(Note: this is one continual workshop divided into 3 segments)

Presenters
Isabelle Kohler, Mikhail Golovko, Rawi Ramautar, Bert Wouters and Peter Lindenburg

Description
In this workshop, we will focus on the fundamentals and novel developments that have been carried out in the field of liquid-phase separation techniques hyphenated to mass spectrometry in clinical metabolomics. In the first segment, we will start with a general introduction on the use of liquid-based separation techniques, including hydrophilic interaction chromatography (HILIC) and supercritical fluid chromatography (SFC), in metabolomics, and also discuss quantitative MS – focusing on practical challenges (i.e. matrix effects, validation, etc.), and possible solutions. In the first and second segment, attention will be paid to LC-MS in lipidomics covering both challenges and practical concerns. After that, attention will be paid to the utility of capillary electrophoresis – mass spectrometry (CE-MS) for metabolomics. Miniaturization in sample preparation and LC will be discussed in the last segment. Unique metabolomics-based applications will be used to illustrate the concepts presented, with a special emphasis on the practical aspects and typical challenges encountered using such techniques.

12:30 – 2:15 | Introduction, challenges, and possible solutions

• Recent developments in liquid-phase separation techniques: introduction, high-throughput and high-resolution approaches (Dr. Isabelle Kohler)
• LC-MS in lipidomics: challenges and practical aspects (Dr. Mikhail Golovko) – Part one

2:30pm - 4:15pm | Novel techniques and applications

• LC-MS in lipidomics: challenges and practical aspects (Dr. Mikhail Golovko) – Part two
• CE-MS in metabolomics: concept, applications and challenges (Dr. Rawi Ramautar)

4:30pm - 6:15pm | Miniaturization in sample preparation and separation

• Novel developments in miniaturized techniques: from sample preparation to detection (Dr. Bert Wouters and Dr. Peter Lindenburg)

Presenters
Stacey Reinke, Tim Ebbels, and Mai Yamamoto

Description
Understanding complex biological systems at multiple levels of biological organization requires combined knowledge from different types of experiments to obtain a comprehensive picture of a system's function. Researchers today, have a plethora of 'omics' (metabolomics, transcriptomics, proteomics) methodologies to choose from and implement in their research allowing them to build a detailed picture of a given organism and to look for interactions between different levels of information. A single set of 'omic' data can be studied and interpreted separately, however integrating the knowledge from multiple data sets into a single model of a system can result in greater statistical power and biological interpretation. Integration of such diverse data sets presents a major challenge in the field of biomarker discovery, precision medicine and systems biology.

Workshop objectives

1. Provide a theoretical and practical introduction to multi-omic data integration
2. Inform attendees about the currently available tools used to integrate ‘omic’ data from different platforms
3. Demonstrate best practices for data fusion

Workshop outcomes

1. Learn how to perform multi-omic data integration
2. Gain better understanding about how data integration can facilitate biomarker discovery

Theme Alignment: New Frontiers

Presenters
Amina Bouslimani, Madeleine Ernst, Justin van der Hooft, Julia M. Gauglitz, Anupriya Tripathi, Kathleen Dorrestein, Pieter Dorrestein

Description 
This workshop will introduce automated tandem mass spectrometry-based dereplication using the Global Natural Products Social Molecular Networking (GNPS) platform and unsupervised substructure discovery using MS2LDA.

Workshop Objectives

1. how to submit mass spectrometry data to GNPS
2. how to run a mass spectral molecular networking job on the GNPS interface and which parameters are important to consider
3. how to browse through the results on the GNPS interface
4. how to run an MS2LDA job on the ms2lda.org website and which parameters are important to consider
5. how to browse through the results on the ms2lda.org interface

Workshop Outcomes
TBD

Theme Alignment: Technology

Presenter
Jianguo (Jeff) Xia, Jasmine Chong (TA)

Description
Multi-omics data integration and systems metabolomics are two active research areas in current computational metabolomics. We have developed a series of user-friendly tools for comprehensive analysis of common omics data, including metabolomics (MetaboAnalyst, metaboloanalyst.ca), transcriptomics (NetworkAnalyst, networkanalyst.ca) and microbiomics (MicrobiomeAnalyst, microbiomeanalyst.ca). Leveraging these resources, we introduce MultiomicsAnalyst and OmicsNet to support statistics and network-based approaches for multi-omics integration and systems metabolomics. The workshop will start with the introduction of the key concepts, our implementations and important results. After 45-minute introduction, workshop participants will continue with a 90 minute "hands-on" lab where they will be encouraged to use their own data and to process it with our web-based tools. Alternately, participants may work with example datasets provided with our tools. The instructor (plus TAs) will assist participants in completing these tasks.

