–170. doi:10.1111/j.1567-1364.2011.00774.x.
   PubMed Web of Science ®Google Scholar
• Song YC, Li H, Ye YH, Shan CY, Yang YM, Tan RX. Endophytic naphthopyrone metabolites are co-inhibitors of xanthine oxidase, SW1116 cell and some microbial growths. FEMS Microbiol Lett. 2004;241(1):67–72. doi:10.1016/j.femsle.2004.10.005.
   PubMed Web of Science ®Google Scholar
• Koyama K, Ominato K, Natori S, Tashiro T, Tsuruo T. Cytotoxicity and antitumor activities of fungal bis (naphtho-γ-pyrone) derivatives. J Pharmacobiodyn. 1988;11(9):630–635. doi:10.1248/bpb1978.11.630.
   PubMedGoogle Scholar
• Kim S-K, Dewapriya P. Anticancer potentials of marine-derived fungal metabolites. In: Marine microbiology. John Wiley & Sons, Ltd; 2013. 237–245. doi:10.1002/9783527665259.ch14.
   Google Scholar
• Traven A, Naderer T. Central metabolic interactions of immune cells and microbes: prospects for defeating infections. EMBO Rep. 2019;20.
   PubMed Web of Science ®Google Scholar
• Bouslimi A, Ouannes Z, Golli EE, Bouaziz C, Hassen W, Bacha H. Cytotoxicity and oxidative damage in kidney cells exposed to the mycotoxins ochratoxin a and citrinin: individual and combined effects. Toxicol Mech Methods. 2008;18(4):341–349. doi:10.1080/15376510701556682.
   PubMed Web of Science ®Google Scholar
• Hetherington AC, Raistrick H. Studies in the biochemistry of micro-organisms. part XIV.—On the production and chemical constitution of a new yellow colouring mater, citrinin, produced from glucose by penicillium. Philos Trans R Soc Lond Ser B Contain Pap Biol Character. 1931;220:269–295.
   Google Scholar
• Zain ME. Impact of mycotoxins on humans and animals. J Saudi Chem Soc. 2011;15(2):129–144. doi:10.1016/j.jscs.2010.06.006.
   Web of Science ®Google Scholar
• Kong HH, Morris A. The emerging importance and challenges of the human mycobiome. Virulence. 2017;8(3):310–312. doi:10.1080/21505594.2017.1279780.
   PubMed Web of Science ®Google Scholar
• Joyce AR, Palsson B. The model organism as a system: integrating ‘omics’ data sets. Nat Rev Mol Cell Biol. 2006;7(3):198–210. doi:10.1038/nrm1857.
   PubMed Web of Science ®Google Scholar
• Gehlenborg N, O’Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D. Visualization of omics data for systems biology. Nat Methods. 2010;7(S3):S56–S68. doi:10.1038/nmeth.1436.
   PubMedGoogle Scholar
• Berger B, Peng J, Singh M. Computational solutions for omics data. Nat Rev Genet. 2013;14(5):333–346. doi:10.1038/nrg3433.
   PubMed Web of Science ®Google Scholar
• Vogel C, Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 2012;13(4):227–232. doi:10.1038/nrg3185.
   PubMed Web of Science ®Google Scholar
• de Bekker C, Smith PB, Patterson AD, Hughes DP, Jacobsen ID. Metabolomics reveals the heterogeneous secretome of two entomopathogenic fungi to ex vivo cultured insect tissues. PLoS ONE. 2013;8(8):e70609. doi:10.1371/journal.pone.0070609.
   PubMed Web of Science ®Google Scholar
• Palsson B. Metabolic systems biology. FEBS Lett. 2009;583(24):3900–3904. doi:10.1016/j.febslet.2009.09.031.
   PubMed Web of Science ®Google Scholar
• Systems biology - bernhard palsson -. Google Books.
   Google Scholar
• Shoaie S, Nielsen J. Elucidating the interactions between the human gut microbiota and its host through metabolic modeling. Front Genet. 2014;5. doi:10.3389/fgene.2014.00086.
   PubMed Web of Science ®Google Scholar
• Mardinoglu A, Gatto F, Nielsen J. Genome-scale modeling of human metabolism - a systems biology approach. Biotechnol J. 2013;8(9):985–996. doi:10.1002/biot.201200275.
   PubMed Web of Science ®Google Scholar
• Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2017;35(1):81–89. doi:10.1038/nbt.3703.
