Research graph
References from Modeling approaches for probing cross-feeding interactions in the human gut microbiome. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/s41586-019-1058-x
10.1038/s41586-019-1058-x · External reference
Impact of bacterial metabolites on gut barrier function and host immunity: A focus on bacterial metabolism and its relevance for intestinal inflammation
10.3389/fimmu.2021.658354 · 2021 · External reference
10.3390/nu13051655
10.3390/nu13051655 · External reference
10.1126/science.aad2602
10.1126/science.aad2602 · External reference
10.1038/s41396-021-00937-7
10.1038/s41396-021-00937-7 · External reference
First 1000 days of life: Consequences of antibiotics on gut microbiota
10.3389/fmicb.2021.681427 · 2021 · External reference
10.1038/nrmicro.2017.58
10.1038/nrmicro.2017.58 · External reference
Ecology-guided prediction of cross-feeding interactions in the human gut microbiome
10.1038/s41467-021-21586-6 · 2021 · External reference
Design of synthetic human gut microbiome assembly and butyrate production
10.1038/s41467-021-22938-y · 2021 · External reference
Species deletions from microbiome consortia reveal key metabolic interactions between gut microbes
10.1128/msystems.00185-19 · 2019 · External reference
A multidimensional perspective on microbial interactions
10.1093/femsle/fnz125 · 2019 · External reference
Impact of N-Acyl-homoserine lactones, quorum sensing molecules, on gut immunity
10.3389/fimmu.2020.01827 · 2020 · External reference
10.1016/j.tim.2021.01.012
10.1016/j.tim.2021.01.012 · External reference
10.1371/journal.pgen.1009541
10.1371/journal.pgen.1009541 · External reference
Antimicrobial peptides in gut health: A review
10.3389/fnut.2021.751010 · 2021 · External reference
10.1038/s41577-021-00506-1
10.1038/s41577-021-00506-1 · External reference
10.1038/nrmicro3552
10.1038/nrmicro3552 · External reference
Characterization of the luminal and mucosa-associated microbiome along the gastrointestinal tract: results from surgically treated preterm infants and a murine model
2021 · External reference
10.1111/1462-2920.12599
10.1111/1462-2920.12599 · External reference
10.1111/1462-2920.13589
10.1111/1462-2920.13589 · External reference
10.1039/c8np00009c
10.1039/c8np00009c · External reference
Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B 12 production by intestinal symbionts
10.1128/mbio.00770-17 · 2017 · External reference
Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis
10.1038/ncomms15393 · 2017 · External reference
10.1016/j.biotechadv.2017.09.005
10.1016/j.biotechadv.2017.09.005 · External reference
10.1016/j.csbj.2020.11.035 · Admitted local publication
10.1038/nrmicro2737
10.1038/nrmicro2737 · External reference
10.1371/journal.pcbi.1002363
10.1371/journal.pcbi.1002363 · External reference
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox vol 3.0
10.1038/s41596-018-0098-2 · 2019 · External reference
10.1021/sb4001307
10.1021/sb4001307 · External reference
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis
10.1038/s41540-021-00178-6 · 2021 · External reference
Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions
10.1186/s12915-020-00775-7 · 2020 · External reference
Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in Parkinson’s Disease
10.1016/j.celrep.2019.10.035 · 2019 · External reference
10.1146/annurev-micro-031021-084116
10.1146/annurev-micro-031021-084116 · External reference
10.1038/s41564-018-0307-3
10.1038/s41564-018-0307-3 · External reference
10.1016/j.csbj.2020.11.043
10.1016/j.csbj.2020.11.043 · External reference
10.1038/ismej.2012.158
10.1038/ismej.2012.158 · External reference
Simulation and modeling of dietary changes in the infant gut microbiome
2018 · External reference
10.1039/c2lc40074j
10.1039/c2lc40074j · External reference
Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem
10.1007/bf00228615 · 1993 · External reference
The HMITM module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro
10.1186/1471-2180-14-133 · 2014 · External reference
A microfluidics-based in vitro model of the gastrointestinal human–microbe interface
10.1038/ncomms11535 · 2016 · External reference
10.1016/j.cmet.2015.07.001
10.1016/j.cmet.2015.07.001 · External reference
Understanding the interactions between bacteria in the human gut through metabolic modeling
10.1038/srep02532 · 2013 · External reference
10.1073/pnas.1219451110
10.1073/pnas.1219451110 · External reference
Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium
10.1186/s12866-014-0282-7 · 2014 · External reference
Mucin cross-feeding of infant Bifidobacteria and Eubacterium hallii
10.1007/s00248-017-1037-4 · 2018 · External reference
Bile acids drive the newborn’s gut microbiota maturation
10.1038/s41467-020-17183-8 · 2020 · External reference
Evidence of distinct pathways for bacterial degradation of the steroid compound cholate suggests the potential for metabolic interactions by interspecies cross-feeding
10.1111/1462-2920.12407 · 2014 · External reference