Workshop objectives

1. To understand the goals and challenges in multi-omics integrations
2. To understand the main concepts in current approaches
3. To understand the results and limitations

Workshop outcomes

1. Pathway and network-based approaches to derive systems insights directly from global metabolomics data
2. Integrating different omics data sets using several statistical methods and biological networks
3. Using several powerful visual analytics approaches to reveal patterns and unique trends for multi-omics data sets.

Theme Alignment: Technology

Presenters
Denise M. Scholtens (Northwestern University), Raji Balasubramanian (University of Massachusetts Amherst)

Description
In this 2-hour hands-on workshop, we will provide an overview of selected methods for graphical model estimation and network modeling, with application to metabolomics. Metabolomic data can be effectively represented as networks, in which nodes represent individual metabolites and edges between pairs of nodes represent dependencies between metabolite pairs. Within this framework, we will describe methods for graphical model estimation such as the gLasso (Hastie, T. and Tibshirani, R., 2008) that are useful for describing the conditional relationships between metabolite pairs in a p>n setting. We will also highlight methods for multiple group graphical model estimation (Danaher, P. et al., 2014) and differential network analysis, such as DINGO (Ha, M. J. et al., 2014). Examples will be provided highlighting application of these techniques in clinical research. This workshop will include hands-on introduction to these techniques including application to example metabolomics datasets using the R software environment.

Workshop objectives

1. Explain the use of network models in metabolomics studies
2. Apply R programming to analyze metabolomics network data
3. Visualize network models using R

Workshop outcomes

1. Create R objects for network modeling using the igraph R package
2. Perform differential network analyses using R

Theme Alignment: Biomedical Applications

Presenters
Ilana Rogacehv (Asaph Aharoni labs-Wezzmann Israel), Saleh Alseekh (MPIMPP-golm), Ric de Vos (WUR), Jose L. Rambla (IBMCP)

Description
Workshop will present and discuss latest advances in natural and generated variability in Plant Metabolomes (short presentations and round table).

Workshop objectives
Each of the 4 temptative Speaker cover different approaches and submetabolomes as well as different species from model species, fruit and non fruit, etc. 2) Round table with all speakers (discussion conducted by workshop chair and open to public particpation) to discuss: Plant Metabolomics groups in National Metabolomic Networks, Present and future challenges in Plant Metabolomics, identify any specific issues in Plant Metabolomics that need plant networking

Workshop outcomes
State of the art in the field of Variability in Plant Metabolomes Specific issues in Plant Metabolomics that require plant specific networking

Theme Alignment: Plant, Food, Environmental and Microbial applications

Presenters
Marnix H. Medema (Wageningen University), Stefan Verhoeven (Netherlands eScienceCenter), Florian Huber (Netherlands eScienceCenter), Lars Ridder (Netherlands eScienceCenter), Simon Rogers (University of Glasgow), Justin J.J. van der Hooft (Wageningen University)

Description
The recent increase in publicly available metabolome and genome data comes with novel opportunities. Here, we will brainstorm and discuss how to exploit this data goldmine by linking information across omics disciplines with a particular focus on linking the results of genome mining for "biosynthesis hotspots" in the form of biosynthesis gene clusters that encode for the production of specialized metabolites to metabolomics data. Our workshop is of relevance to metabolomics researchers interested in multiple structural annotation strategies including the use of phylogenetic information and combined use of genome & metabolome mining. Our workshop will be structured as follows: i) welcome and introduction of basic concepts of genome and metabolome mining with a focus on genome mining (antiSMASH, BiG-SCAPE) ii) discussion groups around: a) available data platforms and a brainstorm on how to enable better reuse of data for linking, b) brainstorm on possible ways to correlate and link genome and metabolome data sets, and c) brainstorm on possible structural/functional annotation information exchange between genome and metabolome. This will accommodate participants with different expertise and background.

