Hello, and thank you for listening to the MicroBinfeed podcast. Here, we will be
discussing topics in microbial bioinformatics. We hope that we can give you some
insights, tips, and tricks along the way. There is so much information we all
know from working in the field, but nobody writes it down. There is no manual,
and it's assumed you'll pick it up. We hope to fill in a few of these gaps. My
co-hosts are Dr. Nabil Ali Khan and Dr. Andrew Page. I am Dr. Lee Katz. Both
Andrew and Nabil work in the Quadram Institute in Norwich, UK, where they work
on microbes in food and the impact on human health. I work at Centers for
Disease Control and Prevention and am an adjunct member at the University of
Georgia in the U.S. Hello and welcome to the MicroBinfeed podcast. Today we are
talking about systematics, specifically SEC code, nomenclature code for
prokaryotes described from sequence data. Joining us to talk about it are co-
authors on the recent publication, Marika Palmer and Miguel Rodriguez. Marika
Palmer is a postdoctoral researcher in the School of Life Sciences at the
University of Nevada, Las Vegas, and Miguel Rodriguez is an assistant professor
of bioinformatics at the University of Innsbruck in the Departments of
Microbiology and the Digital Science Center. So welcome to you both. Hi Nabil,
thank you. Thank you for having us. All right, so let's start off with something
simple. I mentioned this word systematics. What is systematics? Let's give it to
Miguel perhaps. Sure. Yeah, so systematics is a generic term to refer to the
discipline studying the classification and naming of organisms, of biological
organisms, and in general, the distinction is made between the actual
classification of organisms, which is called taxonomy, versus the rules and
regulations for naming those groups, or those taxa, which is called
nomenclature, and the joint study of naming and classification of biological
entities in general is typically referred to as systematics. Okay, good. So
today we're not strictly talking too much on the taxonomy side, I guess, not
really. So please don't get upset with that little bit of disclaimer out of the
way. I wanted to ask you both actually, what do you do regularly in your work?
What's your organism of choice or area of expertise? And how do you both know
each other and got involved with this project? So first off, in terms of
organisms that we work with, I actually don't work on a specific group of
organisms as such. I've been fortunate to be part of collaborations that work
with a lot of cultivated organisms, so typically from soil and oftentimes
rhizobial cultures. So it would be nitrogen fixing bacteria that actually live
in symbiosis with legumes. But I'm also part of a research group that looks at
microbes from extreme environments. So in the research group of Brian Edlund, we
kind of use a lot or spend a lot of our time looking at novel microbes that
haven't been cultured before and try to cultivate them and also try to
understand their ecology. So we basically work with bacteria and archaea. And
what I'm personally most involved with is oftentimes an archaea from hot
springs. But I've also actually started working more on the virome of extreme
environments as well. So I actually look at some viral DNA and from a
biotechnological perspective, what we can learn and what we can use from all of
the genetic diversity out there. From my side, similar to Marika, I have an
interest mostly in microbial ecology, so I don't really work with one specific
organism, although I have been going back and forth for many years since my
master's on taxonomy and genomics of Santomonas. So that's if I had to pick one
organism, that might be the one. More recently, I'm working with the micro
bacterium as well and some freshwater pelagic bacteriales also. But it might be
Santomonas, the one that I favor. Yeah, I mostly work on environmental genomics
of towards microbial ecology, the understanding of whole communities and whole
microbial assemblages, rather. And we really we met with Marika through the
C-Code group. We have actually never met in person. Wow, fantastic. So, I mean,
Lee and I don't meet up that often either. So, you know, so since you mentioned
both your backgrounds, that puts you and you mentioned C-Code, what is C-Code
then and what is the problem C-Code is trying to solve? My relation to C-Code is
mostly one of necessity. As I mentioned, I'm very interested in ecology and one
of the foundational pillars of ecology is consistent systematics. And we have an
issue in the field where we have learned quite a lot about a large number of
species through their genomes for which we just don't have stable names. And so
through that problem, I got I got interested first in taxonomy and later on in
nomenclature and in the issues of stability of names, the stability of names. So
basically, if you think about nomenclature as all that, it's often described as
the language used for us to actually be able to communicate the diversity and
specific organisms to make sure that we're referring to consistent things and
that we're effectively able to communicate about those things. So in terms of
the C-Code, this is basically a set of rules that governs how we form names for
the organisms that are not yet able to cultivate or that we have genome