10.1093/femsre/fuw045
10.1093/femsre/fuw045 · External reference
10.1080/19490976.2017.1290756
10.1080/19490976.2017.1290756 · External reference
Bifidobacteria and butyrate-producing colon bacteria: Importance and strategies for their stimulation in the human gut
10.3389/fmicb.2016.00979 · 2016 · External reference
Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria
10.1111/1462-2920.14454 · 2019 · External reference
Examination of hydrogen cross-feeders using a colonic microbiota model
10.1186/s12859-020-03923-6 · 2021 · External reference
Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota
10.3389/fmicb.2014.00674 · 2014 · External reference
10.1111/1462-2920.13767
10.1111/1462-2920.13767 · External reference
10.1038/nature17626
10.1038/nature17626 · External reference
Glycan complexity dictates microbial resource allocation in the large intestine
10.1038/ncomms8481 · 2015 · External reference
10.1038/nature13995
10.1038/nature13995 · External reference
10.1016/j.fm.2017.09.001
10.1016/j.fm.2017.09.001 · External reference
10.1016/j.jmb.2019.09.023
10.1016/j.jmb.2019.09.023 · External reference
10.1016/j.jtbi.2011.03.008
10.1016/j.jtbi.2011.03.008 · External reference
10.1038/nbt.3703
10.1038/nbt.3703 · External reference
10.1016/j.tim.2016.06.011
10.1016/j.tim.2016.06.011 · External reference
Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product
10.1128/aem.70.10.5810-5817.2004 · 2004 · External reference
10.1038/s41559-019-1080-2
10.1038/s41559-019-1080-2 · External reference
Microbial competition reduces metabolic interaction distances to the low µm-range
10.1038/s41396-020-00806-9 · 2021 · External reference
10.1073/pnas.1601306113
10.1073/pnas.1601306113 · External reference
10.1093/nutrit/nux036
10.1093/nutrit/nux036 · External reference
10.1016/j.smrv.2020.101340
10.1016/j.smrv.2020.101340 · External reference
10.1016/j.cmet.2014.11.008
10.1016/j.cmet.2014.11.008 · External reference
10.1016/j.cell.2014.09.048
10.1016/j.cell.2014.09.048 · External reference
10.1016/j.chom.2015.03.006
10.1016/j.chom.2015.03.006 · External reference
CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention
10.1073/pnas.2019336118 · 2021 · External reference
Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
10.1186/s40168-018-0584-3 · 2018 · External reference
Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss
10.1186/s12918-018-0588-4 · 2018 · External reference
10.1073/pnas.1421834112
10.1073/pnas.1421834112 · External reference
Deciphering functional redundancy in the human microbiome
10.1038/s41467-020-19940-1 · 2020 · External reference
10.1086/282586
10.1086/282586 · External reference
10.1371/journal.pcbi.1007524
10.1371/journal.pcbi.1007524 · External reference
A diverse community to study communities: integration of experiments and mathematical models to study microbial consortia
2021 · External reference
Perspectives and challenges in microbial communities metabolic modeling
10.3389/fgene.2017.00088 · 2017 · External reference
10.3389/fmicb.2016.00673
10.3389/fmicb.2016.00673 · External reference
A tool for statistical and multi-objective calibration of Rule-based models
10.1038/s41598-019-51546-6 · 2019 · External reference
10.1016/j.mib.2021.05.003
10.1016/j.mib.2021.05.003 · External reference
Deciphering microbial interactions in synthetic human gut microbiome communities
10.15252/msb.20178157 · 2018 · External reference
Community structure follows simple assembly rules in microbial microcosms
10.1038/s41559-017-0109 · 2017 · External reference
Modeling metabolic interactions in a consortium of the infant gut microbiome
10.3389/fmicb.2017.02507 · 2017 · External reference
Improved calibration of a solid substrate fermentation model
2011 · External reference
A combinatorial algorithm for microbial consortia synthetic design
10.1038/srep29182 · 2016 · External reference
10.1038/nprot.2009.203
10.1038/nprot.2009.203 · External reference
10.1038/nbt.1672
10.1038/nbt.1672 · External reference
10.1371/journal.pcbi.1006541
10.1371/journal.pcbi.1006541 · External reference
Reconstructing genome-scale metabolic models with merlin
10.1093/nar/gkv294 · 2015 · External reference
10.1093/nar/gkv1070
10.1093/nar/gkv1070 · External reference
10.1093/nar/gkv1164
10.1093/nar/gkv1164 · External reference
10.1093/bioinformatics/btu321
10.1093/bioinformatics/btu321 · External reference
gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
10.1186/s13059-021-02295-1 · 2021 · External reference
10.1093/nar/gky537
10.1093/nar/gky537 · External reference
10.1371/journal.pcbi.1006146
10.1371/journal.pcbi.1006146 · External reference
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species
10.7554/elife.61968 · 2020 · External reference
AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
2020 · External reference
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
10.1093/bioinformatics/btab622 · 2021 · External reference
10.1186/s40168-019-0689-3
10.1186/s40168-019-0689-3 · External reference
