New term for Microbiological cultures

[davidgarciam]

I'm trying to refine my use of ontologies during sample submission to the ENA, specifically in the fields "broad-scale environment", "local environment", and "environmental medium". However, finding the best set of ENVO descriptors for my samples has been difficult. This is the context: we (1) collect stool samples from donors and culture them using different culture media. After incubation, we collect samples of the microbes present in the culture. Also, (2) we use a bioreactor for middle-term experiments instead of running a conventional liquid culture.

In the first case, I feel the best definition for describing the source of the sample would be "microbiological culture". However, this is not a listed ontology. At the same time, this is connected to the fact that the inoculum was obtained from human feces, so I chose human feces metagenomes [2705415] as the scientific name and fecal material [ENVO_00002003] as the broad-scale environment. In the second case, I selected instead "bioreactor metagenome" as the scientific name to highlight the use of a bioreactor.

In the documentation of environment ontology for host-associated microbial samples of Genomic Standard Consortium, the "broad-scale environment" should reflect the ecosystem in which the host is found. But once I take the stool sample and put it in a culture, is the connection to the host lost? In my opinion, it should reflect both things. The fecal material was obtained from a human host and then cultivated in the lab, so the environmental medium should be "culture medium".

Having a category to distinguish samples taken from microbial cultures can allow us to differentiate the microbial diversity observed in natural environments from that observed in vitro. The closest terms are cell culture [ENVO_02000008], culturing environment [ENVO_01000312], and cell culturing [ENVO_01001815]. However, the dbxref Wikipedia:Cell_culture states that "In practice, the term 'cell culture' now refers to the culturing of cells derived from multicellular eukaryotes, especially animal cells, in contrast to other types of culture that also grow cells, such as plant tissue culture, fungal culture, and microbiological culture". Another close one is cultured organic material [ENVO_01001820], but it needs a definition.

I propose the creation of a new term for "microbiological culture". Re-wording the definition found in Wikipedia (https://en.wikipedia.org/wiki/Microbiological_culture), it would be:

Microbiological culture = a controlled artificial environment created using a specific culture medium that supports the growth and proliferation of microorganisms under defined laboratory conditions.