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Network analysis suggests a potentially 'evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities.

Sam Ma Z, Guan Q, Ye C, Zhang C, Foster JA, Forney LJ - Sci Rep (2015)

Bottom Line: To the best of our knowledge, there has been no report on the bacterial interactions within the milk microbiome.One sub-network is a fully connected complete graph consisting of seven genera as nodes and all of its pair-wise interactions among the bacteria are facilitative or cooperative.In contrast, the interactions in the other sub-network of eight nodes are mixed but dominantly cooperative.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources &Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.

ABSTRACT
The critical importance of human milk to infants and even human civilization has been well established. Yet our understanding of the milk microbiome has been limited to cataloguing OTUs and computation of community diversity. To the best of our knowledge, there has been no report on the bacterial interactions within the milk microbiome. To bridge this gap, we reconstructed a milk bacterial community network based on Hunt et al. Our analysis revealed that the milk microbiome network consists of two disconnected sub-networks. One sub-network is a fully connected complete graph consisting of seven genera as nodes and all of its pair-wise interactions among the bacteria are facilitative or cooperative. In contrast, the interactions in the other sub-network of eight nodes are mixed but dominantly cooperative. Somewhat surprisingly, the only 'non-cooperative' nodes in the second sub-network are mutually cooperative Staphylococcus and Corynebacterium that include some opportunistic pathogens. This potentially 'evil' alliance between Staphylococcus and Corynebacterium could be inhibited by the remaining nodes that cooperate with one another in the second sub-network. We postulate that the 'confrontation' between the 'evil' alliance and 'benign' alliance and the shifting balance between them may be responsible for dysbiosis of the milk microbiome that permits mastitis.

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Related in: MedlinePlus

Bacterial network of the human milk microbiome reconstructed using the data sets of Hunt et al.(2011): Figure (1a) and (1b) show the two disconnected sub-networks (components) of the breast milk bacterial network; Figure (1c) and (1d) are the same components, corresponding to (1a) and (1b), respectively, assuming the Staphylococcus and Corynebacterium nodes were eliminated. The green line represents a positive correlation (cooperative interaction) while the red line represents a negative correlation (non-cooperative interaction). Obviously, when the two mutually cooperative players Staphylococcus and Corynebacterium are removed, the whole network becomes totally cooperative (Figure 1c & 1d).
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f1: Bacterial network of the human milk microbiome reconstructed using the data sets of Hunt et al.(2011): Figure (1a) and (1b) show the two disconnected sub-networks (components) of the breast milk bacterial network; Figure (1c) and (1d) are the same components, corresponding to (1a) and (1b), respectively, assuming the Staphylococcus and Corynebacterium nodes were eliminated. The green line represents a positive correlation (cooperative interaction) while the red line represents a negative correlation (non-cooperative interaction). Obviously, when the two mutually cooperative players Staphylococcus and Corynebacterium are removed, the whole network becomes totally cooperative (Figure 1c & 1d).

Mentions: The pair-wise relationships among 15 genera were measured by Spearman rank correlation coefficients with p-value of 0.05, and the computed values of Spearman correlation coefficients with R-statistics package (www.r-project.org) were feed into Cytoscape network analysis software34 and Gephi35. The Graphcrunch236 software was applied to further compare the reconstructed milk microbiome network with several standard models of complex networks. The results of network analysis are exhibited in Figure 1 and Table 1.


Network analysis suggests a potentially 'evil' alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities.

Sam Ma Z, Guan Q, Ye C, Zhang C, Foster JA, Forney LJ - Sci Rep (2015)

Bacterial network of the human milk microbiome reconstructed using the data sets of Hunt et al.(2011): Figure (1a) and (1b) show the two disconnected sub-networks (components) of the breast milk bacterial network; Figure (1c) and (1d) are the same components, corresponding to (1a) and (1b), respectively, assuming the Staphylococcus and Corynebacterium nodes were eliminated. The green line represents a positive correlation (cooperative interaction) while the red line represents a negative correlation (non-cooperative interaction). Obviously, when the two mutually cooperative players Staphylococcus and Corynebacterium are removed, the whole network becomes totally cooperative (Figure 1c & 1d).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4317708&req=5

f1: Bacterial network of the human milk microbiome reconstructed using the data sets of Hunt et al.(2011): Figure (1a) and (1b) show the two disconnected sub-networks (components) of the breast milk bacterial network; Figure (1c) and (1d) are the same components, corresponding to (1a) and (1b), respectively, assuming the Staphylococcus and Corynebacterium nodes were eliminated. The green line represents a positive correlation (cooperative interaction) while the red line represents a negative correlation (non-cooperative interaction). Obviously, when the two mutually cooperative players Staphylococcus and Corynebacterium are removed, the whole network becomes totally cooperative (Figure 1c & 1d).
Mentions: The pair-wise relationships among 15 genera were measured by Spearman rank correlation coefficients with p-value of 0.05, and the computed values of Spearman correlation coefficients with R-statistics package (www.r-project.org) were feed into Cytoscape network analysis software34 and Gephi35. The Graphcrunch236 software was applied to further compare the reconstructed milk microbiome network with several standard models of complex networks. The results of network analysis are exhibited in Figure 1 and Table 1.

Bottom Line: To the best of our knowledge, there has been no report on the bacterial interactions within the milk microbiome.One sub-network is a fully connected complete graph consisting of seven genera as nodes and all of its pair-wise interactions among the bacteria are facilitative or cooperative.In contrast, the interactions in the other sub-network of eight nodes are mixed but dominantly cooperative.

View Article: PubMed Central - PubMed

Affiliation: Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources &Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.

ABSTRACT
The critical importance of human milk to infants and even human civilization has been well established. Yet our understanding of the milk microbiome has been limited to cataloguing OTUs and computation of community diversity. To the best of our knowledge, there has been no report on the bacterial interactions within the milk microbiome. To bridge this gap, we reconstructed a milk bacterial community network based on Hunt et al. Our analysis revealed that the milk microbiome network consists of two disconnected sub-networks. One sub-network is a fully connected complete graph consisting of seven genera as nodes and all of its pair-wise interactions among the bacteria are facilitative or cooperative. In contrast, the interactions in the other sub-network of eight nodes are mixed but dominantly cooperative. Somewhat surprisingly, the only 'non-cooperative' nodes in the second sub-network are mutually cooperative Staphylococcus and Corynebacterium that include some opportunistic pathogens. This potentially 'evil' alliance between Staphylococcus and Corynebacterium could be inhibited by the remaining nodes that cooperate with one another in the second sub-network. We postulate that the 'confrontation' between the 'evil' alliance and 'benign' alliance and the shifting balance between them may be responsible for dysbiosis of the milk microbiome that permits mastitis.

Show MeSH
Related in: MedlinePlus