NUMIEP - MSB-TBSN

MSB-TBSN

International Research Network
in Translational Systems Biology and Nutriomics
for the Development of Precision Nutrition in Health Promotion
and the Prevention of Non-Communicable Diseases

Precision Nutrition→ Microbiome → Epigenome → Health Axis

Welcome to the MSB-TBSN Project – building a global framework for precision nutrition and translational systems biology

The MSB-TBSN initiative is an international strategic partnership focused on advancing Translational Systems Biology (TSB) and nutriomics as key drivers of precision nutrition. Despite rapid progress in multiomics, the integration of diet, microbiome, and epigenome within a unified translational framework remains limited and insufficiently coordinated. The list of strategic, supporting and network MSB-TBSN Partners

The project aims to establish a sustainable international research network integrating the nutriome to microbiome to metabolome to epigenome to transcriptome to phenotype axis, with direct relevance to health promotion and prevention of non-communicable diseases, including cancer, cardiovascular, metabolic, neurodegenerative, and autoimmune disorders.

Our goal is to develop a dynamic TSB ecosystem that connects research institutions through a shared digital platform enabling data integration, joint analyses, and development of multiomic resources. The network will use advanced approaches such as high-throughput multiomics, experimental and human models, and artificial intelligence to accelerate translation into precision nutrition strategies.

Through coordinated research, education, and mobility activities, the project will strengthen international collaboration and support training of the next generation of scientists. Ultimately, MSB-TBSN aims to advance systems-level understanding of the diet, microbiome, and epigenome interplay, enabling evidence-based interventions that promote healthy longevity and reduce the burden of non-communicable diseases.

INTRODUCTION

Keywords: International Strategic Partnership, Research and Education, Research Network, Translational Systems Biology (TSB), Precision Nutrition, Diet, Functional Foods, Nutriomics, Nutrigenomics, Nutriom, Microbiome, Metabolome, Epigenome, Health Promotion, Disease Prevention, Precision Medicine, Cancer, Neurodegenerative Diseases, Autoimmune Diseases, Cardiovascular Diseases, Obesity, Premature Aging.

Project Assumptions

The international strategic partnership presented in this project addresses the lack of sustainable and coordinated research networks in Poland and abroad in the field of Translational Systems Biology (TSB) and nutriomics, supporting the development of a new research area, precision nutrition, with particular focus on the nutriome, microbiome, and epigenome axis and its relevance for public health promotion. Establishing a TSB research network will also provide significant support for advancing nutritional aspects of precision medicine and the prevention of non-communicable diseases (NCDs), including cancer, neurodegenerative, cardiovascular, and metabolic diseases. The project aims to strengthen existing collaborations, expand them, and lay the foundations for a lasting partnership that enables long-term scientific, educational, research, and implementation cooperation, exchange of experience, and development of stable institutional collaboration mechanisms. The network expansion will include the creation of an online TSB platform integrating partner databases, as well as the active recruitment and incorporation of new specialized participants from around the world with high research, development, and educational potential. As a result, an international, dynamic, and self-developing TSB research network based on multiomic analyses will emerge, significantly enhancing the scientific and educational potential of our institution and partner units and increasing their international visibility. This network will enable joint projects and the preparation of proposals for prestigious national programs such as NCN, NCBiR, and ABM, as well as European grants, including European Research Council (ERC) Starting, Consolidator, Advanced, and Synergy Grants, and projects under Horizon Europe, including Marie Skłodowska-Curie Actions (MSCA). Future projects will utilize cutting-edge technologies, including the application of artificial intelligence (AI), and conduct research at the intersection of biology, dietetics, and translational medicine. These projects will employ innovative research concepts, leveraging the experience and potential of international partners, enabling interdisciplinary and multicenter research at the highest level, increasing publication potential, and contributing to the training of the next generation of scientists and specialists in translational systems biology and precision nutrition.