sequences for that we can use as the basis for naming those organisms. All
right. So I'm still wrapping my head around systematics versus taxonomy. So
let's say you find new bacteria that you can only sequence. You can't culture
it. It's in the lake. Do you give it a genus and species and you just you leave
the family name up till later? So if you're able to actually so this comes into
the classification, which the C-Code doesn't govern. So no code of nomenclature
governs the taxonomy of the organism. So your taxonomic freedom isn't impeded by
what any code of nomenclature gives as guidance for naming those microbes. But
if you've used if you have a genome for an organism that you can or cannot
cultivate and you want to name this organism because you have used whatever set
of criteria that you think is logical and justified to show this is a new
organism, then it can either be depending on what analyses you've done or what
decisions you've made in terms of the taxonomy of that organism, decide to call
it a new species. Or if it's sufficiently novel to be a new genus, you can give
it a genus and a species name because you have to have a type for the genus that
you're describing. And depending on how novel they are and depending what
criteria you use, it could become a new family or a new order level lineage as
well. And then you would ideally, I think, if you're sure in terms of what the
taxonomy of that organism should be, ideally you should describe all of those
intermediate ranks as well, up to the point that the last existing parent taxon
exists. So if you have a sufficiently novel organism to potentially be the first
representative of a new order, ideally you should describe the order, family,
genus, and then the species, or at least name them if you're not providing
descriptions for them, and then associate your order that you've now generated
to accommodate that taxon to a parent taxon, so in other words, a class. That
makes a lot of sense. So one of the questions, a simple question then, you sort
of mentioned it, but just firstly, so what C code is trying to do doesn't step
on the toes of taxonomic assignment like GTDB, for instance, right? I'm just
going to say that. Yeah. Yeah. So just to reiterate something that Marika
mentioned that is very, very important. So the principle one of the C code ends
with nothing in the C code may be construed to restrict the freedom of taxonomic
opinion or action. And that's, so that's right at the beginning. That's
principle one. So the C code is meant to provide a stable system to generate
names, but how those organisms are grouped, meaning how the taxonomy is
developed, that depends on, of course, the authors and the peer review system.
Nice. Right. And you both use this thing of, Marika kind of hinted on it and you
keep using this word, stable naming. I mean, if I call you, I call you, I call
you Miguel, that's stable. We're done, right? So why can't I call it, you know,
cuties and just be done with it? So ultimately, I mean, no taxonomic system and
rules that govern the naming, so the nomenclature would be completely static.
or stable, because I think that would actually prevent scientific progress, but
ultimately, what we aim to strive for, at least, would be some stability in that
taxonomic system. But it's okay if we're not in full agreement on the taxonomy
of organisms, as long as we have stable names for them. So ultimately, our
taxonomic opinion might differ over time as we learn more information about a
specific taxon, and then we might assign it to an already existing genus,
transfer it to an already existing genus, or change the name to reflect our
current taxonomic understanding of it. But ultimately, having the names in place
to be sure that we're referring to a particular organism, that's the kind of
stability that we're aiming for. So maybe it's a good moment to introduce the
idea of the principle of priority. That really is what is at the root of the
question of stability. So the principle of priority is a principle that has been
developed across codes of nomenclature for different organisms to deal with the
fact that our taxonomic opinions change, and there might be parallel groups
working in the same taxa. And the main idea of the principle of priority is that
any one taxon that is named would retain that name so far as that name is valid
under a given code of nomenclature. Valid and correct. And on the other hand,
one name that has been validly and correctly assigned to a taxon cannot be used
for any other taxon in the future. So once it has been published, validly and
correctly published, it's a reserved moniker for that taxon, and that is really
what is allowing this degree of stability. That doesn't exist, or that didn't
exist for uncultured prokaryotes between 2001 and the publication of the SIG
code, because the code of nomenclature for prokaryotes required the deposition
of strains into culture collections in two different countries. Yeah, so then I
guess we should lead into the crib that people were using, which is they just
named the things candidatus, which is a catch-all for anything that hasn't been
formally assigned, and that's not regulated at all. So, right, so I could write
