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Definitions of some terms used in discussing microbial-host symbiosis |
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| Term |
Definition |
Comments |
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| Host organism |
The primary eukaryote minus all of its multiple microbiomes |
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| Host genome |
The entire genetic complement of the primary eukaryotic organism that was obtained by vertical transmission |
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| 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 [5-8] |
| 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 |
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| Hologenome |
The symbiome's genome |
Includes all genes from the host and all symbionts |
Ehrlich et al. Genome Biology 2008 9:225 doi:10.1186/gb-2008-9-6-225 |
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