Scientific and Economic Justification

Translational Systems Biology (TSB) is an interdisciplinary field that integrates multiomic data, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, to understand complex biological mechanisms and their applications in translational medicine and health promotion. According to the WHO Europe 2025 report, non-communicable diseases such as cancer, cardiovascular, neurodegenerative, and metabolic diseases, as well as obesity and diabetes, account for approximately 74 percent of global deaths, including a substantial proportion of preventable mortality. Globally, these conditions generate costs of up to USD 514 billion per year, including healthcare expenditures and productivity losses. Numerous studies indicate that effective prevention and health promotion, including dietary interventions, could substantially reduce both incidence and social and economic costs. Despite growing interest in the effects of diet and functional foods on the microbiome and the microbiome’s influence on the epigenome, the literature lacks studies integrating the diet, microbiome, and epigenome axis and its impact on gene expression regulation, cellular function, and human health. Therefore, a scientific gap exists in the systemic, multilevel integration of this axis within TSB, which requires collaboration among multiple specialized teams and the implementation of interdisciplinary and innovative research. In response to this need, we propose the development of an International Strategic Partnership aimed at creating a TSB Research Network that will systematically and coordinately advance knowledge in this area, support the training of future scientific staff, and promote international research collaboration.

Competence

Our team has long been engaged in academic and student exchange, joint publications, and collaboration with international partners. Examples include the preparation and coordination of an NCN OPUS 30 grant under the LAP/Weave mechanism, involving collaboration among units from countries including Poland, Czechia, Canada, and the United States, and participation in the project HORIZON-WIDERA-2026-06-ERA-04.

Structure, Sustainability, and Activities

To ensure sustainability and formal integration within the university structure, an Interfaculty Center for Translational Systems Biology (MCTBS) will be established as the institutional coordinating unit for the network. The Center will integrate research and educational competencies within the project, support the development of multiomic and nutriomic research, particularly in relation to the diet, microbiome, and epigenome axis, and enhance research and teaching quality through joint scientific and educational initiatives. The project will implement key activities, including student and staff exchanges; participation in study visits, internships, seminars, and conferences; strengthening research and teaching quality through MCTBS; support for joint research, grant applications, publications, and databases; and networking and collaboration development through the TSB online platform, meetings, seminars, mentoring, and workshops.

Strategic Partnership

The project partnership within the International Research Network MSB-TBSN is structured as an open, scalable, and continuously evolving collaboration framework comprising strategic, supporting, and network partners (see list).
The University of Agriculture in Krakow (URK), acting as the applicant, coordinates the network through the Interfaculty Center for Translational Systems Biology and Nutriomics (CTBSN), which serves as the institutional hub for the integration of research, education, and collaboration.
The partnership is designed as an open system aimed at strengthening internationalisation, institutional cooperation, and long-term academic collaboration in translational systems biology and nutriomics. Its development supports the integration of multiomic research domains, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, the microbiome, and nutriomics.
The network enables the development of a shared interoperable data environment and a digital platform facilitating collaboration, mentoring, mobility, and knowledge exchange. It also supports joint activities such as staff and student exchanges, study visits, training, workshops, publications, and grant applications, contributing to improved research quality, increased international visibility, and the sustainability of collaboration in precision nutrition, precision medicine, and non-communicable disease prevention.
In the framework of the network, partners will exchange educational and research and development expertise. The list of partners who have signed letters of intent to join the initiative is available on a dedicated page: MSB-TBSN Partners.

Deliverables

The project will establish and operationalize the International Research Network in Translational Systems Biology and Nutriomics (NUMIEP-SYS), integrating partners from from all aver the world to support long-term scientific and educational collaboration. The Interfaculty Center for Translational Systems Biology (MCTBS) will serve as the institutional coordinating unit, ensuring integration of research, education, and network activities and supporting sustainability. A TSB online platform will be developed to integrate partner databases, enable data sharing, and facilitate communication and collaboration across the network. The project will ensure data harmonisation, metadata standardisation, and FAIR-compliant deposition of multiomic datasets, including genomic, epigenomic, transcriptomic, and metabolomic data. The NUMIEP-SYS Atlas will be developed and published as an integrated multiomic resource describing the diet–microbiome–epigenome axis, including preliminary biomarkers and system-level insights. Joint scientific outputs will include peer-reviewed publications and proof-of-concept results, alongside joint grant applications submitted to national and international funding schemes such as NCN, NCBiR, ABM, Horizon Europe, ERC, and MSCA. The project will implement a mobility and training programme with exchanges, workshops, seminars, and training in multiomics, translational systems biology, and AI, as well as joint educational materials and modules supporting precision nutrition and translational systems biology. A sustainability strategy will be developed to ensure continuation, expansion, and institutional embedding of the network beyond the project duration.