a paper and say, I have candid, you know, Alikhani, and be done with it. And,
you know, you could do the same, you could use a similar name and it could all
be colliding and very, very confusing. Right, so what's the rationale, take us
to candidatus as an explanation and how you see it, that as a problem. Yeah, so
funnily enough, there is actually one regulation for candidatus, the only one
that I'm aware of, and is that it cannot be assigned to organisms that are
cultivated. If it's cultivated, you cannot name it candidatus, and we can talk
about that later, but there are other reasons why the regulations of the ICMP
might not be compatible with naming organisms, even if they are already
cultivated. There are other reasons, but the problem with not having priority
for these names is that we end up, and we have seen it in practice, we end up
with a flurry of names that are all referring to the same taxa. So we have many
synonyms, and we can potentially have also names being reused to refer to
different taxa. So we have homonyms, which is really the main objective of
nomenclature is to have one taxa on one name. That really is it. And of course,
if we don't have, if we have synonyms and homonyms, that one job of the whole
discipline is, well, goes. And the fact that candidatus isn't regulated in any
way whatsoever, in terms of how names are formed or what you need in place to be
able to name something, means that there are very many candidatus taxa, which
don't have an actual species that it's associated with. So we could be talking
about families or orders or classes, but we don't have an anchor point of a
specific organism for that name. So there's, in literature, there's a lot, like
a plethora of candidatus taxa that only refer to higher taxonomic ranks and not
to specific species either. So if I now find species X, which actually belongs
to class Y that someone described as a candidatus class at some point, there's
technically nothing that prevents me from just giving it whatever name I want.
And then ultimately, the name that's assigned to the class, like the higher
ranks as candidatus names, kind of gets lost in literature and there is not a
good track record of where those names have gone and what they are actually
referring to. Maybe I can again introduce here another concept to expand on what
Marika is explaining, and it's the concept of the nomenclatural type. Since we
don't know a priori what biological diversity is like, and what will we find in
the future, we have a really hard time naming it. Even if we knew, it will be
hard just because there is so much biological diversity. But not knowing in
advance makes it even harder. And so the genius idea behind most or all
nomenclatural codes is that we can assign an anchor and anything that is similar
enough to that anchor gets the same name. It's doing a heavy lifting here, but
that's part of the freedom of taxonomic opinion. And of course it varies
depending on the rank of the taxon. But it is a very clever idea that again goes
sideways when we have something like a name of a phylum, but no specific anchor
for it. There is no one representative of that phylum that means anything closer
to this one organism, similar enough to this one organism, gets that name. If in
five years we decide that there is too much diversity contained within this
taxon and we want to split it, which one of the two parts gets the name and
which one gets renamed? There is no way of deciding, no objective way of
deciding. So that's why it's important to name things from the bottom up.
Defining one type material or one nomenclatural type for the species and then
from the species up to genus or family and so on. And really what we are trying
to do here with the SIG code is simply saying that the type, the nomenclatural
type of species and subspecies can be the genome. It doesn't have to be a pure
culture deposited in two different countries, in culture collections in two
different countries. It can be just their genome. So you mentioned that a genome
could define the thing, the nomenclature, or it might be defined by how closely
related it is and that term is ambiguous. So when someone defines one of these
terms, are there a bunch of properties that they put in with that? So usually, I
mean, when we're talking about species delineation or taxon delineation, people
are free to use a variety of information to ultimately delimit that taxon one
way or another. But I might believe genealogical concordance is the best way to
circumscribe species and to look for species boundaries. So for cohesive groups
that are analogous to species, whereas someone else might believe average
nucleotide or identity should form the basis of all of those decisions. And
typically in prokaryotic taxonomy, when we're talking about species delineation,
it's often seen as a polyphasic approach. So you try to use a range of different
information and get the consensus of that to ultimately delimit the species. So
as more genome data has become available, we've progressively moved towards
using genome data as the basis for identifying those species boundaries. And
that's something that can be used for both cultivated organisms with genomes
available and uncultivated organisms for which we have genomes available. So
