Journal Article

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

Stirling, Erinne, Xu, Jianming, Ye, Shudi, Röttjers, Lisa, Faust, Karoline, Liu, Shan, Gilbert, Jack A., Knight, Rob, Jansson, Janet K., Cardona, Cesar, Ma, Bin, Wang, Yiling

2020

Overview

Background Microbial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset. Results This non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. 2NmSq7Q5noeLTtkrbKwa4L Video abstract Conclusion This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Animals / association pattern, earth microbiomes, genelist edges, network hubs, negative associations, specialist edges, topological properties / Bacteria - genetics / BASIC BIOLOGICAL SCIENCES / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Co-occurrence patterns / Datasets / Earth microbiomes / Evolution / Genelist edges / Hypotheses / Medical Microbiology / Microbial Consortia / Microbial Ecology / Microbial Genetics and Genomics / microbial network topology / Microbiology / Microbiomes / Microbiota / Microorganisms / Mutualism / Negative co-occurrence / Network hubs / Predation / Saline water / Soil / Soil Microbiology / Specialist edges / Structure-function relationships / Virology