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Improvements in sequencing technologies and reduced experimental costs haveresulted in a vast number of studies generating high-throughput data. Althoughthe number of methods to analyze these "omics" data has also increased,computational complexity and lack of documentation hinder researchers fromanalyzing their high-throughput data to its true potential. In this chapter wedetail our data-driven, transkingdom network (TransNet) analysis protocol tointegrate and interrogate multi-omics data. This systems biology approach hasallowed us to successfully identify important causal relationships betweendifferent taxonomic kingdoms (e.g. mammals and microbes) using diverse types ofdata.

Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions