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Table 3 Correlation and topological properties of the microbiome networks

From: A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community

 BacteriaFungi
NTEGBEGBFOCFOCMR15th day27th dayNT + FOCEGB + EGBFOC
Number of nodesa186252288174293279290283186158
Number of edgesb2666369843265669270551954826349333
Positive edgesc2386088043073899239035463541289284
Negative edgesd2828180191770315164912856049
Modularitye0.8730.7560.6310.7800.2430.3810.2460.2120.8710.828
Number of communityf39322934191521212925
Network diameterg77197111191077
Average path lengthh1.8352.1025.5331.8492.8373.4492.7672.8361.7901.589
Average degreei1.4302.5243.4171.87419.3489.69517.91417.0531.8762.108
Average clustering coefficientj0.1750.2080.1860.2180.2880.2540.2920.2640.2700.286
Densityk0.0080.0100.0120.0110.0660.0350.0620.0600.0100.013
  1. Note: R, cucumber root surrounding soil samples; M, soil sampled from the site between the cucumber root and inoculation site; 15th day, soils sampled on the 15th day; 27th day, soils sampled on the 27th day; NT, no FOC or strain EGB solid culture; EGB, strain EGB solid culture only; EGBFOC, both FOC and EGB solid culture; FOC, FOC only
  2. aMicrobial taxa (at the genus level) with at least one significant (p < 0.001) and strong (r > 0.7 or ≤ 0.7) correlation. R language and corr.test() were used for correlation analysis
  3. bNumber of connections obtained by R language analysis (R 2017, 4version 3.5.3)
  4. cPositive correlation (> 0.7 with p < 0.01) between two microbial taxa
  5. dNegative correlation (≥ 0.7 with p < 0.01) between two microbial taxa
  6. eStructure with high-density connections between nodes (inferred by Gephi)
  7. fA community is defined as a group of nodes that are densely connected internally (Gephi)
  8. gThe longest distance between nodes in the network, measured in number of edges (Gephi)
  9. hAverage network distance between all pair of nodes or the average length of all edges in the network (Gephi)
  10. iThe average number of connections of every node in the network (Gephi)
  11. jThe average clustering coefficient is defined as the mean value of individual coefficients (Gephi)
  12. kThe density used to measures how close the network is to complete. A complete graph has all possible edges and density equal to 1 (Gephi)