Advancing Research Skills: Training on Microbial Metaproteomics

Between 5–23 May 2025, three Junior Research Fellows: Deep Bhattacharya, Evgenyi Brik, Chanaka Nishan Premathilaka from the Institute of Veterinary Medicine and Animal Sciences, took part in international training cycle on Advanced Microbial Metaproteomics, hosted in hybrid form under the guidance of Senior University Lecturer Dr. Mikael Niku from the University of Helsinki. The three-week hybrid programme focused on developing theoretical knowledge and practical skills in metaproteomics, a cutting-edge area at the intersection of microbiology, proteomics, and computational biology. 

Led by Dr. Mikael Niku, Senior University Lecturer and Adjunct Professor at the University of Helsinki, the training was designed to introduce participants to advanced proteomic analysis tools and workflows used to study microbial communities, especially in relation to extracellular vesicle (EV) proteomics. Dr. Niku, known for his work on maternal microbiota and fetal immune development, brought both scientific depth and pedagogical expertise to the course.

The training journey unfolded in three carefully structured phases:

• The first week offered a foundation of knowledge through curated readings and access to a private Moodle platform, where participants explored essential literature and pre-recorded lectures.

• The second week brought students together for interactive, on-site sessions. Here, they engaged in expert-led lectures, collaborative discussions, and live data analysis workshops.

• The final week was devoted to completing individual analyses and preparing project reports that synthesized theory with practice.
  
  

The programme featured a stellar lineup of guest lecturers from top European research institutions:

🔬 Dr. Valerie Schiml guided students through metaproteomic workflows, data acquisition techniques (DDA and DIA), and the use of MaxQuant and Perseus for data analysis.

🧬 Dr. Mohieddin Jafari shared insights into the evolution of proteomics as a discipline, highlighting its integration with systems biology and bioinformatics.

🧫 Dr. Anna Kaisanlahti explored how microbial extracellular vesicles from the gut influence fetal development, offering a compelling view of molecular cross-talk in the maternal–fetal interface.

💻 Dr. Tanja Holstein conducted a hands-on session on Unipept, demonstrating how peptide-based metaproteomics can reveal taxonomic and functional insights from complex microbial datasets.

Participants left the course equipped with a robust skill set, including:

• Confidence in analyzing proteomics data using MaxQuant and Unipept

• Understanding of mass spectrometry workflows and data interpretation

• Practical experience with bioinformatics tools that are easily transferable to their personal research environments

• A deeper appreciation of how microbial proteomics intersects with developmental biology, immunology, and translational research
  
  

This training cycle not only expanded scientific knowledge—it fostered collaboration, curiosity, and the development of critical research skills that participants will carry forward in their careers. It stands as a model for interdisciplinary learning and international academic exchange in the field of microbiome and proteomic sciences.