envo microbiome

[kaiiam]

Cross link to #672

There has been much discussion about a microbiome class, the latest being in #805.

Resulting from pco/issues/22 the term PCO:microbial community was created.

In pco/issues/70 @pbuttigieg stressed that having microbiome be a synonym of microbial community would create semantic fuzziness, further that in his discussions with Barry Smith they came to the agreement that:

ENVO would host microbiomes under or close to "biome", as the communities have adapted to and often define their hosting environment. PCO:microbial community would be used to axiomatise this.

Currently there exists the an OHMI:microbiome class, subclass to ENVO:biome, with definition:

A biome that consists of a complex mixture of microorganisms that reside in a specific environmental niche.

In obi/issues/990 @ramonawalls stressed that the OHMI definition is semantically messy, confounding biome and microbial community, although some refer to "microbiome" that way, microrganisms living in a certain time or place, it is not consistent with the ecological theory of a biome which as stated in the definition of ENVO:biome concerns evolutionary adaptation:

A biome is an ecosystem to which resident ecological communities have evolved adaptations.

Hence I propose the creation of an ENVO:microbiome term with definition:

A biome which is determined by the microbial communities resident within an ecosystem to which such microbial communities have evolved adaptations.

Axioms: subclass of ENVO:biome determined by some PCO:microbial community has exact synonym microbial biome

In this definition, I hope to capture the idea that due to the fast generation time of microbes their adaptation to an environment is on a much different time scale then that of macro organisms. Thus in an ecosystem which is not a biome, i.e. the macrobiota have not yet evolved adaptations, the microbes likely have, or are very quickly and continuously adapting and are thus part of the microbiome existing within the larger ecosystem. Thus a microbiome could exist within a (macro) ecosystem which is itself not a biome.

Such definition would contrast that given by the human microbiome project (https://doi.org/10.1038/nature06244)

A microbiome is the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.

Perhaps it is more similar to the original definition of microbiome written in NM Burge Editor, Fungi in Biological Control Systems. Manchester University Press, 1988 on pg 176 (re cited by https://doi.org/10.1016/j.humic.2017.05.004):

A convenient ecological framework in which to examine biocontrol systems is that of the microbiome. This may be defined as a characteristic microbial community occupying a reasonably well defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity.

[pbuttigieg]

The term is used in many ways, which leads us to this problem.

Definition clean up:

A biome which is determined by its resident microbial communities.

The rest you get from the superclass. We may want to start making statements of climax communities to be clear that we don't mean any community that happens to be there, but this should be done in the biome class itself.

There are several other publications on this that that we discussed with Oliver, Barry, et al. These include: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/

A presentation we contributed to and commented on is available here

Structurally, I don't mind if OHMI or ENVO hosts the microbiome class, as long as the OHMI definition is revised. The definitions of the subclasses in OHMI need attention too. ENVO will then add classes for microbiomes that are not host-associated. If OHMI will deal with host-associated microbiomes, then ENVO can fill the gap for non-host, environmental microbiomes (e.g. soil, ocean, etc).

@zhengj2007 @cmungall @ramonawalls @phismith @yongqunh should be part of this conversation and decision.

[zhengj2007]

@pbuttigieg OHMI developers discussed the term extensively. We improved the definition of OHMI: 'microbiome' (OHMI_0000003) lately. microbiome: A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.

Unfortunately the latest release version is not loaded into the ontobee yet.

Besides, we submitted a poster to ICBO regarding the term and related terms aiming to get feedback from microbiome and ontology community at large. Hope we can discuss it f2f at the ICBO meeting.

[cmungall]

Having microbiome be a subclass of envo:biome makes a certain amount of terminological sense

but recall the envo definition: A biome is an ecosystem to which resident ecological communities have evolved adaptations.

Are all microbiomes biomes according to this definition? It seems really hard operationally to determine if the community has evolved adaptations. Remember for many practical purposes we want to talk about microbiomes in perturbed environments.

What is the use case for this class? How will it be used?

