Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

Genetic Co-Occurrence Network across Sequenced Microbes

The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through the resulting phenotype. In this regard, contemporary genomes can be used as molecular records that reveal associations of various genes working in their na...

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied ...

Fluvial network organization imprints on microbial co-occurrence networks.

Recent studies highlight linkages among the architecture of ecological networks, their persistence facing environmental disturbance, and the related patterns of biodiversity. A hitherto unresolved question is whether the structure of the landscape inhabited by organisms leaves an imprint on their ecological networks. We analyzed, based on pyrosequencing profiling of the biofilm communities in 1...

Supporting Information of “Genetic Co-Occurrence Network Across Sequenced Microbes”

Quantification of correlogy and anti-correlogy We downloaded orthology data from the Kyoto Encyclopedia of Genes and Genomes (KEGG, November 2009) [1], and surveyed the presence or absence of each ortholog across different bacterial species. To avoid possible biases arising from redundant genomes, we considered only one subspecies from each species if it contains multiple subspecies. Also, we e...

Lagged Co-Occurrence Analysis reveals gender differences of co-occurrence patterns in personal narratives