Looking for guidance on Microbial Association Networks (MANs) Inference with samples from different metagenomics/metatranscriptomics studies

Question

[sebasar1245]

Hello,

I'm Sebastian, working on my MSc thesis, aiming to create a knowledge graph of the wastewater treatment microbiome. We're using Netcomi for constructing Microbial Association Networks (MANs) from MGnify database metagenomics and metatranscriptomics data. Specifically, we are using the CCLasso method. However, we are facing these challenges and have some questions:

• Insufficient Samples: Many MGnify studies lack enough samples for MANs inference, leading us to combine data from various studies. Is combining samples from different studies a viable strategy for MANs inference in this context?
• Data Heterogeneity: The data exhibits variability in sequencing technologies (e.g., Illumina Hiseq, Nextseq, Nanopore, etc), experiment types (metagenomics, assembly, or metatranscriptomics), sampling countries, and other variables. How best can we account for the data's heterogeneity in our analyses using Netcomi?

Your expertise and advice would be incredibly valuable. Thanks for your time and assistance.

Sebastian