On this first day, we will talk about the plans for the week, discuss our backgrounds and expectations, and listen to introductory presentations from the participants. 

The data generation part of the workshop will consist of a number of workstations illustrating the different steps of data generation: sample embedding and cryo-sectioning using Leica CM3050S, laser-microdissection using Leica LDM7, sample digestion and ultrasonication using Covaris LE220, library preparation using a Tecan Fluent 780 liquid-handler and pre-sequencing quality-check using qPCR and fragment analysis. The participants will visit all workstations in small groups and get hands-on experience using these different methods.

After a short recap of the previous day, we will hold lectures on the bioinformatic processing of the generated data. The topics covered will include generation of reference genome catalogues using long-read sequencing, obtaining quantitative estimations of microbial community compositions from micro-samples, and quality-filtering strategies to obtain high-quality data. The participants will have the opportunity to process data and start preparing their presentations.

The morning will be dedicated to data analysis, focusing on the unique spatial information obtained from micro-samples. In the afternoon, there will be lectures on complementary methods including fluorescence in-situ hybridisation and spatial metabolomics, which allow the validation and enrichment of micro-scale spatial metagenomic data.

On the last day, we will have a final summary of the course and listen to the final presentations of the participants. Finally, we will have a short round of course assessment and evaluation.