June 2023 Newsletter

From the co-administrators

Dear members of the Metaproteomics Initiative,

We are delighted to bring you the third edition of our newsletter! Here, our primary goal is to foster communication and interaction among community members by sharing valuable information. In this edition, we provide you with updates from our monthly meetings, CAMPI status updates, the presence of our Initiative at international conferences, and research highlights contributed by members like you! We continue to be grateful for the content you share, and we encourage you to reach out to us if you would like your research to be featured in future newsletters.

Your continued support and active participation in the Metaproteomics Initiative are greatly appreciated. We hope that many of you can join us and engage in discussions regarding the Initiative and its projects.

Kind regards, Tim Van Den Bossche and Benoit Kunath

Executive Board Digest

The Metaproteomics Initiative joins HUPO!

HUPO logo

We are thrilled to announce that the Metaproteomics Initiative is now also recognized as an Initiative by the Human Proteome Project (HUPO, https://www.hupo.org/Metaproteomics), next to our existing recognition from the European Proteomics Association (EuPA, https://eupa.org/eupa-initiatives/metaproteomics/).

More specifically, we’ll become part of the Biology/Disease-driven pillar of the Human Proteome Project (B/D-HPP). This project focuses on supporting the broad application of state-of the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human diseases. Metaproteomics, as you all know, enables us to study the complex interactions between microbial communities and their human hosts. By strengthening ties between HUPO and the Metaproteomics Initiative, we aim to further unravel the role of microbiomes in human health and disease.

We will, of course, keep you updated about this collaboration in future newsletters as we embark on this exciting journey together!

Standardization in metaproteomics

We invite you to participate in a Google survey aimed at addressing the challenges of standardization in metaproteomics. As the field rapidly evolves with customized protocols and refined analysis methods, reproducibility and comparability between studies become increasingly difficult.

Your insights will help to identify the most pressing priorities and steps needed to achieve standardized practices, ensuring the reliability and reproducibility of metaproteomic experiments. Therefore, we ask for your participation in a 5-minute survey to shape the future of this field.

Thanks in advance for your contribution!

CAMPI-2: Sample handling

CAMPI-2 has led to a collaboration between 10 laboratories in Europe and the US, where five protocols for metaproteome stabilization are being compared. These protocols have been designed for two different microbiota samples: human feces and soil. This will provide a standard procedure for sample handling, one of the main challenges in metaproteomics studies.

Here’s what’s been happening: The CAMPI-2 participants have successfully stabilized the entire sample set, including soil and stool samples, using the different protocols. We are now moving on to the next crucial step: sample processing, which involves protein extraction and digestion. We aim to complete this phase by the end of July.

CAMPI-3: Taxonomic and Functional Annotation of Metaproteomics Data

CAMPI-3, the latest study initiated by the Metaproteomics Initiative, has been launched.

The CAMPI-3 study aims to:

To facilitate your participation, we have prepared two datasets: a ground-truth “synthetic community” dataset and a biological dataset. These MS datasets and associated protein databases will serve as the foundation for your analyses. To get involved, we encourage you to download the data from https://metaproteomics.org/campi3/download and leverage the provided reporting templates and metrics to ensure standardized sharing of results.

We value your contributions and understand the importance of maintaining confidentiality. Rest assured that all submissions will be treated with the utmost confidentiality and kept anonymous throughout the study.

If you have any questions or require further information about CAMPI-3, please visit z.umn.edu/campi3faqs. Moreover, the project coordinators (pjagtap@umn.edu, peterssl@ornl.gov and benoit.kunath@uni.lu) are ready to assist you at every step of the process. Don’t hesitate to reach out to them.

Ready to submit your results? Please contact Anonymizer at ningzhibin@gmail.com

Recap of the 5th Metaproteomics Symposium: Unlocking Microbiome Functions

The historical Popes’ Palace in Avignon, France, set the stage for the highly anticipated 5th Metaproteomics Symposium, held on April 25-27, 2023, under the auspices of EuPA. This remarkable event brought together 110 participants from around the world to share their ground-breaking discoveries and innovations in the field of metaproteomics. Under the theme “Unlocking microbiome functions”, the symposium served as a dynamic platform for advancing our understanding of microbial communities and their intricate functioning.

