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Table 1 Definitions of some terms used in discussing microbial-host symbiosis

From: What makes pathogens pathogenic

Term Definition Comments
Host organism The primary eukaryote minus all of its multiple microbiomes  
Host genome The entire genetic complement of the primary eukaryotic organism that was obtained by vertical transmission  
Microbiome An interacting group of microorganisms that share an ecological niche within the host such as the gut, nasopharynx or the skin [6] Nearly all microbiomes are multispecies in character; however, even within a species they tend to be polyclonal in nature [58]
Core genome All the genes that each member of a species possesses [4] Specifically in bacteria and perhaps other nonsexual haploid organisms (whose reproduction is not dependent on chromosome synapsis and meiosis)
Distributed genes All the genes that are not shared by all strains of a species [4] Specifically in bacteria and perhaps other nonsexual haploid organisms (whose reproduction is not dependent on chromosome synapsis and meiosis).
Supragenome or pangenome Core genome plus all of the distributed genes of a species [2, 31] Specifically for bacteria and perhaps other nonsexual haploid organisms (whose reproduction is not dependent on chromosome synapsis and meiosis).
Symbiome The organismal ecosystem complete with the eukaryotic host and all of its associated microbiomes  
Hologenome The symbiome's genome Includes all genes from the host and all symbionts