Workshop objectives
With this workshop, we aim for the following, namely to: - Introduce genome mining workflows to the metabolomics community. We will especially focus on introducing the genome mining tools antiSMASH and BiG-SCAPE to the metabolomics community. - Brainstorm on how these genome mining workflows and genome data in general can be linked to metabolome data to further both scientific fields. - Inform the audience on latest cutting-edge developments in the field of linking biosynthesis gene clusters to their molecular products and also provide them an opportunity to shape these developments by providing feedback and suggestions.

Workshop outcomes
After attending this workshop, the participants will have an: - Understanding of basic concepts and motivation of genome mining and metabolome mining. - Overview of existing tools that aid in linking genome and metabolome data for structural annotation of natural products. - Motivation behind state-of-the-art and emerging platforms and tools enabling the linking of metabolome and genome

Theme Alignment: Technology

Presenters
Melissa Fitzgerald, Katharina Herzog, and Tetyana Benzeroual

Description
This workshop primarily targets Early Career Researchers (Undergraduate, Graduate, Postdoctoral Associates) to create awareness on career development and planning. It is divided into four parts and are meant to get participants thinking about their career path, where they would like to be, and how to get there. Session one will involve building up your career development strategy and will include areas such as negotiating your career and creating your storyline. Session two will cover communicating effectively with focus on public speaking and pitching skills. Session four will focus on your talent and will discuss how volunteering could be beneficial for your career. The final session will conclude with speakers from a variety of sectors such as academia, consulting, government, entrepreneurship and new ventures, and industry. The invited speakers will discuss their professional career pathways and how they get there.

Workshop objectives

1. To build up the career development strategy of students and ECRs.
2. Tips on how to communicate effectively: Public speaking and pitching skills
3. To show volunteering can help your career.
4. Make attendees aware of career pathways outside the academe.

Workshop outcomes
Participants will leave this workshop with a better understanding of the tools that are available to them and how they can use the resources around them to propel their career transition.

Theme Alignment: TBD

Presenters
Cyrille Thinnes, Ronan M.T. Fleming

Description
To facilitate the integrative analysis of metabolomic data in their biochemical context, we have developed the Virtual Metabolic Human (VMH, www.vmh.life). The VMH hosts and interlinks the human and associated gut microbe metabolic reconstructions with an extensive nutrition database and hundreds of metabolic diseases using standardized nomenclature. Extensive manual curation protocols enabled the high standard and information coverage of the VMH-hosted genome-scale metabolic reconstructions, i.e., the complete computational representation, for both human and microbes, of known metabolism in relations to the underlying gene, protein, and biochemical networks. This workshop will provide an overview of the VMH database and its capabilities, introduce each resource, including the underlying human and microbiome metabolic reconstructions, as well as the nutrition and the inherited metabolic disease resources. You will learn how to browse the resources, visualize metabolic pathways, design personalized diets, and download your results. We will demonstrate how to interface the VMH with the Constraint-Based Reconstruction Analyses (COBRA) Toolbox to perform metabolic modeling and thereby, accelerate the generation of mechanism-based hypothesis. The VMH and the COBRA Toolbox are valuable tools for metabolomics studies as they interlink measured metabolites with known human and microbial pathways, nutrition and diseases.

Workshop objectives

1. To demonstrate the information captured in the VMH and how they can be useful for metabolomics studies
2. To obtain an overview of the basic principles of constraint-based modeling
3. To present metabolic modeling, using the COBRA toolbox, as a data analysis tool to connect metabolite measurements with pathways

Workshop outcomes

1. Use of VMH for metabolomic data query
2. Overview of simulation opportunities with metabolomic data using the COBRA toolbox
3. Visualization of metabolomic data on the human metabolic map using the COBRA toolbox

Theme Alignment: Biomedical Applications

Presenters
Keeva Cochrane (EMBL-EBI), Venkata Chandrasekhar Nainala (EMBL-EBI), Marie Phelan (University of Liverpool), Moderator Geerten Vuister (University of Leicester)