I want to make a plea for keeping things simple and easier for curators. I would like to avoid populating another shadow hierarchy, e.g. tundra {ecosystem, biome, microbiome}

[kaiiam]

What is the use case for this class? How will it be used? I want to make a plea for keeping things simple and easier for curators. I would like to avoid populating another shadow hierarchy, e.g. tundra {ecosystem, biome, microbiome}

@cmungall I agree and also want to make things easier for curators. My thinking was that there could be a single hierarchy which is intended specifically for the annotation of omic data. It doesn't have to be the microbiome hierarchy for concern over identifying adaptation but I've been putting together these putative microbiome classes drawing from the JGI GOLD / EBI MGNIFY term hierarchy, providing determined by axioms to environmental features material entities and systems (ecosystem and or biome) in the hopes of integrating information from a variety of envo hierarchies into one which is convenient for annotators of microbe omics data to use.

My thinking is that this structure replicates current best practices of MIXS annotated data which asks users to supply Biome environmental features and environmental material classes. That we would have these pre-composed microbiome classes which can be used in the annotation of existing large datastores GOLD/MGNIFY but when reasoned over, other MIXS annotated data (with the triad of annotation terms) would hopefully reason into the proposed microbiome hierarchy. Does this make sense?

[phismith]

Here are the definitions I have been proposing (they are logically slightly tidied up versions of definitions in ENVO)

system =def. A material entity consisting of multiple components that are causally integrated

environmental system= def. A system which has the disposition to environ one or more material entities.

a environs b = def. a includes b (partially or wholly) within its site and a causally influences b

ecosystem = def. an environmental system that environs living organisms

biome =def. an ecosystem that is determined by an ecological community

determined by = def. a system is determined by an entity if the removal of that entity would cause the collapse of that system

community = def. a collection of organisms connected by social or biological relations (biotic interactions)

ecological community = def. a community of at least two different species living in a particular area.

microbiome = def. a biome determined by an ecological community of microbiota

[pbuttigieg]

Thanks all, for input.

@zhengj2007

microbiome: A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.

This is an improvement and is aligning more with the 1988 usage.

However, this definition is not different from any microbial ecosystem, so it's a somewhat of misuse of the biome concept (which is not an OHMI issue, the microbial ecology community doesn't have a disciplined usage).

It also diverges from the ENVO biome definition pattern.

Unfortunately the latest release version is not loaded into the ontobee yet.

@kaiiam and others will need the release soon to evaluate their next steps.

Besides, we submitted a poster to ICBO regarding the term and related terms aiming to get feedback from microbiome and ontology community at large. Hope we can discuss it f2f at the ICBO meeting.

ICBO isn't really the place for representative feedback on this issue, I think. I don't plan on attending this year due to other meeting commitments (coincidentally concerning ocean microbiomes).

@cmungall

Having microbiome be a subclass of envo:biome makes a certain amount of terminological sense

but recall the envo definition: A biome is an ecosystem to which resident ecological communities have evolved adaptations Are all microbiomes biomes according to this definition? It seems really hard operationally to determine if the community has evolved adaptations. Remember for many practical purposes we want to talk about microbiomes in perturbed environments.

There's rampant ambiguity in this term's usage and we'll just have to make an operational decision to bring some consistency to the chaos. Yes, it is hard to operationally determine if adaptation has occurred, and perhaps we need to think about climax communities rather than site-based evolution (even for macro-biomes).

"Microbiomes" of perturbed environments is a doubly messy issue where researchers are simply reusing a trendy term. Microbiota of a perturbed environment is more accurate, unless the perturbed state is stable enough for a climax community to develop and hold (e.g. acid mine drainage microbiome).

What is the use case for this class? How will it be used?

@kaiiam has a number, the GSC would be able to use it to refine the MIxS annotations, our IOC-UNESCO GOOS Microbial EOV data efforts will use it, etc.

