Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci. 2008;105(6):2117–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ahmed I, Roy B, Khan S, Septer S, Umar S. Microbiome, metabolome and inflammatory bowel disease. Microorganisms. 2016;4(2):20.
Article
PubMed Central
CAS
Google Scholar
Grigorescu I, Dumitrascu DL. Implication of gut microbiota in diabetes mellitus and obesity, vol. 12, Acta Endocrinologica Foundation; 2016. p. 206–14.
Google Scholar
Xu M, Xu X, Li J, Li F. Association between gut microbiota and autism spectrum disorder: a systematic review and meta-analysis, vol. 10, Frontiers media S.a; 2019.
Google Scholar
Cheung SG, Goldenthal AR, Uhlemann AC, Mann JJ, Miller JM, Sublette ME. Systematic review of gut microbiota and major depression, vol. 10, Frontiers media S.a; 2019.
Google Scholar
Donia MS, Fischbach MA. Small molecules from the human microbiota. Science. 2015;349(6246):1254766.
Article
PubMed
PubMed Central
CAS
Google Scholar
Martinet L, Naômé A, Deflandre B, Maciejewska M, Tellatin D, Tenconi E, et al. A single biosynthetic gene cluster is responsible for the production of bagremycin antibiotics and ferroverdin iron chelators. mBio. 2019;10(4):7.
Article
Google Scholar
Kolodziejczyk AA, Zheng D, Elinav E. Diet–microbiota interactions and personalized nutrition, vol. 17, nature publishing group; 2019. p. 742–53.
Google Scholar
Baldini F, Heinken A, Heirendt L, Magnusdottir S, Fleming RMT, Thiele I. The microbiome modeling toolbox: from microbial interactions to personalized microbial communities. Bioinformatics (Oxford, England). 2019;35(13):2332–4.
Article
CAS
Google Scholar
Embree M, Liu JK, Al-Bassam MM, Zengler K. Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc Natl Acad Sci. 2015;112(50):15450–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bauer E, Thiele I. From network analysis to functional metabolic modeling of the human gut microbiota. mSystems. 2018;3(3):27.
Article
Google Scholar
Großeholz R, Koh CC, Veith N, Fiedler T, Strauss M, Olivier B, et al. Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen enterococcus faecalis. Systems Biol Appl. 2016;2(1):1–9.
Google Scholar
Åkesson M, Förster J, Nielsen J. Integration of gene expression data into genome-scale metabolic models. Metab Eng. 2004;6(4):285–93.
Article
PubMed
CAS
Google Scholar
Palsson B. Systems biology: properties of reconstructed networks; 2006.
Book
Google Scholar
Orth JD, Thiele I, Palsson BO. What is flux balance analysis? vol. 28: Nature Publishing Group; 2010. p. 245–8.
Gottstein W, Olivier BG, Bruggeman FJ, Teusink B. Constraint-based stoichiometric modelling from single organisms to microbial communities, vol. 13: Royal Society of London; 2016.
Khandelwal RA, Olivier BG, Röling WF, Teusink B, Bruggeman FJ. Community flux balance analysis for microbial consortia at balanced growth. PLoS One. 2013;8(5):e64567.
Article
CAS
PubMed
PubMed Central
Google Scholar
Resendis-Antonio O, Reed JL, Encarnación S, Collado-Vides J, Palsson B. Metabolic reconstruction and modeling of nitrogen fixation in rhizobium etli. PLoS Computat Biol. 2007;3(10):1887–95.
Article
CAS
Google Scholar
Diener C, Gibbons SM, Resendis-Antonio O. MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota. mSystems. 2020;5(1):21.
Article
Google Scholar
El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst Biol. 2014;8(1):41.
Article
PubMed
PubMed Central
CAS
Google Scholar
Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. Nov., comb. nov. Int J Syst Evol Microbiol. 2002;52(6):2141–6.
CAS
PubMed
Google Scholar
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BT. A detailed genome-wide reconstruction of mouse metabolism based on human recon 1. BMC Syst Biol. 2010;4(1):140.
Article
PubMed
PubMed Central
CAS
Google Scholar
Heinken A, Sahoo S, Fleming RMT, Thiele I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes. 2013;4(1):28–40.
Article
PubMed
PubMed Central
Google Scholar
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018;36(3):272–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, et al. The virtual metabolic human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019;47(D1):D614–24.
Article
CAS
PubMed
Google Scholar
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63.
Article
CAS
PubMed
Google Scholar
Ji BW, Sheth RU, Dixit PD, Tchourine K, Vitkup D. Macroecological dynamics of gut microbiota. Nat Microbiol. 2020;5(5):768–75.
Article
CAS
PubMed
Google Scholar
Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science. 2017;357(6353):802–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watanabe LH, König M, Myers CJ. Dynamic flux balance analysis models in SBML; 2017.
Google Scholar
Gomez JA, Höffner K, Barton PI. DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis. BMC Bioinform. 2014;15(1):18.
Article
Google Scholar
Höffner K, Harwood SM, Barton PI. A reliable simulator for dynamic flux balance analysis. Biotechnol Bioeng. 2013;110(3):792–802.
Article
PubMed
CAS
Google Scholar
Mahadevan R, Edwards JS, Doyle FJ. Dynamic flux balance analysis of diauxic growth in Escherichia coli; 2002.
Book
Google Scholar
Henson MA, Hanly TJ. Dynamic flux balance analysis for synthetic microbial communities. IET Syst Biol. 2014;8(5):214–29.
Article
PubMed
PubMed Central
Google Scholar
Kim OD, Rocha M, Maia P. A review of dynamic modeling approaches and their application in computational strain optimization for metabolic engineering. Front Microbiol. 2018;9:1690.
Article
PubMed
PubMed Central
Google Scholar
Magnúsdóttir S, Thiele I. Modeling metabolism of the human gut microbiome, vol. 51, Elsevier ltd; 2018. p. 90–6.
Google Scholar
Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc Natl Acad Sci. 2015;112(20):6449–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mendoza SN, Olivier BG, Molenaar D, Teusink B. A systematic assessment of current genome-scale metabolic reconstruction tools. Genome Biol. 2019;20(1):1.
Article
Google Scholar
Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk HP, Gophna U, et al. Harnessing the landscape of microbial culture media to predict new organism-media pairings, nature communications, vol. 6; 2015.
Google Scholar
Robador A, LaRowe DE, Finkel SE, Amend JP, Nealson KH. Changes in microbial energy metabolism measured by nanocalorimetry during growth phase transitions. Front Microbiol. 2018;9:1.
Article
Google Scholar
Thiele I, Palsson B. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 2010;5(1):93–121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Magnúsdóttir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2017;35(1):81–9.
Article
PubMed
CAS
Google Scholar
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: the United States department of energy systems biology knowledgebase, vol. 36, nature publishing group; 2018. p. 566–9.
Google Scholar
King ZA, Lu J, Dräger A, Dräger D, Miller P, Federowicz S, et al. BiGG models: a platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 2015;44:515–22.
Article
CAS
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):7542–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, et al. MEMOTE for standardized genome-scale metabolic model testing. Nat Res Forum. 2020;38:272–6.
CAS
Google Scholar
Babaei P, Shoaie S, Ji B, Nielsen J. Challenges in modeling the human gut microbiome. Nat Biotechnol. 2018;36(8):682–6.
Article
CAS
PubMed
Google Scholar
Magnúsdóttir S, Heinken A, Fleming RMT, Thiele I. Reply to challenges in modeling the human gut microbiome. Nat Biotechnol. 2018;36(8):686–91.
Article
PubMed
CAS
Google Scholar
Pryor Rosina R, Norvaisas P, Marinos G, Best L, Thingholm LB. Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy. Cell. 2019;178(6):1299–312.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RM, Thiele I. Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. 2019;7(1):75.
Article
PubMed
PubMed Central
Google Scholar
Devika NT, Raman K. Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models. Sci Rep. 2019;9(1):1–9.
Article
CAS
Google Scholar
Kuang E, Marney M, Cuevas D, Edwards RA, Forsberg EM. Towards predicting gut microbial metabolism: integration of flux balance analysis and untargeted metabolomics. Metabolites. 2020;10(4):1.
Article
CAS
Google Scholar
Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555(7695):210–5.
Article
CAS
PubMed
Google Scholar
Turnbaugh Peter JP, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. Nature. 2007;449(7164):804–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Henry Christopher SC, DeJongh M, Best AA, Frybarger PM, Linsay B. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28(9):977–82.
