Modeling metabolism of the human gut microbiome

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

An obesity-associated gut microbiome with increased capacity for energy harvest

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100

Human gut microbiome viewed across age and geography

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815

A metagenome-wide association study of gut microbiota in type 2 diabetes

Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762

Obesity alters gut microbial ecology

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176

The impact of the gut microbiota on human health: an integrative view

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710

Gut microbiota composition correlates with diet and health in the elderly

Claesson, M. J., Jeffery, I. B., Conde, S., Power, S. E., O’Connor, E. M., Cusack, S., Harris, H. M. B., Coakley, M., Lakshminarayanan, B., O’Sullivan, O., et al. (2012) · Nature · doi:10.1038/nature11319 · Cited by 3,314

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., & Siuzdak, G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812874106 · Cited by 2,677

The Microbiota-Gut-Brain Axis

Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

Heinken, A., Ravcheev, D. A., Baldini, F., Heirendt, L., Fleming, R. M. T., & Thiele, I. (2019) · Microbiome · doi:10.1186/s40168-019-0689-3 · Cited by 340

Gut reactions: Breaking down xenobiotic–microbiome interactions

Clarke, G., Sandhu, K. V., Griffin, B. T., Dinan, T. G., Cryan, J. F., & Hyland, N. P. (2019) · Pharmacological Reviews · doi:10.1124/pr.118.015768 · Cited by 319

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Heinken, A., Hertel, J., Acharya, G., Ravcheev, D. A., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01628-0 · Cited by 310

Reconstructing organisms in silico: genome-scale models and their emerging applications

Fang, X., Lloyd, C. J., & Palsson, B. O. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00440-4 · Cited by 292

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Dukovski, I., Bajić, D., Chacón, J. M., Quintin, M., Vila, J. C. C., Sulheim, S., Pacheco, A. R., Bernstein, D. B., Riehl, W. J., Korolev, K. S., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00593-3 · Cited by 234

Metabolic Engineering: Methodologies and Applications

Volk, M., Tran, V. G., Tan, S., Mishra, S., Fatma, Z., Boob, A. G., Li, H., Xue, P., Martin, T. A., & Zhao, H. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00403 · Cited by 217

A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016

NIH Human Microbiome Portfolio Analysis Team (2019) · Microbiome · doi:10.1186/s40168-019-0620-y · Cited by 215

The role of the microbiome in ovarian cancer: mechanistic insights into oncobiosis and to bacterial metabolite signaling

Sipos, A., Ujlaki, G., Mikó, E., Maka, E., Szabó, J., Uray, K., Krasznai, Z. T., & Bai, P. (2021) · Molecular Medicine · doi:10.1186/s10020-021-00295-2 · Cited by 153

Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics

Tan, X., Letendre, J. H., Collins, J. J., & Wong, W. W. (2021) · Cell · doi:10.1016/j.cell.2021.01.017 · Cited by 134

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers

Hale, V. L., Jeraldo, P., Chen, J., Mundy, M. B., Yao, J. Z., Priya, S., Keeney, G., Lyke, K. J., Ridlon, J. M., White, B. A., et al. (2018) · Genome Medicine · doi:10.1186/s13073-018-0586-6 · Cited by 127

Understanding the host-microbe interactions using metabolic modeling

Jansma, J., & Aidy, S. E. (2021) · Microbiome · doi:10.1186/s40168-020-00955-1 · Cited by 106

Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells

Greenhalgh, K., Ramiro‐Garcia, J., Heinken, A., Ullmann, P., Bintener, T., Pacheco, M. P., Bagińska, J., Shah, P., Frachet, A., Halder, R., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.04.001 · Cited by 98

Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis

Heinken, A., Hertel, J., & Thiele, I. (2021) · npj Systems Biology and Applications · doi:10.1038/s41540-021-00178-6 · Cited by 93

A Big World in Small Grain: A Review of Natural Milk Kefir Starters

Nejati, F., Junne, S. G., & Neubauer, P. B. (2020) · Microorganisms · doi:10.3390/microorganisms8020192 · Cited by 89

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

Jenior, M. L., Moutinho, T. J., Dougherty, B. V., & Papin, J. A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007099 · Cited by 83