Project Management

The project will be coordinated by the University of Agriculture in Krakow (URK), which is responsible for overall management, financial control, reporting, and scientific coordination led by the Principal Investigator. The management structure will include the Principal Investigator, thematic leaders, and a Scientific and Program Advisory Board ensuring strategic oversight and coordination. Administrative and financial support will be provided by URK to ensure efficient budget execution and compliance with programme requirements. Data management will cover harmonisation, metadata standardisation, and FAIR-compliant storage in a centralised repository enabling integration and reuse of multiomic datasets. International coordination will be maintained through regular online meetings, seminars, and annual partner meetings. Progress will be monitored via periodic reports, performance indicators, and evaluation by the Advisory Board, while risk management will address scientific, organisational, and financial risks through continuous monitoring and adaptive mitigation strategies. Communication and dissemination will be supported via the TSB platform, publications, conferences, and outreach activities. Training and capacity building will develop competencies in multiomics, data analysis, and international collaboration. The management framework will ensure sustainability, scalability, integration of new partners, and support for future projects and funding applications.

Summary

The project will establish a sustainable, international, and dynamic TSB network integrating multiomic and nutriomic data to develop precision nutrition strategies. The network will address a key research gap resulting from the lack of comprehensive analysis of the diet, microbiome, and epigenome axis and its impact on gene expression, biological system function, and health outcomes relevant to disease prevention. The strategic partnership will enhance scientists’ competencies in advanced technologies, data analysis, and participation in international consortia. The project will result in an online TSB platform integrating partner databases, atlases, and potential biomarkers and therapeutic targets. These structures will support future research, the development of preventive strategies and interventions, and the training of the next generation of scientists and specialists in translational systems biology and precision nutrition.

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NUMIEP project

Multiomics-guided mechanistic understanding of gut microbiome-mediated epigenome reprogramming in response to functional food–based dietary intervention

NUMIEP is a scientific research initiative dedicated to advancing basic science that supports long-term health. The gut microbiome is increasingly recognised as a “hidden organ” — a vast, still underexplored ecosystem with profound influence on human physiology. The project aims to uncover the causal mechanistic links connecting diet, the gut microbiome, and the epigenome. Using iodine- and selenium-biofortified lettuce as a model functional food, we study how dietary components reshape microbial communities and how microbiome-derived metabolites drive epigenetic and functional reprogramming of colonic epithelial cells.
NCN OPUS-LAP project — My role: scientific concept co-author, USA consortium partner (in-kind contribution), scientific advisor for the Microbiome–Epigenome–Transcriptome axis.

popular-science materials

What is Precision Nutrition ?

This short video introduces precision nutrition as an approach that tailors dietary recommendations to individual differences in genetics, metabolism, and lifestyle. It emphasizes that variability in responses to diet requires moving beyond one-size-fits-all guidelines toward personalized strategies. By integrating advances in basic and translational research, precision nutrition aims to improve health outcomes, support human development, and help prevent or mitigate chronic diseases and aging.

Systems Biology: A Short Overview

This short video explains that predicting biological systems is fundamentally more complex than in chemistry or physics due to the immense number of interacting components within living cells. Because human cognition cannot track these processes simultaneously, systems biology relies on computational and mathematical modeling to simulate cellular functions and predict system behavior. By integrating real-world physicochemical constraints, such models enable analysis of complex biological interactions, improving understanding of cellular systems, supporting drug development, and optimizing therapeutic interventions. The video highlights collaborative efforts to develop computational tools and databases that facilitate the construction and analysis of multi-level biological models, advancing the ability to make biology more predictable and applicable in medicine.

