New term Bacterial persistence

[gocentral]

Hello,

I’d like to request a new GO term for Bacterial persistence.

Category: Process

Definition: Bacterial pathogen that persists in host for the host’s lifetime, characterized by a clinically latent state where the pathogen has undergone metabolic slowdown and remains quiescent without any overt disease symptoms. Many different mechanisms are used by bacteria to avoid the immune system.

Synonyms: Dormancy, Latency, Non-replicating persistence.

Could be a child of GO:0022611, Dormancy process

See PMID 20056478, 12407411 for some discussion. This seems also to occur in chickens, and so I have deliberately not restricted it to mammals.

Reported by: aauchincloss

Original Ticket: geneontology/ontology-requests/7163

[gocentral]

Andrea,

It is generally better to use the word "symbiont" rather than pathogen, in order to be consistent with the rest of the GO, and also because pathogen is a loaded term, particularly if you are talking about a clinically latent state, where the bacteria is not playing a pathogen role.

I also wonder if you are talking about a bacteria type, or even phenotype, rather a process based on the definition you have given. I would suggest rewriting the definition.

name: bacterial persistance def: A dormancy process that allows a bacterial symbiont to persist in a host for the host's lifetime. Such a process is typically characterized by the bactera having a clinically latent state involving a metabolic slowdown without any overt disease symptoms. Additional aspects of a bacterial persistance process may involve mechanisms to avoid the host's immune system. is_a: GO:0022611 ! dormancy process

Thanks,

Alex

Original comment by: addiehl

[gocentral]

• assigned_to: nobody --> jl242

Original comment by: mah11

[gocentral]

Hi, I hope I'm answering this in the correct way. I am currently working on Mycobacterium tuberculosis (MYCTU), which I don't think anyone would ever characterize as a symbiont. Do I understand that this same term might then be used to characterize for example Rhizobium association with a plant and MYCTU association with a human? No, I guess not is the answer, as Rhizobia do not really undergo metabolic slowdown. I really have to say that for MYCTU I don't find the term "pathogen" to be a problem, however symbiont does give me serious problems... What now?

Thanks, Andrea

Original comment by: aauchincloss

[gocentral]

Andrea,

Thanks for your response. "Symbiosis" and "symbiont" are used with a broader meaning in the GO than many people consider:

[Term] id: GO:0044403 name: symbiosis, encompassing mutualism through parasitism namespace: biological_process alt_id: GO:0043298 alt_id: GO:0044404 def: "An interaction between two organisms living together in more or less intimate association. The term host is usually used for the larger (macro) of the two members of a symbiosis. The smaller (micro) member is called the symbiont organism. Microscopic symbionts are often referred to as endosymbionts. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs." [GOC:cc, http://www.free-definition.com] comment: Note that this term encompasses all symbiotic relationships between species along a continuum from mutualism through to parasitism, as outlined in the definition. subset: goslim_generic subset: gosubset_prok synonym: "host-pathogen interaction" RELATED [] synonym: "symbiosis" EXACT [] synonym: "symbiotic interaction" EXACT [] synonym: "symbiotic interaction between host and organism" RELATED [] synonym: "symbiotic interaction between organisms" EXACT [] synonym: "symbiotic interaction between species" EXACT [] synonym: "symbiotic interaction with other non-host organism" RELATED [] is_a: GO:0044419 ! interspecies interaction between organisms

It is not uncommon for even biologists, to consider only the mutualistic and commensal meanings of symbiosis. However the GO has chosen to use a broader meaning based on long periods of discussion with experts in microbial pathogenesis. Thus the GO uses "symbiosis" and "symbiont" even to describe the interactions of potential pathogens, such as Mycobacterium tuberculosis, with their hosts.

And indeed, the GO generally avoids the use of the word "pathogen" to describe organisms. Whether or not an organism plays the role of being a pathogen depends very much on individual hosts and indeed the particular environment in the host. Mycobacterium tuberculosis can be present asymtomatically for years in some people, even throughout their entire lives. In such cases it is not playing a pathogen role. It is important that the definition of the term you suggest encompasses the fact that other types of bacteria, even those not commonly considered pathogens, may persist for years in a host, sometimes using similar mechanisms of persistence to types of bacteria that may on occasion play the role of being a pathogen.

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Hello Alex, Well then I guess symbiont is the term to use. Thanks for your help, Andrea

Original comment by: aauchincloss

[gocentral]

Answered in another SF item. New terms:

Added new terms:

entry into dormancy by symbiont in host ; GO:0085014 dormancy maintenance of symbiont in host ; GO:0085015 dormancy exit of symbiont in host ; GO:0085016

Original comment by: jl242

[gocentral]

• status: open --> closed-fixed

Original comment by: jl242