Article
CAS
PubMed
Google Scholar
Garza DR, Van Verk MC, Huynen MA, Dutilh BE. Towards predicting the environmental metabolome from metagenomics with a mechanistic model. Nat Microbiol. 2018;3(4):456–60.
Article
CAS
PubMed
Google Scholar
Zhao L, Zhang F, Ding X, Wu G, Lam YY, Wang X, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151.
Article
CAS
PubMed
Google Scholar
Duboc H, Rajca S, Rainteau D, Benarous D, Maubert MA, Quervain E, et al. Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases. Gut. 2013;62(4):531–9.
Article
CAS
PubMed
Google Scholar
Bauer E, Zimmermann J, Baldini F, Thiele I, Kaleta C. BacArena: individual-based metabolic modeling of heterogeneous microbes in complex communities. PLoS Comput Biol. 2017;13(5):e1005544.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bauer E, Thiele I. From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s diseasera. Syst Biol Appl. 2018;4(1):1–9.
Google Scholar
Green N, Miller T, Suskind D, Lee D. A review of dietary therapy for IBD and a vision for the future. Nutrients. 2019;11:5.
Article
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.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep. 2014;7(4):1104–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gardner JJ, Hodge BMS, Boyle NR. Multiscale multiobjective systems analysis (MiMoSA): an advanced metabolic modeling framework for complex systems. Sci Rep. 2019;9(1):1–15.
Article
CAS
Google Scholar
Sen P, Orešič M. Metabolic modeling of human gut microbiota on a genome scale: an overview. Metabolites. 2019;9:2.
Article
CAS
Google Scholar
García-Jiménez B, García JL, Nogales J. FLYCOP: metabolic modeling-based analysis and engineering microbial communities, in bioinformatics; 2018.
Google Scholar
Fouladiha H, Marashi SA. Biomedical applications of cell- and tissue-specific metabolic network models, vol. 68: Academic Press Inc; 2017. p. 35–49.
Wang Y, Kim R, Hinman SS, Zwarycz B, Magness ST, Allbritton NL. Bioengineered systems and designer matrices that recapitulate the intestinal stem cell niche. Cell Mol Gastroenterol hepatol. 2018;5Elsevier Inc:440–453.e1.
Article
PubMed
PubMed Central
Google Scholar
Turski MP, Turska M, Paluszkiewicz P, Parada-Turska J, Oxenkrug GF. Kynurenic acid in the digestive system–-new facts, new challenges. International J Tryptophan Res. 2013;6:IJTR.S12536.
Article
CAS
Google Scholar
Kuc D, Zgrajka W, Parada-Turska J, Urbanik-Sypniewska T, Turski WA. Micromolar concentration of kynurenic acid in rat small intestine short communication. Amino Acids. 2008;35:503–5.
Article
CAS
PubMed
Google Scholar
Fallingborg J. Intraluminal pH of the human gastrointestinal tract. Dan Med Bull. 1999;46(3):183–96.
CAS
PubMed
Google Scholar
Kastl AJ, Terry NA, Wu GD, Albenberg LG. The structure and function of the human small intestinal microbiota: current understanding and future directions, vol. 9: Elsevier Inc; 2020. p. 33–45.
Hoek MJ, Merks RM. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. BMC Syst Biol. 2017;11(1):56.
Article
PubMed
PubMed Central
CAS
Google Scholar
Vandeputte Doris D, Falony G, Vieira-Silva S, Tito RY, Joossens M. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. 2016;65(1):57–62.
Article
CAS
PubMed
Google Scholar
Chan SH, Friedman ES, Wu GD, Maranas CD. Predicting the longitudinally and radially varying gut microbiota composition using multi-scale microbial metabolic modeling. Processes. 2019;7(7):394.
Article
CAS
Google Scholar
Persi E, Duran-Frigola M, Damaghi M, Roush WR, Aloy P, Cleveland JL, et al. Systems analysis of intracellular pH vulnerabilities for cancer therapy. Nat Commun. 2018;9(1):1–11.
Article
CAS
Google Scholar
Zomorrodi AR, Islam MM, Maranas CD. D-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol. 2014;3(4):247–57.
