5th IMS

"Unlocking microbiome functions"

DAY-1 TUESDAY, 25th April 2023

8:30 Registration and Welcome Coffee
9:30 Opening and Welcome

9:45 Inaugural talk -  Perspectives on the impact and future of metaproteomics for microbiome research
Hettich Robert - Oak Ridge National Laboratory, USA

Session 1: Metaproteomics in Health and Disease

Chair: Uzzau Sergio

10:30 "Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease"
Wolf Maximilian - University of Bielefeld, Germany

10:45 "Ultra-fast metaproteomics profiling of type-2-diabetes oral microbiome using PASEF DIA"
Samodova Diana - University of Copenhagen, Denmark

11:00 "Evaluation of the effect of 93 chemicals on the Simplified Human Gut Microbiota Model (SIHUMIx) using a high-throughput in vitro screening and metaproteomics"
Castañeda-Monsalve Victor - Helmholtz Centre for Environmental Research, Germany

11:15 "Microbiome-derived metabolites as biomarkers for anal cancer screening"
Saenz Johan - University of Hohenheim, Germany

11:30 "Getting more insights in the respiratory microbiota of cystic fibrosis patients"
Hachemi Hamid - CEA - ProGénoMix Platform, France

11:45 "Metaproteomics and 16S rRNA analysis for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis"
Monteoliva Lucia - Universidad Complutense de Madrid, Spain

12:00 "Market outlook for metaproteomics, a feedback from Phylogene"
Metton Isabelle - Phylogene, France

12:30 - 14:00 LUNCH BREAK

14:00  Digging out the major plant-microbe interactions occurring in soil
Keynote - Lidbury Ian - University of Sheffield, England

Session 2: Environmental Metaproteomics

Chair: Matallana-Surget Sabine and Heldal Hagen Live

14:45 "What do we gain from scaled-down environmental metaproteomes? An example in a critical marine microbiome"
Held Noelle - ETH Zurich, Switzerland

15:00 "Data Independent Acquisition Metaproteomics of a Natural Marine System Reveal Peptide Predictors of Algal Blooms"
Timmins-Schiffman Emma - University of Washington, USA

15:15 "Effect of diet on the gut microbiota of the freshwater sentinel Gammarus fossarum "
Dumas Thibaut - CEA - ProGénoMix Platform, France 

15:30 "Dynamics of hyperhalophilic microbial communities submitted to long-term cyclic disturbances: a metagenomic and metaproteomic case study."
Bosch Rafael - Universitat de les Illes Balears (UIB), Spain

15:40 - 16:10 COFFEE BREAK

16:10 "Polysaccharide-degrading potential of microbiomes in agricultural field denitrification beds"
Arntzen Magnus - Norwegian University of Life Sciences, Norway

16:30 "The power of teamwork - Investigating the nutritional cycle of a symbiotic microbial community with tandem mass spectrometry"
D'Angelo Grace - Max Planck Institute of Marine Microbiology, Germany

16:40 "Unraveling Functionality and Taxonomic Shifts of a Hydrocarbon-Degrading Bacterial Consortia using Metaproteomics"
Al Haid Ali - University of Sheffield, England

16:50 "Evaluating the benefit of dia-PASEF approaches and sample-specific database strategies for metaproteomics of very complex microbiomes"
Schmit, Pierre-Olivier - Bruker, France

17:05 Poster session

DAY-2 Wednesday, 26th April 2023

09:00  Host-Microbiome Interactions in Early Life: Focus on Gut Fungi
Keynote - Pettersen Veronika K - UiT The Artic University of Norway, Norway

Session 3: New Methods in Metaproteomics

Chair: Seifert Jana

09:45 "Expanding the Characterization of Microbial Ecosystems using DIA-PASEF Metaproteomics"
Gomez Varela David - University of Vienna, Austria

10:05 "Optimized gene annotation for accurate protein sequence database construction in metaproteomics and data-independent acquisition metaproteomics"
Qiao Liang - Fudan University, China

10:20 "The first ground truth dataset for the assessment of differential expression analyses in metaproteomics and more"
Kunath Benoit - University of Luxembourg, Luxembourg

10:35 "Investigating rumen microbiome functions through seaweed-based nutritional manipulation"
Ferrillo Alessandra - Norwegian University of Life Sciences, Norway

10:45 - 11:15 COFFEE BREAK

11:15 "Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics"
Li Leyuan - University of Ottawa, Canada

