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Abstract
Microbial network construction is a popular explorative data analysis technique in microbiome research. Although a large number of microbial network construction tools has been developed to date, there are several issues concerning the construction and interpretation of microbial networks that have received less attention. The purpose of this perspective is to draw attention to these underexplored challenges of microbial network construction and analysis.
Highlights
To date, the microbial composition of thousands of samples from hundreds of ecosystems has been resolved, thanks to high-throughput sequencing [1]
It has been applied to identify taxa sharing a common role in an ecosystem such as oxygen-producing cyanobacteria in a seasonally stratified lake [3], to link taxa to a function of interest such as carbon flux in the oceans [4], and to predict biotic interactions [5]
In contrast to networks built for macroorganisms, which are based on observations of biotic interactions between individuals, a microbial network is constructed from a count table obtained from sequencing data
Summary
The microbial composition of thousands of samples from hundreds of ecosystems has been resolved, thanks to high-throughput sequencing [1]. A node in a microbial network can represent different units depending on the selected sequencing data processing pipeline and taxonomic level, and the choice of the unit matters for network construction and interpretation. The challenge of rare taxa discussed below is less pronounced for a microbial network constructed on class level.
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