Design of synthetic microbial consortia for gut microbiota modulation

Vázquez-Castellanos, J. F., Biclot, A., Vrancken, G., Huys, G. R. B., & Raes, J. (2019) · Current Opinion in Pharmacology · doi:10.1016/j.coph.2019.07.005 · Cited by 85

Plant Genetics as a Tool for Manipulating Crop Microbiomes: Opportunities and Challenges

Clouse, K. M., & Wagner, M. R. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.567548 · Cited by 73

The gut microbiota promotes the pathogenesis of schizophrenia via multiple pathways

Yuan, X., Kang, Y., Zhuo, C., Huang, X., & Song, X. (2019) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2019.02.152 · Cited by 77

Riboflavin instability is a key factor underlying the requirement of a gut microbiota for mosquito development

Wang, Y., Eum, J. H., Harrison, R. E., Valzania, L., Yang, X., Johnson, J. A., Huck, D. T., Brown, M. R., & Strand, M. R. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101080118 · Cited by 74

A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations

Muller, E., Algavi, Y. M., & Borenstein, E. (2021) · Microbiome · doi:10.1186/s40168-021-01149-z · Cited by 76

Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids

Chang, F., Siuti, P., Laurent, S., Williams, T., Glassey, E., Sailer, A. W., Gordon, D. B., Hemmerle, H., & Voigt, C. A. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00887-y · Cited by 68

In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids

Schleyer, G., Shahaf, N., Ziv, C., Dong, Y., Meoded, R. A., Helfrich, E. J. N., Schatz, D., Rosenwasser, S., Rogachev, I., Aharoni, A., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0336-y · Cited by 68

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

Noecker, C. A., Chiu, H.-C., McNally, C. P., & Borenstein, E. (2019) · mSystems · doi:10.1128/msystems.00579-19 · Cited by 66

Factors Affecting Gut Microbiome in Daily Diet

Su, Q., & Liu, Q. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.644138 · Cited by 60

Integrated molecular approaches for fermented food microbiome research

Walsh, A. M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., & Cotter, P. D. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad001 · Cited by 56

Evidence for a multi-level trophic organization of the human gut microbiome

Wang, T., Goyal, A., Dubinkina, V. B., & Maslov, S. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007524 · Cited by 55

An extended reconstruction of human gut microbiota metabolism of dietary compounds

Blasco, T., Pérez-Burillo, S., Balzerani, F., Hinojosa-Nogueira, D., Lerma-Aguilera, A., Pastoriza, S., Cendoya, X., Rubio, Á., Gosalbes, M. J., Jiménez‐Hernández, N., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25056-x · Cited by 52

Synthetic gut microbiome: Advances and challenges

Mabwi, H. A., Kim, E., Song, D., Yoon, H. S., Pan, C., Komba, E. V. G., Ko, G., & Cha, K. H. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.12.029 · Cited by 54

Gut microbiome-metabolome interactions predict host condition

Shtossel, O., Koren, O., Shai, I., Rinott, E., & Louzoun, Y. (2024) · Microbiome · doi:10.1186/s40168-023-01737-1 · Cited by 49

The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health

Eetemadi, A., Rai, N., Pereira, B. M. P., Kim, M., Schmitz, H. H., & Tagkopoulos, I. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00393 · Cited by 51

Defining the nutritional input for genome-scale metabolic models: A roadmap

Μαρίνος, Γ., Kaleta, C., & Waschina, S. (2020) · PLoS ONE · doi:10.1371/journal.pone.0236890 · Cited by 50

Metabolic Modeling of Cystic Fibrosis Airway Communities Predicts Mechanisms of Pathogen Dominance

Henson, M. A., Orazi, G., Phalak, P., & O’Toole, G. A. (2019) · mSystems · doi:10.1128/msystems.00026-19 · Cited by 46

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

Guéniche, A., Périn, O., Bouslimani, A., Landemaine, L., Misra, N., Cupferman, S., Aguilar, L., Clavaud, C., Chopra, T., & Khodr, A. (2022) · Pathogens · doi:10.3390/pathogens11020121 · Cited by 47

Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome

Bernstein, D. B., Dewhirst, F. E., & Segrè, D. (2019) · eLife · doi:10.7554/elife.39733 · Cited by 44

The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence

Gündoğdu, A., & Nalbantoğlu, Ö. U. (2023) · Nutrition · doi:10.1016/j.nut.2023.112118 · Cited by 45