I anticipate annotators will be able to use this to clarify that their sample is focused on microbial ecology. For example, a MIxS 4 annotation would be able to state:

biome: polar desert biome [ENVO:01000186], sea ice microbiome [ENVO:########] feature: sea ice hummock [ENVO:01001537] material: second-year sea ice [ENVO_03000072]

MIxS 5 may shake this up a bit, but the intention is similar.

For other cases, it allows a declaration of what the expected community fingerprint is going to be. The data can then be checked against the "average" fingerprint of the background or baseline X microbiome and flags can be raised if there's significant deviation (e.g. a perturbation).

I want to make a plea for keeping things simple and easier for curators. I would like to avoid populating another shadow hierarchy, e.g. tundra {ecosystem, biome, microbiome}

While the biome-ecosystem(-zone) pattern needs to be made more consistent, that's not a shadow hierarchy (I still don't fully understand what you mean by this): each of those environmental entities is a different thing (if the biome interpretation of microbiome is taken).

We have very different annotator profiles. The only way I see to make it simple for them is to create subsets that bundle together terms that best suit their needs, as we did with NEON, EMP, and others.

@kaiiam

My thinking was that there could be a single hierarchy which is intended specifically for the annotation of omic data.

This will break the point of the tri-part MIxS annotation. Having three ENVO fields allows annotators to "zoom in" on their target community's environment. If you had "surface sea water microbiome" as the only biome term for an Ocean Sampling Day or TARA Oceans sample, it's essentially redundant with "surface seawater" as the material. Something like "oceanic mesopelagic zone biome" is more informative. As shown above, the microbiome class could be added to a macro-scale biome annotation to qualify it.

...providing determined by axioms to environmental features material entities and systems (ecosystem and or biome) in the hopes of integrating information from a variety of envo hierarchies into one which is convenient for annotators of microbe omics data to use.

Even with this step (which is a good one), we're still not likely to completely remove the need for other biome classes, unless you duplicate the biome hierarchy entirely (which would be confusing)

My thinking is that this structure replicates current best practices of MIXS annotated data which asks users to supply Biome environmental features and environmental material classes.

Keep in mind this will change in MIxS 5, allowing more freedom in what can be added to each slot.

In summary, I think we have the following actions to consider:

• Revise the biome definition to include ecosystems with climax communities (whether or not they actually evolved there)
• Revise the definition of microbiome to align to the above
• Add a comment to the microbiome definition which
  • acknowledges the ambiguity of the term
  • points to PCO 'microbial community' as an alternative.
  • notes that perturbed environments that have not reached their microbial steady-state are not to be treated as microbiomes - request a PCO class for these, such as "microbial community associated with a deforestation in an ENVO:'tropical broadleaf forest biome'" or similar
• Create documentation for annotators.

[pbuttigieg]

PS: @kaiiam's single class approach (linked to a bunch of others) will work well for systems that don't follow MIxS patterns and only want one descriptor. It would also be an asset for text mining solutions.

[yongqunh]

Attached is the OHMI ICBO poster. OHMI_ICBO2019.pdf The definitions presented in the poster were the outcome of many discussions from the OHMI community, esp. among the authors of the poster in the recent months.

As defined in the poster document, we pretty much follow the proposal given by the paper: Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome. 2015;3:31. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-015-0094-5 Note that this paper has been cited for over 200 times since its publication in 2015, indicating its wide recognization.
Copied from the paper: "Microbiome This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of “biome,” the biotic and abiotic factors of given environments. " "Microbiota The assemblage of microorganisms present in a defined environment. "

Aligned with the paper, we think that the microbiome and microbial community have different meanings and cannot be synonyms or alternative terms.

I also agree that the upper level terms along the hierarchy need revisit and updates if needed.

[pbuttigieg]

Thanks @yongqunh

The definitions presented in the poster were the outcome of many discussions from the OHMI community, esp. among the authors of the poster in the recent months.

Naturally, it's a tricky term and would need quite a bit of discussion.

Note that this paper has been cited for over 200 times since its publication in 2015, indicating its wide recognization.

Unfortunately, a citation count doesn't tell us much and the term is still used in very different ways in the microbial ecology community.