those are all really useful. Are those actually saved as something in the C code
repository? Like this is the anchor and these are the properties that would make
it similar to this anchor? Yes. So that goes back, that goes now to what we call
the C code registry. So this, because we, in the C code, the C code is not tied
to any one journal, which means all of the peer reviewed sites.  Scientific
literature is a fair game and we cannot possibly scan all possible, all
different proposals of taxa, of new taxa, taxa names. So we have, instead of
tying the SIG code to a specific journal, what we have done is we have created a
queryable repository that is called the SIG code registry. And in the SIG code
registry, there are a series of minimum data, minimum information that is
required to propose the name, a new name, and one of them is the description. So
the description is the description of a taxon is where the circumscription of
that taxon is located. Sometimes that can be extensive, two or three paragraphs
talking about their ecophysiology and their metabolism and so on. Sometimes it
can be a couple of sentences saying this taxon is circumscribed on the basis of,
you know, GTDB, RED indexes or average amino acid identity or average nucleotide
identity. And, and under no code, is there actually a requirement for, so under
the SIG code, there's also not a requirement, an absolute requirement for an
actual description paragraph or what has typically been called a protologue, but
basically the evidence for the novelty of that organism, the idea is that that
needs to be presented in the effective publication. So the actual paper that
gives you the evidence that this is something new, that's the idea that at least
in that paper, there needs to be sufficient evidence to be convincing that this
is a novel taxon. And even though I might not necessarily agree with that
particular paper, that's again, the taxonomic opinion where we need to draw a
distinction between taxonomy and the nomenclature of it. I think Marika used
here a term that maybe some of your listeners may not know, and it's effective
publication. That's another important concept in the nomenclature of codes. The
effective publication is the manuscript where the taxon is described, where the
evidence Where the name is mentioned, where the name is given. Where the name is
proposed, yes. Which ideally is all the science behind all the evidence of
novelty of that taxon, right? It's the vehicle through which the authors
described all the process. And that is also captured by the SIG code. One of the
last requirement, the last mandatory requirement for the naming of an organism
in the SIG code is that the effective publication is deposited in the SIG code
registry. Yes. So I can't just name something and validate it without an actual
paper being published on the novelty of that organism. Okay, so a couple of
observations from that. It actually sounds that this is actually a really
important problem. I suppose it sounds like a fairly common problem where if you
have, say, a data set or you have data points sort of displayed on a chart and
you're trying to do clustering on that, you often have an interesting problem of
deciding where those boundaries are at a complex data set. And one tactic that
you seem to be describing is to pick a centroid and base your clustering around
that. And that seems to be a fairly effective way of doing it. And that seems to
be what you're applying here, using a specific genome as that centroid. The
other thing I'll point out is this issue of runaway naming is not restricted to
naming species, but I'm sure people have encountered very weird, complicated
problems with naming of genes, which doesn't have any such structure. You know,
the gene, you'll read a paper and it'll describe an operon, you'll think that's
very interesting. You'll read another paper in another species, it'll describe
the similar operon and go, oh, that's kind of similar. And you're like, no, it's
actually the same thing. It's just the same thing. They named it in Yersinia
something, they named it in E. coli something else, and no one's actually
bothered to go back and reconcile those namings. The people who work in the
species know, but as an outsider, you're just going to get, you're going to have
to figure that out on your own. So to me, this sounds like really important
stuff to sort of address before it gets out of, I'm presuming that you're
setting this up before it gets out of hand, before we have way too many genomes
to deal with. It's also worth saying, I wanted to also say that when we're
specifying an amenglytral type, it doesn't necessarily mean that it's the mid-
weight organism genome of the organism. It doesn't mean that it's the most
typical or the most average of that taxon at all. But yeah, if you were to
cluster things based on average nucleotide identity or whatever, then using a
mid-weight approach would make sense. But the type doesn't necessarily have to
be a typical representative of that taxon. One of the things I wanted to ask is
actually, this thing of this, the suggestion of using a genome sequence as that
mid-weight is not necessarily that, it's not that controversial because in
classic taxonomy, surely this is something taken into consideration, right? Yes.