Article
CAS
PubMed
Google Scholar
Shoaie S, Ghaffari P, Kovatcheva-Datchary P, Mardinoglu A, Sen P, Pujos-Guillot E, et al. Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metab. 2015;22(2):320–31.
Article
CAS
PubMed
Google Scholar
Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837–48.
Article
CAS
PubMed
Google Scholar
Chan SHJ, Simons MN, Maranas CD. SteadyCom: predicting microbial abundances while ensuring community stability. PLoS Comput Biol. 2017;13(5):e1005539.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rinninella E, Raoul P, Cintoni M, Franceschi F, Miggiano GAD, Gasbarrini A, et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 2019;7:1.
Article
CAS
Google Scholar
Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;(6):174, 1406–1423.e16.
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci. 2011;108(SUPPL. 1):4554–61.
Article
CAS
PubMed
Google Scholar
Zinöcker MK, Lindseth IA. The western diet–microbiome-host interaction and its role in metabolic disease, vol. 10, MDPI AG; 2018.
Google Scholar
Vogt NM, Kerby RL, Dill-McFarland KA, Harding SJ, Merluzzi AP, Johnson SC, et al. Gut microbiome alterations in Alzheimer’s disease. Sci Rep. 2017;7:1.
Article
CAS
Google Scholar
Kong G, Cao KAL, Judd LM, Li SS, Renoir T, Hannan AJ. Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington's disease. Neurobiol Dis. 2020;135:104268.
Article
CAS
PubMed
Google Scholar
Sun MF, Shen YQ. Dysbiosis of gut microbiota and microbial metabolites in Parkinson's disease. Ageing Res Rev. 2018;45Elsevier Ireland Ltd:53–61.
Article
CAS
PubMed
Google Scholar
Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, et al. Consortium, Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes. bioRxiv. 2019;1:691030.
Google Scholar
Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, et al. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. Genome Med. 2017;9(1):39.
Article
CAS
PubMed
PubMed Central
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
PubMed
PubMed Central
Google Scholar
Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, et al. Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's disease. Cell. 2016;167(6):1469–1480.e12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katzenschlager R, Lees AJ. Treatment of Parkinson's disease: levodopa as the first choice. J Neurol Suppl. 2002;249:ii19.
Google Scholar
van Kessel SP, Frye AK, El-Gendy AO, Castejon M, Keshavarzian A, van Dijk G, et al. Gut bacterial tyrosine decarboxylases restrict levels of levodopa in the treatment of Parkinson’s disease. Nat Commun. 2019;10(1):1–11.
CAS
Google Scholar
Rekdal VM, Bess EN, Bisanz JE, Turnbaugh PJ, Balskus EP. Discovery and inhibition of an interspecies gut bacterial pathway for levodopa metabolism. Science. 2019;364:6445.
Google Scholar
Coleman JA, Gouaux E. Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Nat Struct Mol Biol. 2018;25(2):170–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fung TC, Vuong HE, Luna CD, Pronovost GN, Aleksandrova AA, Riley NG, et al. Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut. Nat Res Forum. 2019;4:2064–73.
Google Scholar
Hui W, Li T, Liu W, Zhou C, Gao F. Fecal microbiota transplantation for treatment of recurrent C. Difficile infection: an updated randomized controlled trial meta-analysis. PLoS One. 2019;14(1):e0210016.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colman RJ, Rubin DT. Fecal microbiota transplantation as therapy for inflammatory bowel disease: a systematic review and meta-analysis. J Crohn's Colitis. 2014;8(12):1569–81.
Article
Google Scholar
Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M, Onischi C, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149(1):102–109.e6.
Article
PubMed
Google Scholar
Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. Expert consensus document: the international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 2014;11(8):506–14.
Article
PubMed
Google Scholar
Steenbergen L, Sellaro R, van Hemert S, Bosch JA, Colzato LS. A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood. Brain Behav Immun. 2015;48:258–64.
Article
PubMed
Google Scholar
Allen AP, Hutch W, Borre YE, Kennedy PJ, Temko A, Boylan G, et al. Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers. Transl Psychiatry. 2016;6(11):e939.
Article
CAS
PubMed
PubMed Central
Google Scholar
Talani G, Biggio F, Mostallino MC, Locci V, Porcedda C, Boi L, et al. Treatment with gut bifidobacteria improves hippocampal plasticity and cognitive behavior in adult healthy rats. Neuropharmacology. 2020;165:107909.