Description
The NMR pipeline requires locating many different tools in order to properly interface with the data presented. Many tools come at a cost and for the burgeoning community and expanding online resources, this can be prohibitive to probing NMR data and independent appraisal of quality and annotation completion. This workshop provides an overview of open-source tools for facilitating interaction with open-access repository data without the need to purchase software licences:
Section1. Outlining the structure and data available in the EMBL-EBI repository MetaboLights[www.ebi.ac.uk/metabolights] and how to facilitate deposition and download of datasets.
Section2. Accessing data downloaded from MetaboLights via Galaxyproject.org tool tameNMR[github.com/PGB-LIV/tameNMR] (available via PhenoMeNal[phenomenal-h2020.eu/home]) and other tools available via workflow4metabolomics[workflow4metabolomics.org]. This section will look at raw 1D 1H NMR spectra deposited, bin spectra according to annotation provided with deposition and perform simple statistics on the resultant spectra intensity files.
Section3. Analysing 2D NMR via Collaborative Computing Project for NMR (CCPN[ccpn.ac.uk/collaborations/metabolomics]). This includes download of 2D NMR standards from BMRB (Biomolecular Resonance Bank)[hmdb.ca] / HMDB[bmrb.wisc.edu/metabolomics] and overlay with CCPN metabolite library.

Workshop objectives
To gain understanding in formats of NMR data available on online repositories and how to interface with raw NMR data using open-source third party software. To gain understanding as to how to appraise NMR data presented with annotations, identities provided. To explore open-access NMR standard data and compare to experimental NMR data using open-source software.

Workshop outcomes
To learn how to deposit your data to the MetaboLights repository To learn how to visualise experimental NMR data available on the MetaboLights repository using third party software (tameNMR, workflow4metabolomics and CCPN AnalyseMetabolomics). To learn how to map annotations, identities and standard libraries with experimental 1D 1H and 2D NMR data using open-source software (tameNMR and CCPN AnalyseMetabolomics).

Theme Alignment: Technology

(Note: this is one continual workshop divided into 3 segments)

Presenters
Dara Daygon, Yann Guitton, Julia Kuligowski, Jasper Engel, Ron Wehrens, Jos Hageman, Justin van der Hooft, Natasa Giallourou, Keeva Cochrane

Description
Untargeted metabolomics experiments based on 1H-NMR, LC/MS or GC/MS produce large and complex data sets. In this workshop we will introduce the fundamentals of analysis of such data using open source resources. The workshop is divided into three blocks covering data processing; data analysis; and databases, fair data and reproducible research. Throughout the workshop, focus will lie on the practical application of the techniques discussed and correct interpretation of their results. The workshop includes hands-on tutorials using the participants own laptops.
In the first segment the typical steps in data processing for LC-MS, GC-MS and NMR will be discussed. The second block starts with an introduction to multivariate data analysis (MVDA) for metabolomics. Here, the main principles of MVDA will be discussed, mainly in the context of explorative analysis using principal component analysis. Special attention will be paid to the importance of appropriate data pre-processing in MVDA. The second half of session 2 focuses on supervised data analysis. Analysis of a typical case-control study as well as more complex multi-factor experimental designs will be addressed. The third block covers metabolite identification, cross-omic public resources available from EMBL-EBI that can be used to enhance metabolomics analysis and enable cross-omics interpretation, and data management planning.

8:30am – 10:15am: Metabolomics data processing

• Introduction to the Galaxy platform W4M including general data pre-processing principles (Dr. Dara Daygon, Dr. Yann Guitton)
• Practical: Workflow4Metabolomics as a tool for metabolomics data processing (Yann Guitton)
• Data Quality assessment: Signal drift and batch effect correction (Dr. Julia Kuligowski)

10:30am – 12:15pm: Fundamentals of data analysis in metabolomics

• Overview of the use of multivariate statistics in discovery studies (Dr. Jasper Engel)
• Practical: metabolomics data analysis in MetaboAnalyst (Dr. Jasper Engel, Dr. Jos Hageman, Dr. Ron Wehrens)

1:30pm – 3:15pm: Metabolite identification, standards and databases

• Introduction to the (computational) aspects of metabolite identification and panel discussion (Dr. Justin van der Hooft, Dr. Natasa Giallourou)
• Introduction to the MetaboLights database and other cross-omic resources (Dr. Keeva Cochrane)

Presenters
Warwick Dunn (University of Birmingham), Christina Jones (National Institute of Standards and Technology), Claire O’Donovan(European Bioinformatics Institute)

Description
A National Cancer Institute-sponsored Think Tank, held in 2017, highlighted the need for community-wide engagement for improving and systematizing quality assurance (QA) and quality control (QC) practices for untargeted metabolomics. The 'metabolomics Quality Assurance and quality Control Consortium' (mQACC) was established from this initial effort and initially focused on instrumental analysis aspects, while acknowledging that sample collection, storage, and preparation are critical analytical steps. For the purposes of this proposed workshop, QA will be defined as the set of procedures that are performed in advance of analysis of samples that are used to improve data quality and QC will be defined as the set of activities that a laboratory conducts during and after instrumental analysis that are used to demonstrate the quality of project data. A workshop at was held at Metabolomics 2018 to alert the community to the existence of the mQACC and gauge the community's interest in our mission. Since then, the consortium has grown its membership and activities. The current workshop will focus on informing the community about mQACC's progress, furthering community engagement, and training the community on QA and QC for untargeted metabolomics.