Computational Modeling of the Human Microbiome

Chowdhury, S., & Fong, S. S. (2020) · Microorganisms · doi:10.3390/microorganisms8020197 · Cited by 43

CRISPR-Cas9: A method for establishing rat models of drug metabolism and pharmacokinetics

Lu, J., Liu, J., Guo, Y., Zhang, Y., Xu, Y., & Wang, X. (2021) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2021.01.007 · Cited by 42

Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome

Ravcheev, D. A., Moussu, L., Smajić, S., & Thiele, I. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00636 · Cited by 36

AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacitiesPreprint

Heinken, A., Acharya, G., Ravcheev, D. A., Hertel, J., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Preciat, G., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.09.375451 · Cited by 39

Gut Microbiota and Human Body Interactions; Its Impact on Health: A Review

Hajiagha, M. N., Taghizadeh, S., Asgharzadeh, M., Dao, S., Ganbarov, K., Köse, Ş., & Kafil, H. S. (2021) · Current Pharmaceutical Biotechnology · doi:10.2174/1389201022666210104115836 · Cited by 36

Constraint-based modeling in microbial food biotechnology

Rau, M. H., & Zeidan, A. A. (2018) · Biochemical Society Transactions · doi:10.1042/bst20170268 · Cited by 35

Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies

Busato, S., Gordon, M., Chaudhari, M., Jensen, I. T., Akyol, T. Y., Andersen, S. U., & Williams, C. (2022) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2022.102326 · Cited by 38

Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells

Schinn, S., Morrison, C., Wei, W., Zhang, L., & Lewis, N. E. (2021) · Metabolic Engineering · doi:10.1016/j.ymben.2021.03.013 · Cited by 33

Neoagaro-Oligosaccharides Ameliorate Chronic Restraint Stress-Induced Depression by Increasing 5-HT and BDNF in the Brain and Remodeling the Gut Microbiota of Mice

Zhuang, Y., Zeng, R., Liu, X., Yang, L., & Chan, Z. (2022) · Marine Drugs · doi:10.3390/md20110725 · Cited by 32

Gut microbiota and gut tissue metabolites involved in development and prevention of depression

Yu, M., Jia, H., Qin, L.-L., & Zou, Z. (2021) · Journal of Affective Disorders · doi:10.1016/j.jad.2021.10.016 · Cited by 31

What the Gut Tells the Brain—Is There a Link between Microbiota and Huntington’s Disease?

Wronka, D., Karlik, A., Misiorek, J. O., & Przybył, Ł. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054477 · Cited by 32

First and second generation probiotic therapeutics for Inflammatory Bowel Disease

Sireswar, S., Ghosh, I., & Dey, G. (2019) · PharmaNutrition · doi:10.1016/j.phanu.2019.100159 · Cited by 26

Key Technologies for Progressing Discovery of Microbiome-Based Medicines

Young, R. B., Marcelino, V. R., Chonwerawong, M., Gulliver, E. L., & Forster, S. C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.685935 · Cited by 30

An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community

Wang, P., Correia, K., Ho, H.-C., Venayak, N., Nemr, K., Flick, R., Mahadevan, R., & Edwards, E. A. (2019) · The ISME Journal · doi:10.1038/s41396-018-0333-4 · Cited by 25

Gardenia Jasminoides Ameliorates Antibiotic-Associated Aggravation of DNCB-Induced Atopic Dermatitis by Restoring the Intestinal Microbiome Profile

Kim, H. I., Hong, S. H., Lee, S.-Y., Ku, J. M., Kim, M., & Ko, S. (2021) · Nutrients · doi:10.3390/nu13041349 · Cited by 25

Hyperbaric oxygen improves depression‐like behaviors in chronic stress model mice by remodeling gut microbiota and regulating host metabolism

Zhang, B., Dong, W., Ma, Z., Duan, S., Han, R., Zhou, L., Liu, X., & Mao, Y. (2022) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.13999 · Cited by 24

Modelling microbial communities using biochemical resource allocation analysis

Sharma, S. A., & Steuer, R. (2019) · Journal of The Royal Society Interface · doi:10.1098/rsif.2019.0474 · Cited by 20

Adaptation of the Human Gut Microbiota Metabolic Network During the First Year After Birth