Systems Biology and Meta-Omic Analysis of the Human Microbiome

This keynote lecture by Elhanan Borenstein presents a systems biology framework for understanding the human microbiome as a complex, multi-level network of interacting microbial species and metabolic pathways. The talk emphasizes the limitations of traditional microbiome research focused on composition and correlations, and highlights the need for predictive, model-driven approaches that integrate metagenomic and multi-omic data. By applying computational modeling and cross-meta-omic analysis, the speaker demonstrates how it is possible to infer microbial interactions, predict functional changes, and better understand how the microbiome influences host physiology and disease. The lecture underscores the transition from descriptive to mechanistic and predictive microbiome science, with implications for disease research, therapeutic development, and personalized medicine.

How Systems Biology Is Transforming Modern Medicine

This lecture by James Valcourt introduces systems biology as a transformative approach in modern medicine, shifting from studying individual components to understanding complex biological networks. It highlights how advances in computational power enable analysis of large-scale biological data, leading to breakthroughs in areas such as gene regulation, cancer treatment personalization, brain function, and the role of the microbiome in disease. The talk emphasizes that systems biology provides deeper insight into complex health conditions and supports the development of more effective, individualized medical interventions.

Epigenetics microbiome and Aging

This video explains how DNA damage over time leads to “epigenetic drift,” which disrupts normal gene regulation and contributes to aging. It also describes how failures in DNA repair mechanisms accelerate this epigenetic deterioration, helping to explain why cellular function declines with age.
Borrego-Ruiz and Juan J Borrego 2024

Epigenetics Explained: How Diet, Lifestyle & Environment Influence Your Genes

This video explains the basics of epigenetics, focusing on how diet, lifestyle, and environmental factors can influence gene expression without changing DNA sequence. It highlights practical ways to support health through nutrition, daily habits, and environmental awareness, emphasizing that gene activity can be modified through targeted interventions. The video also introduces personalized approaches, such as DNA testing and specific protocols, to optimize individual health and wellbeing based on epigenetic responses.

Nutrigenomics: The Science of Eating Right for Your Genes

This video explains nutrigenomics as the study of how genetic variation influences individual responses to diet and how nutrients can affect gene expression. It highlights key concepts such as gene–diet interactions, epigenetic regulation, and the role of specific genes in metabolism and disease risk. The video emphasizes that understanding these mechanisms enables the development of personalized nutrition strategies to improve health outcomes, support weight management, and prevent chronic diseases, while also acknowledging challenges related to complexity and ethical considerations in the use of genetic data.

Selected Reference Publications

Systems biology approaches to inform precision nutrition

This review highlights the role of systems biology and nutrigenomics in advancing precision nutrition by addressing interindividual variability in diet-related disease risk and responses to dietary interventions. The authors emphasize the importance of identifying metabotypes and understanding inter-organ crosstalk in inflammation and metabolism to stratify risk and predict responses. By integrating biological factors (e.g., age, sex, metabolic phenotypes, genomic profiles) with behavioral traits, systems biology enables targeted dietary recommendations that improve the efficacy of personalized nutrition interventions, particularly for cardio-metabolic health and disease prevention.
Mitchelson KAJ, Ní Chathail MB, Roche HM. Systems biology approaches to inform precision nutrition. Proc Nutr Soc. 2023 May;82(2):208-218. doi: 10.1017/S0029665123002732.

Systems biology of personalized nutrition

This article discusses systems biology in personalized nutrition, emphasizing integration of biological processes across tissues and their interactions with diet and the environment. It introduces “systems flexibility” for real-time assessment of metabolic and homeostatic responses to support individualized dietary recommendations. The review highlights examples involving macro- and micronutrients, genetic variation, and performance goals, and describes modeling approaches combining personalized diagnostics with nutritional interventions to optimize health and wellness outcomes.
van Ommen B, van den Broek T, de Hoogh I, van Erk M, van Someren E, Rouhani-Rankouhi T, Anthony JC, Hogenelst K, Pasman W, Boorsma A, Wopereis S. Systems biology of personalized nutrition. Nutr Rev. 2017 Aug 1;75(8):579-599. doi: 10.1093/nutrit/nux029. Erratum in: Nutr Rev. 2017 Aug 1;75(8):672. doi: 10.1093/nutrit/nux049. PMID: 28969366

Systems biology approaches to understand the effects of nutrition ...