Copied from the paper: "Microbiome This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eurkaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of “biome,” the biotic and abiotic factors of given environments. " "Microbiota The assemblage of microorganisms present in a defined environment. "

This is in reasonably good agreement with the 1988 description. However, it 1) has a confounding and inaccurate usage of habitat, 2) has a very odd parallel of genes and genomes and 3) essentially equates "biome" to ecosystem, which diverges from most treatments of this by organisations that define biomes.

I'm thus not convinced that this is to be treated as dogma.

Aligned with the paper, we think that the microbiome and microbial community have different meanings and cannot be synonyms or alternative terms.

Very much agreed. See https://github.com/PopulationAndCommunityOntology/pco/issues/70

I also agree that the upper level terms along the hierarchy need revisit and updates if needed.

Great - I'll look into this.

[pbuttigieg]

PS: @yongqunh note that the definition of microbiota overlaps with the class discussed here: https://github.com/PopulationAndCommunityOntology/pco/issues/70

Further:

microbiota = def. A collection of microbial organisms that reside in a particular environment.

All collections of microbes reside in some environment. I think this as a synonym of microbial community (in PCO) is best.

[zhengj2007]

@pbuttigieg If need, we may set a call to discuss these terms.

[pbuttigieg]

Sure, it may be easier to cover ground. How's the 25th before 22:00 CEST (20:00 Zulu/UTC)?

[zhengj2007]

@pbuttigieg The date is fine to me. But not sure whether other people who are interested in this topic can join. How about invite the people who would like to attend to make a vote in Doodle? Thanks!

[yongqunh]

I am interested in having a meeting as well. Thanks.

[pbuttigieg]

@zhengj2007 @yongqunh @kaiiam @phismith @cmungall

If you'd like to join in, please indicate your availability on this Doodle poll.

[zhengj2007]

@pbuttigieg Shall we also invite Ramona for Doodle poll?

[pbuttigieg]

@pbuttigieg Shall we also invite Ramona for Doodle poll?

@ramonawalls join the party!

@zhengj2007 please invite anyone you'd like to.

[pbuttigieg]

At the Atlantic Observing Research Alliance Marine Microbiome Workshop, prominent voices are calling for the definition of microbiome to be extended to include eDNA from sloughed off cells.

This will totally separate us from any biome-centric definition, making "microbiome" a pretty arbitrary term.

[yongqunh]

The environmental DNA (eDNA) may be considered as part of the environment, so still under the biome scope. https://news.stanford.edu/news/2014/june/marine-edna-monitoring-062714.html

[pbuttigieg]

So eDNA from a macrorganism is part of a microbiome? Sounds off.

[tnn111]

Is it living? Does it participate in metabolic processes? Or is it just “passing through”?

Does including this help us solve problems?

On Jun 27, 2019, at 15:57, Pier Luigi Buttigieg notifications@github.com wrote:

So eDNA from a macrorganism is part of a microbiome? Sounds off.

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[yongqunh]

If we look for the definition defined in OHMI: microbiome = def. A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside. the eDNA is part of the surrounding environment, it does not have to be living. Also, see the definition in the paper: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-015-0094-5 This definition also allows the inclusion of eDNA. The OHMI microbiome definition is aligned with that.

[cmungall]

Does including this help us solve problems?

This is the key question. I think it may be useful here to start with use cases, and then from those use cases figure out which classes are required and how they need to inter-relate; after that we can decide on the labels. OBO isn't a dictionary or an arbitrer of terminology. If someone wants to annotate to or query a class that is a grouping of eDNA plus DNA from metabolically active organisms then there should be a class for them to do this. But if there is no use case then let's exclude it, there are already too many conceptually similar classes across OBO, let's not proliferate further.

I understand the use cases for much of ENVO - the classes in the feature, biome, and material hierarchies are essential for annotating microbiome samples (and many other non-microbiome use cases of course).