Article
CAS
PubMed
Google Scholar
Markowiak P, Ślizewska K. Effects of probiotics, prebiotics, and synbiotics on human health. MDPI AG. 2017;9:1.
Google Scholar
Brüssow H. Probiotics and prebiotics in clinical tests: an update [version 1; peer review: 2 approved], vol. 8, F1000 research ltd; 2019.
Google Scholar
Douglas AE. Contradictory results in microbiome science exemplified by recent drosophila research. Am Soc Microbiol. 2018;9(1).
Bindels LB, Delzenne NM, Cani PD, Walter J. Opinion: towards a more comprehensive concept for prebiotics. Nat Publ Group. 2015;12:303–10.
CAS
Google Scholar
De Wolfe TJ, Eggers S, Barker AK, Kates AE, Dill-McFarland KA, Suen G, et al. Oral probiotic combination of lactobacillus and bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for clostridium difficile infection. PLoS One. 2018;13:9.
Article
Google Scholar
Korpela K, Salonen A, Vepsäläinen O, Suomalainen M, Kolmeder C, Varjosalo M, et al. Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants. Microbiome. 2018;6(1):1.
Article
Google Scholar
Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, et al. Structural variation in the gut microbiome associates with host health. Nature. 2019;568(7750):43–8.
Article
CAS
PubMed
Google Scholar
Kumar M, Ji B, Zengler K, Nielsen J. Modelling approaches for studying the microbiome. Nat Publ Group. 2019;4:1253–67.
CAS
Google Scholar
Azad MAK, Sarker M, Li T, Yin J. Probiotic species in the modulation of gut microbiota: an overview. Biomed Res Int. 2018;2018.
Liu S, Ren F, Zhao L, Jiang L, Hao Y, Jin J, et al. Starch and starch hydrolysates are favorable carbon sources for Bifidobacteria in the human gut. BMC Microbiol. 2015;15(1):54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vrancken G, Gregory AC, Huys GR, Faust K, Raes J. Synthetic ecology of the human gut microbiota. Nat Publ Group. 2019;17:754–63.
CAS
Google Scholar
Rabesandratana T. Microbiome conservancy stores global fecal samples. Am Assoc Adv Sci. 2018;362:510–1.
CAS
Google Scholar
Das P, Ji B, Kovatcheva-Datchary P, Bäckhed F, Nielsen J. In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis. PLoS One. 2018;13(3):e0195161.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bodor A, Bounedjoum N, Vincze GE, Erdeiné Kis Á, Laczi K, Bende G, et al. Challenges of unculturable bacteria: environmental perspectives. Springer. 2020;19:1–22.
CAS
Google Scholar
Lagier JC, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, et al. Culturing the human microbiota and culturomics. Nat Publ Group. 2018;16:540–50.
CAS
Google Scholar
Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K, Frachet A, et al. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat Commun, 7. 2016;(1):1–15.
van de Wiele T, van den Abbeele P, Ossieur W, Possemiers S, Marzorati M. The simulator of the human intestinal microbial ecosystem (SHIME®), in the impact of food bioactives on health: in vitro and ex vivo models, springer international publishing; 2015. p. 305–17.
Google Scholar
Medlock GL, Carey MA, McDuffie DG, Mundy MB, Giallourou N, Swann JR, et al. Inferring metabolic mechanisms of interaction within a defined gut microbiota. Cell Systems. 2018;7(3):245–257.e7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zeevi D, Korem T, Zmora N, Israeli D, Rothschild D, Weinberger A, et al. Personalized nutrition by prediction of glycemic responses. Cell. 2015;163(5):1079–94.
Article
CAS
PubMed
Google Scholar
Ferrua MJM, Singh RP. Modeling the fluid dynamics in a human stomach to gain insight of food digestion. J Food Sci. 2010;75(7):151–62.
Article
CAS
Google Scholar
Medina Daniel AD, Pinto F, Ortuzar V, Garrido D. Simulation and modeling of dietary changes in the infant gut microbiome. FEMS Microbiol Ecol. 2018;94:9.
Google Scholar
Fisher Charles KC, Mehta P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS One. 2014;9:7.
Google Scholar