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closeA question to the authors
Posted by Robin1 on 08 May 2013 at 20:37 GMT
I'm a Secondary Science teacher and am using information from your paper as background for a lesson I am writing on the ecology of the human microbiome for life science courses, and I'm having some trouble with a few terms. One of the things I want my students to do is draw some inferences from Figure 4. Could you please explain what 'number of edges' means? Is an edge the region between niches? And could you also explain the positive vs. negative connectors. Does the positive line represent positive interactions among phyla, such as mutualistic interactions, and the negative connector, competitive interactions?
RE: A question to the authors
kfaust replied to Robin1 on 17 May 2013 at 09:01 GMT
Dear Robin1,
Figure 4 summarizes relationships between microbial classes. "Number of edges" in this context is the number of inter-class relationships between members of the two classes in the entire co-occurrence network. An edge in Figure 4 means that the members of the two classes connected by that edge are forming inter-class relationships more often than expected by chance.
Since the edges in Figure 4 represent aggregated relationships over many pairs, several mechanisms could contribute to each edge. For instance for a positive edge, some pairs might cross-feed, others might interact in a biofilm or belong to the same successional stage etc. For a negative edge, mechanisms could include adaptation to different niches or competition. Thus, edge interpretation is ambiguous. It is however interesting to observe that some classes (Bacilli and Actinobacteria) form only negative relationships with other classes, with most of these relationships occurring in the oral cavity. Our interpretation of this observation is that members of these classes are sufficiently functionally diverse to fill most available niches in the oral cavity, thereby excluding members from other classes.
I hope this answered your question,
Karoline Faust