The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

This study examines the potential for microbial communities to provide insight into stresses experienced by their eukaryotic host organisms, through profiling of metagenomes and metatranscriptomes. Our study uses plant host-associated microorganisms as an in vivo and in situ microsensor to identify environmental stresses experienced by the microbial community and by the plant. Transcriptionally active host-associated microbial communities are responsive in a highly specific manner to environmental conditions. Conversely, host transcriptome sequencing provides only a very general stress response. This study is a proof-of-concept for the use of microbial communities as microsensors, with a great potential for interrogation of a wide range of host systems.