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.

[pbuttigieg]

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.

This describes a multi-step provenance pathway. MIxS and other GSC standards aren't very good at expressing such things, so it looks like we're going to have to "overload" an ontology term to express more than it should.

Ideally, the GSC would allow you to generate a set of metadata (with ENVO terms) for each step of the way. Alas, we'll see what we can do.

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.

You could use cell culture [ENVO:02000008] for the env_medium.

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.

fecal material [ENVO_00002003] - this is an env_medium term. All materials should be in env_medium.

This is where the provenance pathway issue hits us: the fecal material was the env_medium for obtaining the inoculum, the cell culture for obtaining the DNA etc. Each step in the pathway introduces new artifacts.

In the second case, I selected instead "bioreactor metagenome" as the scientific name to highlight the use of a bioreactor.

I would add bioreactor or one of its subclasses to the env_local_scale property. Remember you can add several.

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".

I wouldn't say the link to the broad scale environment of the host is lost, unless you kept the subjects in isolation in a lab for a few weeks, or they all travelled to the same ecosystem and stayed there for long enough that their gut microbiome would have turned over based on local exposures. The kind of ecosystem they lived in (urban, village, tropical, etc) has an influence on their diet and exposure, so you can add a few broad scale terms in there. For example, if the subject lived in a city in North Germany, I'd toss in some env_broad_scale terms like city [ENVO_00000856],temperate ecosystem [ENVO:01001931].

Again, in the current form of the MIxS standards, you're unfortunately forced to overload these slots. It's a bit weird, but to help people discover your record, you could add an array of fecal material [ENVO_00002003],cell culture [ENVO:02000008] and any other material you sampled in the env_medium slot.

For env_local_scale, I'd consider adding terms describing the anatomical origins of things like intestine environment [ENVO:2100002] as well as things like the bioreactor (env_local) where you extracted a cell culture (env_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.

The dbxref is just a reference, the definition of cell culture is broader and works well for bacteria, archaea, and other things. I'll tighten up the def of cell culture to look like:
"Organic material which is composed primarily of a growth of cells in an artificial medium for experimental research."

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.

I can add that. The label will be "microbial culture" with a broad synonym "microbiological culture" as the latter term is often used more loosely. I'll also add an exact synonym "culture of microorganismal cells".

The definition will be "A cell culture which supports the growth and proliferation of microorganisms."

The IRI/PID will be http://purl.obolibrary.org/obo/ENVO_01001968 so the MIxS value would look like microbial culture [ENVO:01001968]

We don't need to repeat anything in the definition that's already in the definition of the superclass (cell culture) - all properties are inherited.

I'll also bacterial, archaeal, and eukaryotic microbe cell cultures for good measure.