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Fabbrini et al. Microbiome Res Rep 2023;2:25 https://dx.doi.org/10.20517/mrr.2023.25 Page 15 of 18

Edge - In a network analysis, an edge is basically the graphical representation of an interaction between
nodes, which can be positive or negative, weighted and directed or not. In a microbiome network, edges are
typically just positive or negative and weighted, showing a correlation in terms of abundance.

Module - Module refers to a collection of nodes that are closely interconnected with each other, and with
relatively fewer connections to nodes outside the group.

Node characteristics that define the node centrality in a network.
Degree - This refers to the count of edges that connect a chosen node with the rest of the nodes in the
network.

Betweenness centrality - It measures the extent to which a vertex lies on paths between other vertices/
nodes.

Closeness centrality - Reciprocal of distance sums from a specific node to all reachable nodes.

Distance – The total weight of all edges within the shortest path between two nodes.

Hub node - A node that has more connectivity within the network than other nodes, based on the node
centrality values.

Keystone node - A node crucial for the observed network structure, meaning that removing this node from
the network alters significatively its layout. Not all hub nodes are keystones and vice versa, as the definition
of the two differs significantly. Brute force leave-one-out approaches can be used to detect this type of
node [40,75] .

DECLARATIONS
Author contributions
Conceptualization: Fabbrini M, Scicchitano D, Rampelli S
Formal analysis: Fabbrini M, Scicchitano D
Writing-original draft preparation: Fabbrini M, Scicchitano D
Writing-draft revision: Fabbrini M, Scicchitano D, Candela M, Rampelli S, Turroni S
Funding acquisition: Rampelli S, Turroni S
All authors contributed to the article and approved the submitted version.

Availability of data and materials
All the sequences used for the case study are publicly available and the accession list can be found in
Supplementary Data 1.

Financial support and sponsorship
None.

Conflicts of Interest
The authors declare no conflicts of interest.