Workshop objectives

1. Provide a forum for discussion of appropriate QA and QC processes with inclusion of real-life examples
2. Discuss QA and QC principles related to instrumental analysis of biological samples and the reporting of QC-related data
3. Inform attendees about mQACC activities and opportunities to join and contribute to the consortium.

Workshop outcomes

1. Attendees will have improved knowledge of QA and QC practices for untargeted metabolomics and their importance
2. Attendees will have the necessary information on how to join and contribute to mQACC.

Theme Alignment: Technology

Presenters
Justin v.d. Hooft, Fabien Jourdan, Sajjan Singh Mehta, Steffen Neumann, Reza Salek, Tobias Schulze, Hendrik Treutler, Mingxun Wang, Ralf Weber, Egon Willighagen

Description
This workshop aims to bring together spectral library providers, their (power) users, spectra contributors and developers from the bioinformatics ecosystem around spectral libraries. There are several community-driven spectral libraries out there, and we will show some of the advanced possibilities for data access, data linking, sharing and data standards. Other areas covered will be spectral library generation workflows from raw data, and programmatic access and spectral search algorithms. Beyond just metabolite identification, spectral libraries can be mined for further information, such as coverage of metabolites or more generally the chemical space, which in turn can help to fill the gaps. The importance of capturing available metadata for such mining will be discussed as well. The target audience are in particular advanced users of (and contributors to) spectral libraries, computational users of spectral libraries, providers of reference spectra, spectral library maintainers and developers.

Workshop objectives

1. Spectral libraries are an important information source for metabolite identification
2. Defining metadata to make spectra usable for data mining efforts
3. Harmonization of both curation and data exchange standards

Workshop outcomes

1. How to create (and share!) reference spectra
2. FAIR spectral data, linking via InChIKeys, SPLASH, and integration of ELIXIR BioSchemas for interoperability

Theme Alignment: Technology

Presenters
Hunter Mosley, Venkata Chandrasekhar Nainala, Federico Martinez Seidel, Danilo Daloso, and Frederik Dethloff

Description
The aim of this workshop is to give some hands-on examples of the different uses of stable isotope labeled compounds, both in the field of plant metabolomics and human/medical studies. Questions to be raised/discussed: (1) Which questions can be answered using stable isotopes? (2) What can different research fields learn from each other in terms of stable isotope labeling experiments? (3) What needs to be considered for experimental planning of a labeling experiment? (4) Which instruments and software packages are suitable? (5) How to interpret the resulting data? (6) What are the limitations for labeling studies? This workshop primarily targets beginners in the metabolomics field, including early-career researchers, but also everyone who is using stable isotope labeled compounds to complement their own existing research.

Workshop objectives

1. Which questions can be answered using SIRM?
2. What can different research fields learn from each other in terms of SIRM experiments?
3. What needs to be considered for experimental planning?
4. Which instruments and software packages are suitable?
5. How to deposit SIRM data and metadata into public repositories?
6. Can InChI help to represent SIRM spectral assignments in an unambiguous manner?
7. What are the limitations for labeling studies?

Workshop outcomes
Participants can expect to learn about the basics in SIRM during the Workshop. Further, the Workshop aims at enabling participants to delve into specific topics on their own afterwards (keywords, online resources). Finally, we hope to seed ideas and to bring researchers with interest in SIRM together to enable further discussions during the following conference.

Theme Alignment: Technology

Presenter
Douglas McCloskey

Description
Metabolomics is one of the most information rich –omics data types, but the tools available to the majority of researchers for analyzing metabolomics data is limited to exploratory statistics and pathway mapping. While valuable, exploratory statistics and pathway mapping are only the first step towards extracting the maximal amount of value out of metabolomics data. This workshop will cover advanced metabolomics data analysis strategies such as biochemical modeling using constraint-based and kinetic analysis, metabolic flux analysis from isotope labeling experiments, and machine learning including deep learning. The workshop will also cover the experimental design pre-requisites required to successfully execute advanced metabolomics data analysis. And finally, the workshop will describe how advanced data analysis workflows can be implemented in practice in order to derive actionable insights from metabolomics data.

