Table 1 Relevant properties of co-occurrence networks

Size

Nodes

Each node represents a bacterial/archaeal or fungal OTU.

Larger networks contain a greater number of interacting (co-occurring or co-excluding) OTUs.

332

335

335

335

139

142

144

144

Size

Edges

Edges indicate significant co-occurrence or co-exclusion relationships.

Co-occurrence could represent a number of ecological interactions, from predator-prey relationships to commensalism to shared ecological niches [12]. Co-exclusion may represent competition or inhibition.

3698

2995

2088

2261

616

457

669

349

Degree

Mean degree

Degree refers to the number of edges a given node has. Mean degree is the average degree across all nodes in a network [10].

Higher mean degree indicates more co-occurrence or co-exclusion relationships per OTU.

22.28

17.88

12.47

13.50

8.86

6.44

9.29

4.85

Cohesion

Density

Density is defined as the ratio of the number of edges in a given network to the number of edges possible for that many nodes.

High-density networks contain a large proportion of interacting OTUs.

0.067

0.054

0.037

0.040

0.064

0.046

0.065

0.034

Centrality

Centralization index

The degree of organization of a network around specific (central) nodes.

High scores indicate that networks are centralized around one or a few focal nodes; low scores indicate decentralized structure [103].

0.17

0.15

0.11

0.13

0.17

0.10

0.16

0.071

Modularity

Modularity index

Edges belonging to a module minus those that would be expected from a random network with the same number of edges [104].

High modularity indicates more structured communities within a network [104].

0.44

0.49

0.66

0.63

0.45

0.72

0.39

0.77

Number of modules

Modules are groups of OTUs that interact more closely with one another than with other OTUs.

Can represent overlapping ecological niches or phylogenetic groups [19].

14

9

19

13

18

13

16

13