The symposium commenced with an enlightening overview by Robert Hettich, who provided valuable perspectives on the future impact of metaproteomics in microbiome research. The captivating keynote presentations further underscored the vast potential of metaproteomics. Notably, Ian Lidbury delved into the exploration of major plant-microbe interactions occurring in soil, shedding light on their crucial significance. Additionally, Veronika Pettersen focused on host-microbiome interactions in early life, specifically highlighting the role of gut fungi. These insightful talks demonstrated the tremendous progress made in the field and showcased the immense potential of metaproteomics in addressing pressing scientific challenges. Daniel Figeys further broadened the horizons presenting the prospects of metaproteomics in clinical research and drug development.

The symposium featured five different sessions dedicated to unraveling the intricate dynamics of microbial communities in various fields, emphasizing the role of metaproteomics in deciphering complex community interactions. State-of-the-art technologies driving metaproteomics research forward were showcased, including the exploration of DIA methods and advanced bioinformatics tools specifically designed for metaproteomics analysis.

Beyond the scientific sessions, the symposium fostered a spirit of collaboration and partnership, made possible within the Metaproteomics Initiative framework. Attendees had the opportunity to engage in interactive sessions, present posters, and participate in networking events, facilitating vibrant discussions and knowledge sharing. Dedicated roundtable discussions offering a prospectus on a ‘Grand challenge’ and ‘Metadata standards and Repository’ provided a platform to highlight emerging opportunities for the metaproteomics community and address its needs. A session dedicated to the CAMPIs benchmarks allowed participants to gain deeper insights into these studies and their goals while providing input for future CAMPI editions.

The 5th Metaproteomics Symposium concluded with an air of enthusiasm, leaving attendees with new insights, potential collaborations, and a renewed passion for metaproteomics research. We extend our heartfelt gratitude to the speakers, sponsors, and participants who contributed to the resounding success of the symposium.

Houston, We Have a (Microbiome) Problem… (Notes from Metaproteomics@ASMS2023)

The 71st edition of the annual conference for the American Society for Mass Spectrometry (Houston, June 4-8, 2023) which was attended by more than 6000 researchers, also had poster presentations, talks, workshop and a bioinformatics hub session on metaproteomics.

Subina Mehta (University of Minnesota) presented talk on ovarian cancer metaproteomics and Pierre-Olivier Schmit (Bruker Daltonique) presented talk on and DIA-PASEF for metaproteomics. Researchers from Pacific Northwest National Laboratory (Mary Lipton, Paul Piehowski, Kristin Burnum-Johnson), Oakridge National Laboratory (Robert Hettich, Samantha Peters), Ghent University (Tim Van Den Bossche, Tanja Holstein) and University of Minnesota (Pratik Jagtap, Timothy Griffin, Andrew Rajczewski) presented posters and attended the workshop on “Houston, We Have a Microbiome Problem (…and how the Metaproteomics Initiative aims to solve it)” and Bioinformatics Hub on “Metaproteomics”.

The Wednesday evening workshop was attended by almost 50 attendees. The in-person attendees were welcomed by Timothy Griffin, highlighting the importance of mass spectrometry based metaproteomics research. This introduction was followed by Tim Van Den Bossche, who introduced the Metaproteomics Initiative and invited the attendees to join the various activities of the Initiative. Bob Hettich presented the updates from the International Metaproteomics Symposium and also the rationale behind the CAMPI Study.

These presentations were followed by a presentation by Pratik Jagtap announcing the CAMPI3 study. Samantha Peters took part in the discussion and answered questions about some of the details of the CAMPI-3 sample types. Attendees also asked questions regarding plans for the future of Metaproteomics Initiative. The presenters and audience had a lively discussion that covered multiple aspects of metaproteomics ranging from sample preparation to mass spectrometry acquisition to bioinformatics analysis and biological interpretation. Active recruitment identified about 10 attendees who expressed interest in participating in the CAMPI-3 bioinformatics campaign. At the conclusion of the workshop, about a dozen participants hung around for more detailed and personalized discussions.

