In network science, change is good: Historically, network science focused on static networks, in which nodes are connected by permanent links. However, in networked systems ranging from protein-protein interactions to social networks, links change. Although it might seem that permanent links would make it easier to control a system, Li et al. demonstrate that temporality has advantages in real and simulated networks. Temporal networks can be controlled more efficiently and require less energy than their static counterparts. Science , this issue p. 1042

Although the taxonomic composition of the human microbiome varies tremendously across individuals, its gene composition or functional capacity is highly conserved — implying an ecological property known as functional redundancy. Such functional redundancy has been hypothesized to underlie the stability and resilience of the human microbiome, but this hypothesis has never been quantitatively tested. The origin of functional redundancy is still elusive. Here, we investigate the basis for functional redundancy in the human microbiome by analyzing its genomic content network — a bipartite graph that links microbes to the genes in their genomes. We find that this network exhibits several topological features that favor high functional redundancy. Furthermore, we develop a simple genome evolution model to generate genomic content network, finding that moderate selection pressure and high horizontal gene transfer rate are necessary to generate genomic content networks with key topological features that favor high functional redundancy. Finally, we analyze data from two published studies of fecal microbiota transplantation (FMT), finding that high functional redundancy of the recipient’s pre-FMT microbiota raises barriers to donor microbiota engraftment. This work elucidates the potential ecological and evolutionary processes that create and maintain functional redundancy in the human microbiome and contribute to its resilience.

A new computational method to characterize the dynamics of human-associated microbial communities is applied to data from two large-scale metagenomic studies, and suggests that gut and mouth microbiomes of healthy individuals are subjected to universal (that is, host-independent) dynamics, whereas skin microbiomes are shaped by the host environment; the method paves the way to designing general microbiome-based therapies. Microbial communities associated with the human body are complex and highly personalized ecosystems, the ecological dynamics of which are poorly understood. Whether these are mainly host-independent (hence 'universal') or host-specific is an open question, and the answer is critical to the development of microbiome-based interventions. This study reports a new computational method for the characterization of the dynamics of human-associated microbial communities, and applies it to data from two of the largest microbiome studies. The results suggest that gut and mouth microbiomes display universal dynamics, whereas skin microbiomes are shaped by the host environment. These universal gut microbial dynamics are not observed in subjects infected with Clostridium difficile, but reappear following faecal transplantation. Human-associated microbial communities have a crucial role in determining our health and well-being1,2, and this has led to the continuing development of microbiome-based therapies3 such as faecal microbiota transplantation4,5. These microbial communities are very complex, dynamic6 and highly personalized ecosystems3,7, exhibiting a high degree of inter-individual variability in both species assemblages8 and abundance profiles9. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models10, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle11, physiology12 or genetics13, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species7,14. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project9,15 and the Student Microbiome Project16—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection17 but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies18.

Significance: Large-scale biological network analyses often use concepts used in social networks analysis (e.g. finding “communities,” “hubs,” etc.). However, mathematically advanced engineering concepts have only been applied to analyze small and well-characterized networks so far in biology. Here, we applied a sophisticated engineering tool, from control theory, to analyze a large-scale directed human protein–protein interaction network. Our analysis revealed that the proteins that are indispensable, from a network controllability perspective, are also commonly targeted by disease-causing mutations and human viruses or have been identified as drug targets. Furthermore, we used the controllability analysis to prioritize novel cancer genes from cancer genomic datasets. Altogether, we demonstrated an application of network controllability analysis to identify new disease genes and drug targets.

Population structure is a key determinant in fostering cooperation among naturally self-interested individuals in microbial populations, social insect groups, and human societies. Traditional research has focused on static structures, and yet most real interactions are finite in duration and changing in time, forming a temporal network. This raises the question of whether cooperation can emerge and persist despite an intrinsically fragmented population structure. Here we develop a framework to study the evolution of cooperation on temporal networks. Surprisingly, we find that network temporality actually enhances the evolution of cooperation relative to comparable static networks, despite the fact that bursty interaction patterns generally impede cooperation. We resolve this tension by proposing a measure to quantify the amount of temporality in a network, revealing an intermediate level that maximally boosts cooperation. Our results open a new avenue for investigating the evolution of cooperation and other emergent behaviours in more realistic structured populations.