Hacquard et al 2015Plants and their inhabiting microbiome collectively constitute a holobiont in which they have been interacting and evolving with each other Vandenkoornhuyse et al 2015. Plants are heavily inhabited by diverse microbes in every compartment including root stem leaf flower and fruit Lindow. The Human Microbiome Nursing Notes Nursing Mnemonics Nurse Study Notes The gut microbiome consists of the collective genome of microbes inhabiting the gut including bacteria archaea viruses and fungi. . Microbiome is a term that describes the genome of all the microorganisms symbiotic and pathogenic living in and on all vertebrates.