The participants were invited to the Bioinformatics Hub on Metaproteomics at the ASMS on Thursday morning for more expanded discussions on these and related topics. At the Bioinformatics Hub, attendees expressed an interest in a “Beginners Guide to Metaproteomics” manuscript.

Save the Date

6th International Metaproteomics Symposium

We’re thrilled to announce that the next International Metaproteomics Symposium will be held in the stunning Norway. Save the date for this exciting event, scheduled for January 2025!

Stay tuned for further updates.

Metaproteomics articles you don’t want to miss

Our Gut Bugs Function Redundantly

Diversity matters, so does redundancy. Functional redundancy (FR) - the difference between taxonomic and functional diversity, describes the extent to which taxonomically distinct organisms can contribute to ecosystem functioning in similar ways.

FR has been shown to be a common event in the human gut microbiome. However, most previous studies of FR in the human microbiome have been conceptual rather than quantitative. The recent advances in deep metaproteomic techniques allow us to construct a protein-content network of human gut microbiomes and quantify the FR on the proteome level (i.e. FRp).

What does the FRp metric imply? A decrease in FRp may be associated with impaired microbiome stability and resilience. We show that naturally occurring protein-content network of gut microbiomes can preserve high taxonomic richness and high FRp at the same time, while environmental factors such as specific xenobiotics (e.g. antibiotics) and inflammatory bowel disease can significantly decrease the FRp of an individual’s microbiome.

We still have not fully understood the phenomenon of high FRp in our gut microbiome. What does it look like in some other diseases? How does it relate to the resistance and resilience of our microbiota? Can we leverage FRp to combat gut microbiome dysbiosis and diseases? Metaproteomics will continue to facilitate these exciting future explorations, since it opens the door to deepening the understanding of our microbiome functional ecology by examining the proteins – the implementers of microbiome functions.

Read the paper: https://www.nature.com/articles/s41467-023-39149-2

DIA-PASEF opens new frontiers for metaproteomics

David Gómez-Varela’s group at the University of Vienna presented the first report using DIA-PASEF in metaproteomics. The data showed very significant improvements in protein and peptide quantification depth, sensitivity, and reproducibility in complex gut mouse samples. Application to a preclinical disease model of chronic pain revealed new host-microbiome interactions leading to potential clinical interventions.

Building on this first work, new data from Gómez-Varela’s group presented at ASMS 2023 showed the possibility to quantify >45,000 protein groups and hundreds of species and functional pathways from a single LC-MS experiment. They were able to do this using sub-nanomolar peptide amounts (proteins and species could be detected even with only 10 picograms!) and in a short 22-minute effective LC gradient.

The group is actively working on new methodological and bioinformatic developments to push the limits towards deep, reproducible, and ultra-fast profiling of hundreds of samples per day. These new levels of sensitivity could eventually enable single-cell-type analysis in metaproteomics.

Mix24X, a lab-assembled reference

Our team has proposed Mix24X, a new reference dataset to evaluate interpretation procedures for tandem mass spectrometry proteotyping of complex samples, such as microbiomes. This reference is an artificial assembly of individual peptidomes from 24 bacterial reference species.

Mix24X encompasses a wide range of microbial diversity, covering 20 distinct genera and 5 bacterial phyla. Notably, it includes challenging cases such as Shigella flexneri and Escherichia coli, which exhibit significant phylogenetic similarity, as well as several highly sequenced clades and distantly related species. Although Mix24X does not fully replicate the complexity of a true microbiome sample, which comprises numerous species and challenging extracellular matrices, it can help to understand how your data processing pipeline performs in terms of sensitivity and accuracy.

To facilitate ease of use, Mix24X is readily available for download from the PRIDE repository. This dataset can be used to improve bioinformatic tools dedicated to proteotyping microorganisms from complex samples, or to extracting taxonomic or functional information from metaproteomic experiments.

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