Fuertes, A., Pérez-Burillo, S., Apaolaza, I., Vallès, Y., Francino, M. P., Rufián‐Henares, J. Á., & Planes, F. J. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00848 · Cited by 22

Material Engineering in Gut Microbiome and Human Health

Yang, L., Hung, L. Y., Zhu, Y., Ding, S., Margolis, K. G., & Leong, K. W. (2022) · Research · doi:10.34133/2022/9804014 · Cited by 24

A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota

Versluis, D. M., Schoemaker, R., Looijesteijn, E., Muysken, D., Jeurink, P. V., Paques, M., Geurts, J. M. W., & Merks, R. M. H. (2022) · mSystems · doi:10.1128/msystems.00446-22 · Cited by 20

Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling

Chan, S. H. J., Friedman, E. S., Wu, G. D., & Maranas, C. D. (2019) · Processes · doi:10.3390/pr7070394 · Cited by 21

Expanding the drug discovery space with predicted metabolite–target interactions

Nuzzo, A., Saha, S., Berg, E. L., Jayawickreme, C. K., Tocker, J. E., & Brown, J. R. (2021) · Communications Biology · doi:10.1038/s42003-021-01822-x · Cited by 20

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses

Hertel, J., Heinken, A., Fässler, D., & Thiele, I. (2023) · Cell Reports Methods · doi:10.1016/j.crmeth.2023.100615 · Cited by 21

A Computational Framework for Studying Gut-Brain Axis in Autism Spectrum Disorder

Mohammad, F. K., Palukuri, M. V., Shivakumar, S., Rengaswamy, R., & Sahoo, S. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.760753 · Cited by 21

The interaction among Kluyveromyces marxianus G-Y4, Lacticaseibacillus paracasei GL1, and Lactobacillus helveticus SNA12 and signaling molecule AI-2 participate in the formation of biofilm

Wang, X., Ma, K., Zhang, C., Ji, F., Chen, L., Zhang, X., Mahsa, G. C., Azarpazhooh, E., Ajami, M., Rui, X., et al. (2023) · Food Microbiology · doi:10.1016/j.fm.2023.104369 · Cited by 19

Emerging tools and best practices for studying gut microbial community metabolism

Noecker, C. A., & Turnbaugh, P. J. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01074-z · Cited by 20

Not by (Good) Microbes Alone: Towards Immunocommensal Therapies

Leung, C. Y., & Weitz, J. S. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2018.12.006 · Cited by 18

Biogas starter from genome-scale data for methanogenic bioprocessing of protein waste

Chellapandi, P., & Saranya, S. V. (2023) · Systems Microbiology and Biomanufacturing · doi:10.1007/s43393-023-00191-2 · Cited by 17

Syntrophic splitting of central carbon metabolism in host cells bearing functionally different symbiotic bacteria

Ankrah, N. Y. D., Wilkes, R. A., Zhang, F. Q., Zhu, D., Kaweesi, T., Aristilde, L., & Douglas, A. E. (2020) · The ISME Journal · doi:10.1038/s41396-020-0661-z · Cited by 17

Organ-on-Chip Technology for Aerobic Intestinal Host – Anaerobic Microbiota Research

Bossink, E. G. B. M., Segerink, L. I., & Odijk, M. (2021) · Organs-on-a-Chip · doi:10.1016/j.ooc.2021.100013 · Cited by 17

Gut-on-a-Chip for the Analysis of Bacteria–Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet–Microbiota Relationship?

Lee, K. W., Shin, J. S., Lee, C. M., Han, H. Y., Yun, O., Kim, H. W., & Cho, T. J. (2023) · Nutrients · doi:10.3390/nu15051131 · Cited by 15

In silico encounters: harnessing metabolic modelling to understand plant–microbe interactions

Feierabend, M., & Töpfer, N. (2025) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf030 · Cited by 14

Targeting the gut to prevent and counteract metabolic disorders and pathologies during aging

Milenković, D., Capel, F., Combaret, L., Comte, B., Dardevet, D. P., Evrard, B., Guillet, C., Monfoulet, L., Pinel, A., Polakof, S., et al. (2022) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2022.2089870 · Cited by 14

Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics

Li, L., Nielsen, J., & Chen, Y. (2024) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2024.103248 · Cited by 12