Workshop objectives

1. Overview of advanced biochemical modeling methods
2. Overview of advanced statistical methods including machine learning
3. Example applications using metabolomics data to answer biological questions
4. Pre-requisite data processing and experimental design strategies to allow for constructing high throughput biochemical modeling and machine learning pipelines.

Workshop outcomes

1. How to formulate and solve constraint-based, metabolic flux analysis, and kinetic modeling problems
2. How to formulate and solve machine learning problems using metabolomics data
3. Several strategies for designing and executing high throughput biochemical modeling and machine learning pipelines.

Theme Alignment: New Frontiers

Presenters
Philippe Rocca-Serra (UOXF), Jean-Charles Portais (INRA-MetaboHub), Vitaly Selivanov (UB), Celia van Gelder (ELIXIR training platform)

Description
Metabolic reaction rates (fluxes) provide a measure of the in vivo enzymatic activities that cannot be directly available from the transcriptomic, proteomic or metabolomic data alone, even extended with isotopic labeling measurements. Thus, fluxomics is an integral part of the bioinformatics and systems biology toolbox with significant applications in industrial biotechnology, metabolic or protein engineering, nutritional systems biology, toxicology, precision agriculture and crop improvement and network and systems medicine. A successful fluxomic analysis is based on the accuracy of quantitative metabolomic data (extra- and intra-cellular) and isotopic labeling measurements and the reconstruction of metabolic networks that describe the stoichiometry - and when available the regulation- of metabolic reactions. To-date, the community lacks standardized isotopic labeling data repositories, interoperability among the fluxomic tools and metabolic reaction databases and harmonized fluxomic training workflows. The workshop aims at discussing the challenges and the needs of the fluxomics community in harmonization of metabolic reaction databases, flux analysis tools and data repositories, and relevant training, towards standardized fluxomic workflows producing accurate, consistent and reproducible results.

Workshop objectives
The main workshop objectives are to unveil current issues in the standardization of workflows for fluxomic data analysis and discuss the directions for appropriately addressing them. This will be achieved through the following specific actions:

1. The workshop is to be organized as a peer session, where the presenters A-C, described above, will show in 10 min presentations specific aspects/current situation and relevant challenges in the following three parts of the fluxomics workflows: (a) quantitative metabolomic and isotopic labeling data deposition, (b) fluxomics tools and their interoperability and connectivity with extended metabolic reaction databases & (c) fluxomics training needs.
2. Then, the presenters in collaboration with the organizers will coordinate three different teams of the attendees focusing on these themes, respectively, collecting ideas about current needs, challenges and propositions for organizing respective standardization efforts within the fluxomics community (this part of the workshop will last ~30 min).
3. Finally the coordinators of each team will present the results of each discussion and lead a ~30 min final discussion combining the results of the four teams.

Workshop outcomes
Peer session - Interactive workshop enabling the participation of the attendees and collection of ideas/opinions from early career researchers too. Uncovering the current situation with standardization of fluxomic data and their analysis and determining the preferable directions of future work.

Theme Alignment: Technology

Presenters
Rima Kaddurah-Daouk (Duke University Medical Center), Almut Heinken (National University of Ireland), Naama Karu (Leiden University), Christina Jones (NIST), Almut Heinken (National University of Ireland), Richard Beger (FDA)

Description
Metabolism, and specifically the diversity of biochemical signatures produced by the trillions of microbes inhabiting our bodies, have received great attention and are an integral part of clinical and non-clinical studies. There is a pressing need to define the wide range of metabolites influenced by the gut bacteria under normal and gut dysbiosis conditions and to evaluate contribution to the metabolome and correlation with disease. The workshop aims to discuss the current state of the art and explore the methodologies and challenges in the pipeline followed to elucidate the interplay between the gut microbiome and the metabolome. In the session the importance of the gut microbiome in human health will be showcased together with the current knowledge framework on the impact of diet and the exposome on the gut microbiome. The technical aspects of fecal sample collection, metabolite recovery and stability will be discussed alongside the technologies used to detect and quantify microbial-host co-metabolites. Additionally, we will cover the scope of integrating metabolomics and metagenomics data and how it can facilitate biological interpretation.

