Integrating local and global information to identify influential nodes in complex networks

Mukhtar, Mohd Fariduddin; Abas, Zuraida Abal; Baharuddin, Azhari Samsu; Norizan, Mohd Natashah; Fakhruddin, Wan Farah Wani Wan; Minato, Wakisaka; Rasib, Amir Hamzah Abdul; Abidin, Zaheera Zainal; Rahman, Ahmad Fadzli Nizam Abdul; Anuar, Siti Haryanti Hairol

doi:10.1038/s41598-023-37570-7

Cited by 11 publications

(3 citation statements)

References 39 publications

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“…Rather than existing in isolation, microorganisms co-occur in ecological networks that determine the stability of the entire ecosystem and thus the plant's response to biotic/abiotic stresses [23]. The drivers of these networks are the taxa termed as the "most in uential nodes" [24].…”

Section: Discussionmentioning

confidence: 99%

Microbial Influencers and Cotton Leaf Curl Disease (CLCuD) susceptibility: A network perspective

Aqueel,

Badar,

Ijaz

et al. 2024

Preprint

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Background Biotic stresses such as plant viruses e.g. Cotton Leaf Curl Virus (CLCuV) can alter root-associated and leaf-associated microbial diversity in plants. There are complex ecological dynamics at play with each microbe contributing to multitude of biotic and abiotic interactions thus deciding the stability of the plant’s ecosystem in response to disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions as well as the limitations with respect to the depth of sequencing. There is also no real consensus on which network-wide statistics to identify the influential microbial players in a network. Guided by latest developments in network science, particularly, recently published metrics such as Integrated View of Influence (IVI), and some other centrality measures, in this study, we provide an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the Cotton Leaf Curl Disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. Results Our results indicate that the CLCuD resistant Gossypium arboreum possesses an equal share of keystone species which helps it in withstanding ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes whereas in the susceptible variety they are present in the rhizosphere. Based on hubness score, spreading score and IVI, the top 10 occurring keystone species in FDH-228 (resistant) variety were Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. Conclusion Crop health is dependent on the microbiome influencers in its ecosystem. The CLCuD resistant Gossypium arboreum has an abundance of Firmicutes and only limited phyla as opposed to the susceptible variety where there is a vast variety of bacterial phyla in its top keystone species. The stability of the FDH-228 network helps it in handling perturbations better. This approach helps us in deciphering the diseased and healthy plant’s response to viral disease which may be microbially mediated.

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Section: Discussionmentioning

confidence: 99%

Microbial Influencers and Cotton Leaf Curl Disease (CLCuD) susceptibility: A network perspective

Aqueel,

Badar,

Ijaz

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Rather than existing in isolation, microorganisms co-occur in ecological networks that determine the stability of the entire ecosystem and thus the plant’s response to biotic/abiotic stresses ( Afridi et al, 2022 ). The drivers of these networks are the taxa termed the “most influential nodes” ( Mukhtar et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective

Aqueel,

Badar,

Ijaz

et al. 2024

Front. Microbiol.

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Biotic stresses, such as plant viruses, e.g., cotton leaf curl virus (CLCuV), can alter root-associated and leaf-associated microbial diversities in plants. There are complex ecological dynamics at play, with each microbe contributing to a multitude of biotic and abiotic interactions, thus deciding the stability of the plant’s ecosystem in response to the disease. Deciphering these networks of interactions is a challenging task. The inferential research in microbiome is also at a nascent stage, often constrained by the underlying analytical assumptions and the limitations with respect to the depth of sequencing. There is also no real consensus on network-wide statistics to identify the influential microbial players in a network. Guided by the latest developments in network science, including recently published metrics such as Integrated View of Influence (IVI) and some other centrality measures, this study provides an exposé of the most influential nodes in the rhizospheric and phyllospheric microbial networks of the cotton leaf curl disease (CLCuD) susceptible, partially tolerant, and resistant cotton varieties. It is evident from our results that the CLCuD-resistant Gossypium arboreum possesses an equal share of keystone species, which helps it to withstand ecological pressures. In the resistant variety, the phyllosphere harbors the most influential nodes, whereas in the susceptible variety, they are present in the rhizosphere. Based on hubness score, spreading score, and IVI, the top 10 occurring keystone species in the FDH-228 (resistant) variety include Actinokineospora, Cohnella, Thermobacillus, Clostridium, Desulfofarcimen, and MDD-D21. Elusimicrobia, Clostridium-sensu-stricto_12, Candidatus woesebacteria, and Dyella were identified as the most influential nodes in the PFV-1 (partially tolerant) variety. In the PFV-2 (susceptible) variety, the keystone species were identified as Georginia, Nesterenkonia, Elusimicrobia MVP-88, Acetivibrio, Tepedisphaerales, Chelatococcus, Nitrosospira, and RCP2-54. This concept deciphers the diseased and healthy plant’s response to viral disease, which may be microbially mediated.

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“…BC is the fraction of all shortest paths in the network that passes through a given node. The DC, the number of links connected to a node, is one of the most common centrality measures [ 40 ].…”

Section: Clinical Assessmentmentioning

confidence: 99%

Topological alterations in white matter anatomical networks in cervical dystonia

Zhang,

Luo,

Zhong

et al. 2024

BMC Neurol

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Background Accumulating neuroimaging evidence indicates that patients with cervical dystonia (CD) have changes in the cortico-subcortical white matter (WM) bundle. However, whether these patients’ WM structural networks undergo reorganization remains largely unclear. We aimed to investigate topological changes in large-scale WM structural networks in patients with CD compared to healthy controls (HCs), and explore the network changes associated with clinical manifestations. Methods Diffusion tensor imaging (DTI) was conducted in 30 patients with CD and 30 HCs, and WM network construction was based on the BNA-246 atlas and deterministic tractography. Based on the graph theoretical analysis, global and local topological properties were calculated and compared between patients with CD and HCs. Then, the AAL-90 atlas was used for the reproducibility analyses. In addition, the relationship between abnormal topological properties and clinical characteristics was analyzed. Results Compared with HCs, patients with CD showed changes in network segregation and resilience, characterized by increased local efficiency and assortativity, respectively. In addition, a significant decrease of network strength was also found in patients with CD relative to HCs. Validation analyses using the AAL-90 atlas similarly showed increased assortativity and network strength in patients with CD. No significant correlations were found between altered network properties and clinical characteristics in patients with CD. Conclusion Our findings show that reorganization of the large-scale WM structural network exists in patients with CD. However, this reorganization is attributed to dystonia-specific abnormalities or hyperkinetic movements that need further identification.

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Integrating local and global information to identify influential nodes in complex networks

Cited by 11 publications

References 39 publications

Microbial Influencers and Cotton Leaf Curl Disease (CLCuD) susceptibility: A network perspective

Microbial Influencers and Cotton Leaf Curl Disease (CLCuD) susceptibility: A network perspective

Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective

Topological alterations in white matter anatomical networks in cervical dystonia

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