10.4161/gmic.22370
10.4161/gmic.22370 · External reference
10.1080/19490976.2015.1023494
10.1080/19490976.2015.1023494 · External reference
Large-scale metabolic interaction network of the mouse and human gut microbiota
2020 · External reference
10.3390/metabo9020022
10.3390/metabo9020022 · External reference
10.1038/nbt.1614
10.1038/nbt.1614 · External reference
10.1038/nrmicro1023
10.1038/nrmicro1023 · External reference
10.1186/s13059-019-1730-3
10.1186/s13059-019-1730-3 · External reference
10.15252/msb.20198982
10.15252/msb.20198982 · External reference
10.1016/j.xcrm.2020.100138
10.1016/j.xcrm.2020.100138 · External reference
10.1038/s41467-018-07946-9
10.1038/s41467-018-07946-9 · External reference
10.1016/j.ymben.2003.09.002
10.1016/j.ymben.2003.09.002 · External reference
10.1016/s0006-3495(02)73903-9
10.1016/s0006-3495(02)73903-9 · External reference
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli
2020 · External reference
10.1371/journal.pone.0064567
10.1371/journal.pone.0064567 · External reference
Predicting microbial abundances while ensuring community stability
10.1371/journal.pcbi.1005539 · 2017 · External reference
Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling
2019 · External reference
10.1016/j.celrep.2014.03.070
10.1016/j.celrep.2014.03.070 · External reference
10.1371/journal.pcbi.1005544
10.1371/journal.pcbi.1005544 · External reference
10.3390/microorganisms7010014
10.3390/microorganisms7010014 · External reference
The Modulation of Gut Microbiota Composition in the Pathophysiology of Gestational Diabetes Mellitus: A Systematic Review
10.3390/biology10101027 · 2021 · External reference
Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease
10.3389/fphys.2021.715506 · 2021 · External reference
Gut microbiota’s effect on mental health: The gut-brain axis
10.4081/cp.2017.987 · 2017 · External reference
10.1007/s12328-017-0813-5
10.1007/s12328-017-0813-5 · External reference
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
10.1128/msystems.00606-19 · 2020 · External reference
10.1097/00041433-200202000-00002
10.1097/00041433-200202000-00002 · External reference
10.1016/j.cub.2012.08.005
10.1016/j.cub.2012.08.005 · External reference
10.7554/elife.55650
10.7554/elife.55650 · External reference
10.1371/journal.pbio.2000633
10.1371/journal.pbio.2000633 · External reference
10.1371/journal.pone.0148386
10.1371/journal.pone.0148386 · External reference
10.1371/journal.pone.0207072
10.1371/journal.pone.0207072 · External reference
10.1016/j.csbj.2021.06.048
10.1016/j.csbj.2021.06.048 · External reference
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
10.1186/s12859-019-3337-9 · 2020 · External reference
METATOOL: For studying metabolic networks
10.1093/bioinformatics/15.3.251 · 1999 · External reference
Detection of colorectal carcinoma based on microbiota analysis using generalized regression neural networks and nonlinear feature selection
10.1109/tcbb.2018.2870124 · 2020 · External reference
10.3390/jcm9082403
10.3390/jcm9082403 · External reference
10.1158/1940-6207.capr-17-0370
10.1158/1940-6207.capr-17-0370 · External reference
Machine and deep learning meet genome-scale metabolic modeling
10.1371/journal.pcbi.1007084 · 2019 · External reference
10.1038/s41592-021-01205-4
10.1038/s41592-021-01205-4 · External reference
10.1371/journal.pcbi.1002606
10.1371/journal.pcbi.1002606 · External reference
10.1093/nar/gkaa939
10.1093/nar/gkaa939 · External reference
10.1038/nature11209
10.1038/nature11209 · External reference
Methanogen communities in stools of humans of different age and health status and co-occurrence with bacteria
10.1093/femsle/fnv092 · 2015 · External reference
Co-occurrence of anaerobic bacteria in colorectal carcinomas
10.1186/2049-2618-1-16 · 2013 · External reference
10.1016/j.chom.2019.07.004
10.1016/j.chom.2019.07.004 · External reference
Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease
10.1038/srep26087 · 2016 · External reference
Co-occurrence of asthma and the inflammatory bowel diseases: A systematic review and meta-analysis
2018 · External reference
Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism
10.1126/science.aau6323 · 2019 · External reference
10.1016/j.csbj.2021.01.028
10.1016/j.csbj.2021.01.028 · External reference
10.1038/s41564-018-0124-8
10.1038/s41564-018-0124-8 · External reference
Unveiling genomic diversity among members of the species bifidobacterium pseudolongum, a widely distributed gut commensal of the animal kingdom
10.1128/aem.03065-18 · 2019 · External reference
10.1038/s41587-020-0446-y
10.1038/s41587-020-0446-y · External reference
10.1038/nature18848
10.1038/nature18848 · External reference
Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
10.1038/s41598-019-53188-0 · 2019 · External reference
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
10.1371/journal.pcbi.1007127 · 2019 · External reference
10.1038/s41596-021-00593-3
10.1038/s41596-021-00593-3 · External reference