Workshop objectives

1. Presentation of up to date knowledge on the role of the gut-microbiome and metabolome in health and disease
2. Demonstrate best practices for assessment of host-gut microbiota interactions

Workshop outcomes

1. Understand the importance of standardized practices in the study of the microbial-metabolite interplay
2. Dissemination of knowledge and highlight of the future perspectives of gut microbiome – metabolome research.

Theme Alignment: Plant, Food, Environmental and Microbial Applications

Presenters
Rob Vreeken (Janssen Pharmaceutica), Fadi Abdi (Biocrates), Mohamed Bedair (Bayer Crop Science), Adriana Carvalho de Souza (DSM), Doris Jacobs (Unilever)

Description
Over the past decade, Metabolomics has developed, evolved and matured to a level of capability and robustness useful for many applications in industry. However, the gap between academic research and industry application is still large. The potential of Metabolomics has not been completely exploited. In this workshop, we will make an effort to bridge this gap by pointing out opportunities for Metabolomics applications for pharmaceutical, food, agricultural and biotechnology industry. Representatives from different industries will share their views, experiences and ideas on how Metabolomics can create value for a company. Moreover, the opportunities may inspire Metabolomics scientists to pursue their career in industry. On the other hand, we will also talk about the challenges that lie ahead. Questions like what is needed to leverage Metabolomics in industry? How can we overcome bottlenecks in the Metabolomics workflow? How can regulatory aspects be considered? and What role does the Metabolomics Society play? will be addressed. We will conclude the session with a panel discussion where we invite the metabolomics community to express their opinions, ideas and questions.

Workshop objectives

1. To highlight opportunities and challenges for Metabolomics applications in industry
2. To discuss the role of the Metabolomics Society in bridging the gap between academia and industry
3. To inspire Metabolomics scientists

Workshop outcomes

1. A good overview on Metabolomics applications in different industries
2. Starting points on how to overcome major bottlenecks
3. Ways on how to tighten bonds between academia and industry

Theme Alignment: New Frontiers

Presenters
Gabi Kastenmueller (Helmholtz Zentrum München), Natal van Riel (Eindhoven University of Technology), Cynthia Musante (Pfizer), Shauna O’Donovan (Maastricht University), Fianne Sips (Eindhoven University of Technology)

Description
The workshop aims to bring together different communities, in particular researchers studying human metabolism using metabolomics or dynamic mathematical models. Workshop participants will learn about the opportunities that dynamic modelling has to offer in the context of precision medicine and pharmacometabolomics. Open challenges, including the data needed to develop such models, will be discussed. In particular, the workshop will focus on the application of time-series metabolomics data collected after a ‘metabolic challenge’, such as an oral glucose tolerance test (OGTT) or mixed meal test (MMT). Such tests are commonly used in nutrition studies and clinical studies in patients with metabolic disorders (type 2 diabetes, non-alcoholic fatty liver disease). The added value of mechanistic, dynamic models as quantitative and predictive framework for the analysis and interpretation of such data will be shown, which includes the possibility to disentangle intra-individual physiological heterogeneity from variation between individuals that associates with different health conditions.

Workshop objectives

1. To introduce basic principles of mathematical modelling using differential equations.
2. To demonstrate challenges associated with time-series metabolomics in humans.
3. To present case studies of dynamic modeling of time-series and tracer metabolomics.

Workshop outcomes

1. Understanding the potential of dynamic models of human metabolism to analyze time-series metabolomics.
2. Insights in the study design and quantitative approaches that are required.
3. Enhance the interaction of the metabolomics and metabolic modelling communities.

Theme Alignment: New Frontiers

Presenters
Isabel Orf, Agnieszka Smolinska, Pierre-Hugues Stefanuto, and Ana Rita Lima

Description
This workshops aims at giving an introduction to volatomics in human health, covering potential applications, particularities in comparison to classical metabolomics in human health, and analytical methods. Participants will learn from traditional presentations, but also be involved in a open panel discussion at the end of the workshop.

In order to cover both the applications of VOC analysis, as well as basic researchers all speakers are asked to combine their recent research topics with the discussion of one application/technical issue in the field.

Workshop objectives
TBD

Workshop outcomes
TBD

Theme Alignment: TBD