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Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities in complex and contiguous environments. They engage in numerous inter- and intra- kingdom interactions which can be inferred from microbiome profiling data. In particular, network-based approaches have proven helpful in deciphering complex microbial interaction patterns. Here we give an overview of state-of-the-art methods to infer intra-kingdom interactions ranging from simple correlation- to complexdoi:10.1016/j.csbj.2021.05.001 pmid:34093985 pmcid:PMC8131268 fatcat:ba6wne7jprat3jgnngfbzkebq4