This review highlights the application of systems biology in nutritional research to understand how dietary components influence health and prevent disease. By integrating multiple “-omics” approaches—including transcriptomics, proteomics, and metabolomics—systems biology generates comprehensive datasets that enable predictive modeling of individual responses to nutrition. The authors emphasize the role of bioactive food components in counteracting oxidative stress, a key factor in aging and the development of diseases such as neurodegenerative disorders, cancer, metabolic syndrome, and cardiovascular disease. Overall, systems biology provides a powerful framework for elucidating the molecular mechanisms of diet-mediated health benefits and for advancing precision nutrition strategies.
Badimon L, Vilahur G, Padro T. Systems biology approaches to understand the effects of nutrition and promote health. Br J Clin Pharmacol. 2017 Jan;83(1):38-45. doi: 10.1111/bcp.12965. Epub 2016 May 29. PMID: 27062443

Personalized nutrition therapy in critical care ...goals for personalization of nutrition

This article presents 10 expert recommendations for personalized nutrition in critical care to optimize ICU outcomes. Early nutrition (EN preferred, PN if needed) should start within 48 hours. Indirect calorimetry is recommended to guide energy targets (~70% initially, then increasing), while protein should begin low (<0.8 g/kg/d) and be progressively increased (≥1.2 g/kg/d) based on clinical status and kidney function. Monitoring of energy/protein delivery, micronutrients, and muscle status (ultrasound, CT, BIA) is advised. Future approaches include intermittent feeding, anabolic nutrients (HMB, creatine, leucine), and integration of rehabilitation or anabolic agents to support recovery and preserve muscle mass.
Wischmeyer PE, Bear DE, Berger MM, De Waele E, Gunst J, McClave SA, Prado CM, Puthucheary Z, Ridley EJ, Van den Berghe G, van Zanten ARH. Personalized nutrition therapy in critical care: 10 expert recommendations. Crit Care. 2023 Jul 4;27(1):261. doi: 10.1186/s13054-023-04539-x. PMID: 37403125

Precision nutrition: A systematic literature review

This systematic literature review examines the application of machine learning (ML) in precision nutrition, analyzing 60 primary studies out of 4,930 retrieved papers. The review identifies fifteen key problems across seven nutrition and health domains and classifies ML tasks into regression, classification, recommendation, and clustering, mostly using supervised approaches. Across the studies, 30 ML algorithms were applied, with 19 used multiple times, and models were evaluated using 23 different metrics. The findings indicate that integrating ML into precision nutrition can effectively manage complex, multi-dimensional data, improve predictive performance, and enable personalized dietary recommendations, highlighting its potential to enhance research and practical applications in individualized nutrition strategies.
Kirk D, Catal C, Tekinerdogan B. Precision nutrition: A systematic literature review. Comput Biol Med. 2021 Jun;133:104365. doi: 10.1016/j.compbiomed.2021.104365. Epub 2021 Apr 7. PMID: 33866251

Precision nutrition and food biomanufacturing for space missions...

TThis review addresses challenges of long-duration spaceflight nutrition and strategies in precision nutrition and biomanufacturing for autonomous life-support systems. Space-specific stressors—microgravity, radiation, and circadian disruption—affect metabolism, immune function, and gut microbiota, limiting conventional diets. It highlights multi-omics monitoring, AI-driven feedback, and digital twins for personalized nutrition, alongside microbial, plant, and cellular biomanufacturing, as well as technologies like 3D/4D food printing and closed-loop bioreactors integrating food production, metabolism, and waste recycling. Key challenges include reactor stability, biosafety, and multi-species culture management, emphasizing the need for intelligent, self-regulating systems for real-time, dietary support in space.
Liu J, Zeng D, Hu B, Wang W, Hu S, Cifuentes A, Liao G, Long M, Zhao H, Lu W. Precision nutrition and food biomanufacturing for space missions: Toward intelligent and bioregenerative life-support systems. Food Res Int. 2026 May 1;231(Pt 2):118803. doi: 10.1016/j.foodres.2026.118803. Epub 2026 Feb 24. PMID: 41819942.

Advancing Precision Nutrition Through Multimodal Data and Artificial Intelligence

This review addresses challenges and opportunities in precision nutrition driven by interindividual variability in metabolic responses to diet (metabolic heterogeneity). It highlights major sources of variability, including the host genome, gut microbiome, and brain connectome, and their interactions with dietary intake. Advances in multimodal data collection and artificial intelligence enable predictive models integrating genetic, microbial, and brain activity data to forecast individual dietary responses. The review also discusses n-of-1 study designs, wearable technologies, and machine learning to support individualized nutritional decision-making, along with current challenges and future implementation directions.
Fu Y, Zhang K, Miao Z, Yang G, Huang Y, Zheng JS. Advancing Precision Nutrition Through Multimodal Data and Artificial Intelligence. Adv Sci (Weinh). 2026 Mar;13(17):e21111. doi: 10.1002/advs.202521111. Epub 2026 Feb 11. PMID: 41669854.

Multiomics to Predict Individual Responses to Weight Loss Interventions...

This review examines challenges and opportunities in precision nutrition driven by interindividual metabolic variability. It highlights key sources of heterogeneity, including the host genome, gut microbiome, and brain connectome, and their interactions with diet. Advances in multimodal data collection and artificial intelligence enable predictive models integrating genetic, microbial, and brain activity data to forecast individual dietary responses. The review also discusses n-of-1 study designs, wearable technologies, and machine learning for individualized nutritional decision-making, along with current challenges and future directions for implementation.
Haslam DE, Hu FB. Multiomics to Predict Individual Responses to Weight Loss Interventions: A Promising Strategy to Enable Precision Nutrition. Diabetes Care. 2026 Jan 1;49(1):63-65. doi: 10.2337/dci25-0075. PMID: 41418032;

Biological Rhythms, Chrono-Nutrition, and Gut Microbiota: Epigenomics Insights ...

The article explores how circadian rhythms, meal timing, and gut microbiota interact to influence metabolic health through epigenetic mechanisms. It highlights that the temporal pattern of food intake affects gene expression, DNA methylation, and non-coding RNA activity, linking circadian regulation with nutritional signaling and microbial activity. These interactions shape the host’s metabolic and immune landscape, suggesting that aligning eating patterns with circadian rhythms could serve as a non-invasive strategy to optimize metabolism, support well-being, and prevent metabolic disorders.
de Oliveira Melo NC, Cuevas-Sierra A, Souto VF, Martínez JA. Biological Rhythms, Chrono-Nutrition, and Gut Microbiota: Epigenomics Insights for Precision Nutrition and Metabolic Health. Biomolecules. 2024 May 6;14(5):559. doi: 10.3390/biom14050559. PMID: 38785965

Epigenetics in Precision Nutrition.

This article reviews the role of epigenetics in precision nutrition, highlighting that individual responses to diet and lifestyle are influenced not only by the genome and gut microbiome but also by the epigenome, which has been largely overlooked. Epigenetic mechanisms, including DNA methylation, non-coding RNAs, and histone modifications, act as interfaces between the genome and environmental factors, shaping variability in metabolic health and responses to dietary interventions. Evidence indicates that DNA methylation is associated with obesity, diabetes, and cardiovascular disease, and may serve as a marker for personalized nutrition strategies. The review emphasizes the potential of integrating epigenetic data into precision nutrition research to identify novel intervention targets and improve individualized dietary recommendations.
Li X, Qi L. Epigenetics in Precision Nutrition. J Pers Med. 2022 Mar 28;12(4):533. doi: 10.3390/jpm12040533. PMID: 35455649

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