I don't understand what the use case is for a microbiome class, or the existing subclasses we see in OHMI (e.g. fungal microbiome, human microbiome). Which curation community will annotate to these terms? I'm not even sure what an instance of one of these classes is. Is the totality of all microbes environmed in humans? All microbes in one human? All microbes in one subdivision of the gut?

A radical straw-man suggestion: we don't need a microbiome class. We can use ontologies for metabolomics without a metabolome class, we can use ontologies to do proteomics without a proteome class. "ome" constructs are useful for human communication and to galvanize a research strategy etc (I know microbiome not etymologically analogous but the point still holds). In order to do microbiome data science we need classes to represent the structures that influence an organismal community, the cellular and molecular structures of the organisms, the processes that shape those structures, the chemical and macroscopic properties of these things. But do we actually need a class for 'microbiome', and a bunch of subclasses that parallel other hierarchies? What's the use case?

[pbuttigieg]

the eDNA is part of the surrounding environment, it does not have to be living.

Agreed, that works in both cases, as long as it doesn't slip into having the macroorganism itself tag along or the eDNA itself having any major role in defining the microbiome (just as fur left behind on a shrub wouldn't determine a macrobiome)

However, eDNA would also be part of any biome as a circumstantial residue. The emphasis on it is what spooks me.

microbiome = def. A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside.

The issue here is that this could be understood as equivalent to any ecosystem determined by any microbial community. Some tweaking can resolve this.

[yongqunh]

There are many use cases for OHMI study of microbiome. For example, we have systematically annotated and analyzed rheumatic disease associated host-microbiome interactions. We are currently working on gastric cancer and colon cancer related host-microbiome interactions. In addition, we are collaborating with the https://microbiomedb.org and apply OHMI ontology to support the MicrobiomeDB project. We don't have a use case for eDNA, though.

[diatomsRcool]

However, eDNA would also be part of any biome as a circumstantial residue. The emphasis on it is what spooks me.

Agreed

[cmungall]

@yongqunh - I wasn't questioning whether there were causes for studying the microbiome, I was questioning the need for a class in the ontology microbiome, and the existing subclasses, given that what you are doing could be represented using terms from disease, anatomy, and organismal ontologies.

[yongqunh]

@cmungall - I see. Our use cases often need to represent host-microbiome interactions. Note that 'host-microbe interaction' or 'host-bacterium interaction' differs from 'host-microbiome interaction' because the 'host-bacterium interaction' may just mean an interaction between host cells and bacteria in a cell culture plate, which is not a host-microbiome interaction.

[cmungall]

But you could have some other way to say that this is an in-vivo interaction.

Drifting away from the original topic, but what precisely is an instance of a host-microbiome interaction? Obviously I know that there is a relationship between a host and its microbiome, but what is a single instance of this process? What is it's spatial and temporal extent? Does it necessarily involve all members of the microbiome? And the context of microbes, e.g. epithelial cells of host?

[diatomsRcool]

I'm just going to alert @jhpoelen in case he's dealt with this in GloBI

[jhpoelen]

A similar point came up In a recent discussion with friendly folks @beraute Eric Beraute and Rachel Meyer of http://www.ucedna.com in context of eDNA datasets like https://github.com/beraute/Klamath-mountains https://github.com/beraute/Pillar_Point_16S_18S and https://github.com/beraute/Pillar_Point_CO1_16S .

I suggested to model the eDNA samples as a network of co-occurrences (see https://github.com/beraute/Klamath-mountains/issues/4 ) using the RO term http://purl.obolibrary.org/obo/RO_0008506 (ecologically co-occurs with) . I imagine that you can group these co-occurrences and label them as produced by a eDNA sample process at a given time/place. A similar grouping can be used to label the co-occurrences as some microbiome.

[ramonawalls]

Sorry to be late to the party, folks. I think I could sum up my response by saying "I agree with Pier" on most points. I filled out the doodle poll, and I'm looking forward to a call to discuss this.

