Network analysis methods for studying microbial communities: A mini review

Monica Steffi Matchado, Michael Lauber, Sandra Reitmeier, Tim Kacprowski, Jan Baumbach, Dirk Haller, Markus List
2021 Computational and Structural Biotechnology Journal  
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 complex
more » ... ditional dependence-based methods. We highlight common biases encountered in microbial profiles and discuss mitigation strategies employed by different tools and their trade-off with increased computational complexity. Finally, we discuss current limitations that motivate further method development to infer inter-kingdom interactions and to robustly and comprehensively characterize microbial environments in the future.
doi:10.1016/j.csbj.2021.05.001 pmid:34093985 pmcid:PMC8131268 fatcat:ba6wne7jprat3jgnngfbzkebq4