   PubMed Web of Science ®Google Scholar
• Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS. The virtual metabolic human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019;47(D1):D614–D624. doi:10.1093/nar/gky992.
   PubMed Web of Science ®Google Scholar
• Ghaffari P, Mardinoglu A, Asplund A, Shoaie S, Kampf C, Uhlen M, Nielsen J. Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling. Sci Rep. 2015;5(1):8183. doi:10.1038/srep08183.
   PubMedGoogle Scholar
• Martins-Santana L, Nora LC, Sanches-Medeiros A, Lovate GL, Cassiano MHA, Silva-Rocha R. Systems and synthetic biology approaches to engineer fungi for fine chemical production. Front Bioeng Biotechnol. 2018;6:117. doi:10.3389/fbioe.2018.00117.
   PubMed Web of Science ®Google Scholar
• Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun. 2019;10(1):3586. doi:10.1038/s41467-019-11581-3.
   PubMedGoogle Scholar
• Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol. 2012;6(1):24. doi:10.1186/1752-0509-6-24.
   PubMedGoogle Scholar
• Sohn SB, Kim TY, Lee JH, Lee SY. Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. BMC Syst Biol. 2012;6(1):49. doi:10.1186/1752-0509-6-49.
   PubMedGoogle Scholar
• Xu N, Liu L, Zou W, Liu J, Hua Q, Chen J. Reconstruction and analysis of the genome-scale metabolic network of Candida glabrata. Mol Biosyst. 2013;9(2):205–216. doi:10.1039/C2MB25311A.
   PubMedGoogle Scholar
• Chung BK, Selvarasu S, Camattari A, Ryu J, Lee H, Ahn J, Lee H, Lee D-Y. Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microb Cell Factories. 2010;9(1):50. doi:10.1186/1475-2859-9-50.
   PubMedGoogle Scholar
• Brochado AR, Matos C, Møller BL, Hansen J, Mortensen UH, Patil KR. Improved vanillin production in baker’s yeast through in silico design. Microb Cell Factories. 2010;9(1):84. doi:10.1186/1475-2859-9-84.
   PubMedGoogle Scholar
• Mishra P, Lee N-R, Lakshmanan M, Kim M, Kim B-G, Lee D-Y. Genome-scale model-driven strain design for dicarboxylic acid production in Yarrowia lipolytica. BMC Syst Biol. 2018;12(S2):12. doi:10.1186/s12918-018-0542-5.
   PubMedGoogle Scholar
• Frezza C, Zheng L, Folger O, Rajagopalan KN, MacKenzie ED, Jerby L, Micaroni M, Chaneton B, Adam J, Hedley A. Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. Nature. 2011;477(7363):225–228. doi:10.1038/nature10363.
   PubMed Web of Science ®Google Scholar
• Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat Biotechnol. 2010;28(12):1279–1285. doi:10.1038/nbt.1711.
   PubMed Web of Science ®Google Scholar
• Agren R, Mardinoglu A, Asplund A, Kampf C, Uhlen M, Nielsen J. Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Mol Syst Biol. 2014;10(3):721. doi:10.1002/msb.145122.
   PubMed Web of Science ®Google Scholar
• Kumar M, Ji B, Babaei P, Das P, Lappa D, Ramakrishnan G, Fox TE, Haque R, Petri WA, Bäckhed F. Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: lessons from genome-scale metabolic modeling. Metab Eng. 2018;49:128–142. doi:10.1016/j.ymben.2018.07.018.
   PubMed Web of Science ®Google Scholar
• Granata I, Troiano E, Sangiovanni M, Guarracino MR. Integration of transcriptomic data in a genome-scale metabolic model to investigate the link between obesity and breast cancer. BMC Bioinform. 2019;20(S4):162. doi:10.1186/s12859-019-2685-9.
   PubMedGoogle Scholar
• Bauer E, Thiele I. From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease. Npj Syst Biol Appl. 2018;4(1):1–9. doi:10.1038/s41540-018-0063-2.
   PubMedGoogle Scholar
• Das P, Babaei P, Nielsen J. Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. BMC Genomics. 2019;20(1):208. doi:10.1186/s12864-019-5591-7.
   PubMed Web of Science ®Google Scholar
• Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R, Thiele I. Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions. BMC Biol. 2020;18(1):62. doi:10.1186/s12915-020-00775-7.
   PubMed Web of Science ®Google Scholar
• Miraglia F, Colla EM. Parkinson’s disease and molecular mimicry. Cells. 2019;8(3):E222. doi:10.3390/cells8030222.
   PubMed Web of Science ®Google Scholar
• Nuzum ND, Loughman A, Szymlek-Gay EA, Hendy A, Teo WP, Macpherson H. Gut microbiota differences between healthy older adults and individuals with Parkinson’s disease: a systematic review. Neurosci Biobehav Rev. 2020;112:227–241. doi:10.1016/j.neubiorev.2020.02.003.
   PubMed Web of Science ®Google Scholar
• Rosario D, Bidkhori G, Lee S, Bedarf J, Hildebrand F, Le Chatelier E, Uhlen M, Ehrlich SD, Proctor G, Wüllner U, Mardinoglu A. Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease. Cell Rep. 2021;34(9):108807. doi:10.1016/j.celrep.2021.108807.
   PubMed Web of Science ®Google Scholar
• MahmoudianDehkordi S, Arnold M, Nho K, Ahmad S, Jia W, Xie G, Louie G, Kueider‐Paisley A, Moseley MA, Thompson JW. Altered bile acid profile associates with cognitive impairment in Alzheimer’s disease-An emerging role for gut microbiome. Alzheimers Dement J Alzheimers Assoc. 2019;15(1):76–92. doi:10.1016/j.jalz.2018.07.217.
   PubMed Web of Science ®Google Scholar
• Baloni P, Funk CC, Yan J, Yurkovich JT, Kueider-Paisley A, Nho K, Heinken A, Jia W, Mahmoudiandehkordi S, Louie G, Saykin AJ. Identifying differences in bile acid pathways for cholesterol clearance in Alzheimer’s disease using metabolic networks of human brain regions. 2019, p. 782987. doi:10.1101/782987.
   Google Scholar
• Zomorrodi AR, Maranas CD. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol. 2012;8(2):e1002363. doi:10.1371/journal.pcbi.1002363.
   PubMed Web of Science ®Google Scholar
• Shoaie S, Karlsson F, Mardinoglu A, Nookaew I, Bordel S, Nielsen J. Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci Rep. 2013;3(1):1–10. doi:10.1038/srep02532.
   Google Scholar
• Shoaie S, Ghaffari P, Kovatcheva-Datchary P, Mardinoglu A, Sen P, Pujos-Guillot E, De Wouters T, Juste C, Rizkalla S, Chilloux J, Hoyles L. Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metab. 2015;22(2):320–331. doi:10.1016/j.cmet.2015.07.001.
   PubMed Web of Science ®Google Scholar
• Román E, Coman I, Prieto D, Alonso-Monge R, Pla J. Implementation of a CRISPR-based system for gene regulation in candida albicans. mSphere. 2019;4(1):e00001–19. doi:10.1128/mSphere.00001-19.
   PubMed Web of Science ®Google Scholar
• Gonzalez-Angulo AM, Hennessy BTJ, Mills GB. Future of personalized medicine in oncology: a systems biology approach. J Clin Oncol. 2010;28(16):2777–2783. doi:10.1200/JCO.2009.27.0777.
   PubMed Web of Science ®Google Scholar
• Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nat Protoc. 2020;15(1):1–14. doi:10.1038/s41596-019-0254-3.
   PubMed Web of Science ®Google Scholar
• Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet. 2014;15(2):107–120. doi:10.1038/nrg3643.
   PubMed Web of Science ®Google Scholar
• Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, Bartell JA, Blank LM, Chauhan S, Correia K, Diener C. MEMOTE for standardized genome-scale metabolic model testing. Nat Biotechnol. 2020;38(3):272–276. doi:10.1038/s41587-020-0446-y.
   PubMed Web of Science ®Google Scholar
• Machado D, Andrejev S, Tramontano M, Patil KR. Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. Nucleic Acids Res. 2018;46(15):7542–7553. doi:10.1093/nar/gky537.
   PubMed Web of Science ®Google Scholar
• Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol. 2013;9(3):e1002980. doi:10.1371/journal.pcbi.1002980.
   PubMed Web of Science ®Google Scholar
• Mojica FJM, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60(2):174–182. doi:10.1007/s00239-004-0046-3.
   PubMed Web of Science ®Google Scholar
• Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiol Read Engl. 2005;151(3):653–663. doi:10.1099/mic.0.27437-0.
   PubMedGoogle Scholar
• Brouns SJJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJH, Snijders APL, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321(5891):960–964. doi:10.1126/science.1159689.
   PubMed Web of Science ®Google Scholar