[pbuttigieg]

Hi all, we will have a call on the 23rd of July at:

[pbuttigieg]

@jhpoelen

I suggested to model the eDNA samples as a network of co-occurrences (see beraute/Klamath-mountains#4 ) using the RO term http://purl.obolibrary.org/obo/RO_0008506 (ecologically co-occurs with) . I imagine that you can group these co-occurrences and label them as produced by a eDNA sample process at a given time/place.

Yes, this is a good option - co-occurrence is pretty much all that can be securely claimed with the kind of data we handle.

A similar grouping can be used to label the co-occurrences as some microbiome.

Yes and no: co-occurrence is a necessary but not sufficient condition for a specific microbiome (but note that the current fuzziness of the term means that anything goes in most contexts).

[zhengj2007]

@pbuttigieg Can I have the call-in information for today's call? Thanks!

[ramonawalls]

Apologies. This never made it on to my calendar (my fault) and I have a conflict today. If I can, I will join late.

[pbuttigieg]

Hi all, having issues with Zoom, lets try a Google Hangout Join the conversation on Hangouts: https://hangouts.google.com/group/BHkwbCKsXjakcth39

[pbuttigieg]

That's a shame @ramonawalls, you can leave some key points in the chat linked above if you wish

[pbuttigieg]

Hi all,

Here's a meeting summary:

Attendees

@pbuttigieg @kaiiam @yongqunh @zhengj2007 @diatomsRcool Apologies: @cmungall @ramonawalls

Debriefing

The participants of the OHMI/ENVO/PCO teleconference on July 23rd 2019:

Recalling that: The OBO foundry seeks to preserve orthogonality and semantic alignment of the ontologies it federates.

Recognising that: The term "microbiome" is relatively novel, and its usage in the microbial ecology, metagenomics, and related communities is often semantically loose.

Noting that: Microbial communities, microbiota (including mono-population assemblies), microbial ecosystems, and microbial ecosystems with sustained climax communities (i.e. microbial biomes) are all frequently referred to as "microbiomes"

Further noting that: The definition of ENVO:biome is stricter than the intended meaning and current definition of OHMI:microbiome.

Decide to: Relocate OHMI:microbiome, rendering it a subclass of ENVO:ecosystem.

Further decide to: Create a new ENVO class "microbial biome", under ENVO:biome

Further decide to: Add "microbiome" as a related synonym to ENVO:'microbial biome', OHMI:microbiome, PCO:'microbial community', and OHMI:microbiota.

Further decide to: Update the OHMI submission to ICBO to reflect the above.

Note a point of disagreement: In that @pbuttigieg believes the label of OHMI_0000003 (currently "microbiome") should be changed to "microbial ecosystem", with a synonym "microbiome" for consistency and to show the ambiguity in the community usage. @yongqunh believes that this should remain to encourage more consistent usage. @pbuttigieg notes the ENVO stance that ontologies are not standards, but should reflect the ambiguity as a first principle.

Deferred points:

• OHMI:microbiota is more properly placed inside PCO, and imported into OHMI. The definition also needs revision.

[phismith]

Not sure if the attached has any relevant content, but please ignore if not Barry

On Tue, Jun 18, 2019 at 9:09 AM Pier Luigi Buttigieg < notifications@github.com> wrote:

The term is used in many ways, which leads us to this problem.

Definition clean up:

A biome which is determined by its resident microbial communities.

The rest you get from the superclass.

There are several other publications on this that that we discussed with Oliver, Barry, et al. These include: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520061/

A presentation we contributed to and commented on is available here https://docs.google.com/presentation/d/1SfyY6P8bUfYng9rGUTqL-jVTdp3FRBjUFknRbfyY_F4/edit#slide=id.g2837b51eeb_2_476

Structurally, I don't mind if OHMI or ENVO hosts the microbiome class, as long as the OHMI definition is revised. The definitions of the subclasses in OHMI need attention too.

@zhengj2007 https://github.com/zhengj2007 @cmungall https://github.com/cmungall @ramonawalls https://github.com/ramonawalls @phismith https://github.com/phismith @yongqunh https://github.com/yongqunh should be part of this conversation and decision.

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