Meta‐Omics‐ and Metabolic Modeling‐Assisted Deciphering of Human Microbiota Metabolism

Sieow, B. F., Nurminen, T. J., Ling, H., & Chang, M. W. (2019) · Biotechnology Journal · doi:10.1002/biot.201800445 · Cited by 12

Evolutionary Stability of Salmonella Competition with the Gut Microbiota: How the Environment Fosters Heterogeneity in Exploitative and Interference Competition

Müller, J., Spriewald, S., Stecher, B., Stadler, E., & Fuchs, T. M. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.06.027 · Cited by 12

Molecular systems biology approaches to investigate mechanisms of gut−brain communication in neurological diseases

Vandemoortele, B., & Vermeirssen, V. (2023) · European Journal of Neurology · doi:10.1111/ene.15819 · Cited by 10

A Quantitative Systems Pharmacology Model Describing the Cellular Kinetic‐Pharmacodynamic Relationship for a Live Biotherapeutic Product to Support Microbiome Drug Development

Renardy, M., Prokopienko, A. J., Maxwell, J. R., Flusberg, D. A., Makaryan, S., Selimkhanov, J., Vakilynejad, M., Subramanian, K., & Wille, L. (2023) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.2952 · Cited by 10

Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications

Dahal, S., Zhao, J., & Yang, L. (2020) · Biotechnology and Bioprocess Engineering · doi:10.1007/s12257-020-0061-2 · Cited by 9

Modelling the influence of vitamin D and probiotic supplementation on the microbiome and immune response

Franks, S. J., Dunster, J. L., Carding, S. R., Lord, J. M., Hewison, M., Calder, P. C., & King, J. R. (2024) · Mathematical Medicine and Biology A Journal of the IMA · doi:10.1093/imammb/dqae017 · Cited by 8

Towards Predicting Gut Microbial Metabolism: Integration of Flux Balance Analysis and Untargeted Metabolomics

Kuang, E., Marney, M. W., Cuevas, D., Edwards, R. A., & Forsberg, E. M. (2020) · Metabolites · doi:10.3390/metabo10040156 · Cited by 8

A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets

Singh, R. P., Dutta, A., Bose, T., & Mande, S. S. (2022) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2022.100127 · Cited by 10

Quantitative modeling of human metabolism: A call for a community effort

Masid, M., & Vassily Hatzimanikatis, A. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.04.008 · Cited by 7

2′-Fucosyllactose helps butyrate producers outgrow competitors in infant gut microbiota simulations

Versluis, D. M., Schoemaker, R., Looijesteijn, E., Geurts, J. M. W., & Merks, R. M. H. (2024) · iScience · doi:10.1016/j.isci.2024.109085 · Cited by 7

Serum Metabolites Relate to Mucosal and Transmural Inflammation in Paediatric Crohn Disease

Suárez, R., Guruprasad, N., Tata, G., Zhang, Z., Focht, G., McClement, D. G., Navas‐López, V. M., Koletzko, S., Griffiths, A. M., Ledder, O., et al. (2024) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjae085 · Cited by 5

Feeding the World Inside Us: Our Gut Microbiomes, Diet, and Health

McClements, D. J. (2019) · Springer eBooks · doi:10.1007/978-3-030-12995-8_7 · Cited by 5

Systematic interrogation of the distinct metabolic potential in gut microbiomes of inflammatory bowel disease patients with dysbiosisPreprint

Heinken, A., & Thiele, I. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/640649 · Cited by 5

Mapping out the gut microbiota-dependent trimethylamine N-oxide super pathway for systems biology applications

Valenbreder, I., Balăn, S., Breuer, M., & Adriaens, M. E. (2023) · Frontiers in Systems Biology · doi:10.3389/fsysb.2023.1074749 · Cited by 4

Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models

Ortiz, J. P. M., McClure, D. D., Shanahan, E. R., Dehghani, F., Holmes, A. J., & Read, M. N. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1965698 · Cited by 4

Gut Microbiome in Obesity Management

Heshmati, H. M. (2020) · IntechOpen eBooks · doi:10.5772/intechopen.91974 · Cited by 4

Probiotics in mitigation of food allergies and lactose intolerance

Vadala, B. S., Kumar, P., & Dwivedi, M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-823733-5.00022-2 · Cited by 3