Yes. So all major journals of systematics have been requiring genomes to propose
new taxa for very long time already. This is not something new. And in fact, if
I may, in the ICMP back in 1966, the requirement for the proposal of a new
species or subspecies was that you will designate a type strain, or in special
cases, a description, a preserved specimen, preparation, or even an
illustration. So we are really modernizing, bringing back that concept of
freedom on what we use, that we use as the basic information we use, and
modernizing it to include a very, something that happens to be a very stable
kind of data that is also much cheaper to obtain today, which is the genome. And
something that is routinely used for species delineation and delimitation in
cultivated organism, as you said, in traditional prokaryotic taxonomy as well. I
mean, that's something, genomes are cultivated under the ICMP, so the
nomenclature or the code of nomenclature for prokaryotes, like we're already
like validating names under that code using genome data. So it's not, Barney
Whitman always says like, it's not revolutionary, it's evolutionary. It's an
evolutionary change that allows us to actually use the data and the information
that is appropriate for the organisms that we study. You mentioned this thing of
prokaryotes, so it's a sequence and the difference of culture and non culture.
Does the C code apply to everything, cultured, uncultured, and is it only for
bacteria or is it for, how far does that scope extend? Yeah, so on the
distinction of cultivated versus uncultivated, yes, the C code applies to all
prokaryotes, whether they are cultivated or not. You can propose a new name
under the C code, even if the name, the organism is cultivated. There are
reasons why you may have a culture, but you may not be able to validate your
name through the ICMP. One of them is if you have a pure culture, but that
organism is fastidious, it's very difficult to grow. For example, it requires
very high pressures or very low nutrient concentrations or something like that,
or it just takes years to double. That means that realistically you won't be
able to deposit that organism in culture collections, at least not anytime soon.
So that's one limitation, even if the organism is already cultured. Another
limitation is the application, the uneven application of the Nagoya protocol.
The Nagoya protocol regulates access to genetic resources and the fair and
equitable sharing of benefits arising from their utilization. And that
regulation applies differently in different countries, and there are countries
in which that regulation is a lot more strict, like for example, in Brazil, in
South Africa, in South Korea. And what that means is that descriptions coming
from these places will almost never be attached to the transfer of material to
different countries, just because they can't, they just can't regulatorily. And
in some of the countries, depending on the interpretation of those countries
that are signatories to the Nagoya protocol, they might be allowed to export the
culture to a culture collection, which the culture collection could effectively
cultivate and deposit effectively within the culture collection, but then
there's limitations on distributing those cultures to other researchers. And
under the ICMP, there isn't a lot of room for that.  to be any restrictions like
that. So even if you did deposit it, depending on which countries we're talking
about, even if you ended up depositing your culture into international culture
collections, there might be limitations on the actual distribution of those
cultures afterwards, and then under the actual ICMP, they're not able to be
validated, the names. Can I extend Nabil's question just a little bit more? So
he asked about bacteria, but like, I promised you a ridiculous question before.
So what if you found DNA in a mosquito in amber? What if you have a Jurassic
Park experience here, and it might be a eukaryote? Under the C code, it's
currently, the C code is currently to accommodate archaea and bacteria from
sequence, using sequence data as nomenclatural types, but potentially in the
future, I think under the zoological code, you can actually use DNA for
describing the organism. So technically, if it's a eukaryote, and they got DNA,
a Jurassic Park moment, they would be able to describe that organism under the
actual, is it the IC, I don't know, ZN, ZN, the zoological code of the name. I
don't know if it would be Z or Z for the majority of people. Oh, you can, you
can go either way. Definitely, we definitely have an international audience.
Yeah, that requirement, that requirement of living type material is unique to
prokaryotes. So we really are only solving a very specific problem in
prokaryotes. Nobody needs a living oak to name a new species of oak or a living
tiger to name a new species. Or a mating pair. It would be the equivalent of
having a mating pair to be able to name the organism. That you'd have to somehow
maintain and keep somewhere. It needs to be viable going forward. Yeah, so
that's unique to prokaryotes, that problem. Many thanks for coming along today
and having a chat with us. Today, we've been talking about systematics,
specifically SeqCode, which is a nomenclature code for naming prokaryotes
described from sequence data. And talking to us has been Marika Palmer and
Miguel Rodriguez. And you've been with Lee and Nabeel today, and this is the
Microbinfee podcast, and we'll see you next time. The opinions expressed here
are our own, and do not necessarily reflect the views of CDC or the Quadram
Institute.