11:30 "Unravelling metabolic heterogeneity and cross-feeding using metaproteomics and stable isotope labelling"
Kamrad Stephan - University of Cambridge, England

11:45 "Identification of newly synthesized proteins in microbial communities using BONCAT and click chemistry"
Hellwig Patrick - Otto von Guericke University Magdeburg, Germany

12:00 "Constructing a peptide library for faster human gut metaproteomics research"
Sun Zhongzhi - University of Ottawa, Canada

12:10 "MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database"
Cheng Kai - University of Ottawa, Canada

12:20 "Comparison of methods for processing fecal protein extracts on a multiwell plate for metaproteomic analysis"
Deledda Maria Antonietta - University of Sassari, Italy

12:30 - 14:00 LUNCH BREAK

"CAMPIs" Session

14:00 “CAMPIs: vision and objectives”
Hettich Robert- Oak Ridge National Laboratory, USA

14:10 “CAMPI2: Sample preservation”
Uzzau Sergio - University of Sassari, Italy

14:30 “CAMPI3: Extracting functional information”
Jagtap Pratik - University of Minnesota, USA

14:50 General discussion: “Improving methodologies & next CAMPI editions”

“Grand Challenge” Session

15:20 “Grand challenge: a prospectus”
Figeys Daniel - University of Ottawa, Canada

15:50 Round Table: “Opportunities for the community”
Figeys Daniel , Armengaud Jean, Hettich Robert


17:00 EuPA Metaproteomics Initiative Session

17:00 "EuPA MetaP Initiative: Structuring the community"
Van den Bossche Tim - Ghent University, Belgium
Kunath Benoit - University of Luxembourg, Luxembourg


20:30 IMS Dinner

DAY-3 Thursday, 27th April 2023

Session 4: Integrative Multiomics and Bioinformatics

Chair: Muth Thilo and Mesuere Bart

09:00 "An approach to integrate metagenomics, metatranscriptomics and metaproteomics data found in public resources"
Vizcaino Juan Antonio - EMBL-EBI, England

09:20 "The Peptonizer2000: Probability based taxonomic profiling of microbiome samples using PepGM and Unipept"
Holstein Tanja - Bundesanstalt für Materialforschung - und Prüfung, Germany

09:35 "Mistle: Metaproteomic index and spectral library search engine"
Nowatzky Yannek - Bundesanstalt für Materialforschung - und Prüfung, Germany

09:50 "Accessible metaproteomic database construction using iterative homology searching with CHEW"
Kleikamp Hugo - Aalborg University, Denmark

10:05 "Integrative meta-omics in Galaxy and beyond"
Schiml Valerie - Norwegian University of Life Sciences, Norway

10:20 "Unipept Desktop 2.0: construction of targeted reference protein databases for proteogenomics analyses"
Verschaffelt Pieter - Ghent University, Belgium

10:35 - 11:05 COFFEE BREAK

11:05 "Bioinformatic Workflow for Metaproteomic Analysis of Host-Microbe Dynamics in Clinical Samples"
Jagtap Pratik - University of Minnesota, USA

11:20 "PathwayPilot: A User-Friendly Tool for Visualizing Metabolic Pathways and Navigating the KEGG Database"
Vande Moortele Tibo - Ghent University, Belgium

11:30 Round Table – Metadata standards and Repository

Van den Bossche Tim, Heyer Robert, Vizcaino Juan-Antonio

12:30 - 14:00 LUNCH BREAK

Session 5: Trends in Metaproteomics

Chair: Jehmlich Nico

14:00 "Experimental validation that human microbiome phages use alternative genetic coding"
Peters Samantha - Oak Ridge National Laboratory, USA

14:15 "Fecal sample collection and room-temperature storage using swabs with preservation medium enables deep characterization of the human gut metaproteome"
Tanca Alessandro - University of Sassari, Italy

14:30 "A prospectus for tailoring metaproteomics database using MS/MS proteotyping"
Armengaud Jean - CEA - ProGénoMix Platform, France

14:45 "Untargeted data-independent acquisition for metaproteomics of complex microbial samples"
Suomi Tomi - University of Turku, Finland

14:55 "Exploring precision prebiotics to target the gut microbiome in Alzheimer"s disease"
Qin Hongye - University of Ottawa, Canada

15:15 Closing Talk & Perspectives for the field -  Metaproteomic applications in clinical research and drug development
Daniel Figeys - University of Ottawa, Canada

16:15 Concluding discussions and perspectives

17:00 End of the Symposium - Visit of the Pope’s Palace