Engineering Microbial Biofilms for Improved Productivity of Biochemicals Important in Restoration of Degraded Ecosystems

Premarathna, M., Rathnathilaka, T., Seneviratne, G., & Madawala, H. M. S. P. (2022) · Advances in Bioscience and Biotechnology · doi:10.4236/abb.2022.133007 · Cited by 3

Bacterial biomarkers: new aspects of colorectal tumors diagnosis: reality or fantasy

Shahbazi, T., Bakhshi, B., Fazeli, M. S., & Derakhshan-Nezhad, E. (2023) · European Journal of Cancer Prevention · doi:10.1097/cej.0000000000000760 · Cited by 3

Microbiome Engineering towards Disease Therapy

Krishnan, A., & Dasgupta, A. (2024) · Springer eBooks · doi:10.1007/978-981-97-6270-5_5 · Cited by 3

Gut Microbiota Shift in Obese Adolescents Born by Cesarean Section

Novikova, E., Belkova, N. L., Валерьевна, П. А., Romanitsa, A. I., Станиславовна, К. Е., Немченко, У. М., & Rychkova, L. V. (2020) · International Journal of Biomedicine · doi:10.21103/article10(4)_oa19 · Cited by 3

Microbial gatekeepers: unraveling the role of the gut microbiota enzyme DPP4 in diabetes management

Liao, L., Lin, F., & Gao, J. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.09.005 · Cited by 2

Molecular Mechanisms of Gut Microbiota–Immune System Crosstalk: From Mucosal Architecture to Adaptive Immunity Programming

Ciaușu-Sliwa, D., Capotă, R., Bostănaru, A.-C., Năstasă, V., & Mareș, M. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27146246 · Cited by 2

A multifaceted approach to harness probiotics as antagonists on plant based foods, for enhanced benefits to be reaped at a global level

Karunaratne, A. M. (2018) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.9215 · Cited by 3

Microbiome: Current Status and Future Applications

Ramos-Jiménez, R. G., & Morowitz, M. J. (2019) · Success in academic surgery · doi:10.1007/978-3-030-14644-3_14 · Cited by 2

In‐depth characterization of genome‐scale network reconstructions for the in vitro synthesis in cell‐free systems

Schuh, L. K., Weyler, C., & Heinzle, E. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27249 · Cited by 2

Computational framework for exploring the interplay of diet and gut microbiota in autismPreprint

Palukuri, M. V., Shivakumar, S., Sahoo, S., & Rengaswamy, R. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/422931 · Cited by 2

A multiscale spatiotemporal model including a switch from aerobic to anaerobic metabolism reproduces succession in the early infant gut microbiotaPreprint

Versluis, D. M., Schoemaker, R., Looijesteijn, E., Muysken, D., Jeurink, P. V., Paques, M., Geurts, J. M. W., & Merks, R. M. H. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.22.457032 · Cited by 2

Simulations of the infant gut microbiota suggest that complex ecological interactions regulate effects of human milk oligosaccharides on microbial mucin consumptionPreprint

Versluis, D. M., Wijtkamp, C., Looijesteijn, E., Geurts, J. M. W., & Merks, R. M. H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.15.603541 · Cited by 2

Operationalizing Team Science at the Academic Cancer Center Network to Unveil the Structure and Function of the Gut Microbiome

McDonnell, K. (2025) · Journal of Clinical Medicine · doi:10.3390/jcm14062040 · Cited by 1

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

Bauer, E., & Thiele, I. (2018) · mSystems · doi:10.1128/msystems.00209-17 · Cited by 88

Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools

Altamirano, Á., Saa, P. A., & Garrido, D. A. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.035 · Cited by 25

Mapping the Inner Workings of the Microbiome: Genomic- and Metagenomic-Based Study of Metabolism and Metabolic Interactions in the Human Microbiome

Manor, O., Levy, R., & Borenstein, E. (2014) · Cell Metabolism · doi:10.1016/j.cmet.2014.07.021 · Cited by 84

Constraint-based modeling of host-microbe and microbe-microbe metabolic interactions in the human gut

Heinken, A. (2015) · Skemman

Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework

Heinken, A., & Thiele, I. (2015) · Gut Microbes · doi:10.1080/19490976.2015.1023494 · Cited by 107