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Development of the SeqCode: A proposed nomenclatural code for
uncultivated prokaryotes with DNA sequences as type
William B. Whitman
a,
⇑
, Maria Chuvochina
b
, Brian P. Hedlund
c
, Philip Hugenholtz
b
,
Konstantinos T. Konstantinidis
d
, Alison E. Murray
e
, Marike Palmer
c
, Donovan H. Parks
b
,
Alexander J. Probst
f
, Anna-Louise Reysenbach
g
, Luis M. Rodriguez-R
h
, Ramon Rossello-Mora
i
,
Iain Sutcliffe
j
, Stephanus N. Venter
k
a
Department of Microbiology, University of Georgia, Athens, GA, USA
b
The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
c
School of Life Sciences, University of Nevada, Las Vegas, NV, USA
d
School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
e
Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
f
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU),
University of Duisburg-Essen, Essen, Germany
g
Biology Department, Portland State University, Portland, OR, USA
h
Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
i
Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
j
Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
k
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
article info
Article history:
Received 9 November 2021
Revised 30 January 2022
Accepted 31 January 2022
Keywords:
Nomenclatural type
Metagenome
SeqCode
Nomenclatural code
Candidatus
abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The gen-
omes of most type strains have been sequenced, genome sequence similarity is widely used for delin-
eation of species, and phylogenomic methods are commonly used for classification of higher
taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-
uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of
Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last
two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types.
The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot
be deposited into culture collections. Several simplifications relative to the International Code of
Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to
apply and more readily communicated. By simplifying nomenclature with the goal of a unified classifica-
tion, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in
every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and pro-
mote synergies between the ecological, environmental, physiological, biochemical, and molecular biolog-
ical disciplines to more fully describe prokaryotes.
Ó2022 The Author(s). Published by Elsevier GmbH. This is an open access article under the CC BY license
(http://creativecommons.org/licenses/by/4.0/).
Contents
Introduction. . . . . ........................................................................................................ 2
Some general principles of biological nomenclature . . . . . . . . . . .................................................................. 3
Comparison of the ICNP and the SeqCode ..................................................................................... 4
Nomenclatural types. . . . . . . . . . . . . . . . . ..................................................................................... 4
Priority of higher taxa. . . . . . . . . . . . . . . . ..................................................................................... 5
https://doi.org/10.1016/j.syapm.2022.126305
0723-2020/Ó2022 The Author(s). Published by Elsevier GmbH.
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
⇑
Corresponding author.
E-mail address: whitman@uga.edu (W.B. Whitman).
Systematic and Applied Microbiology 45 (2022) 126305
Contents lists available at ScienceDirect
Systematic and Applied Microbiology
journal homepage: www.elsevier.com/locate/syapm
Simplification of the code. . . . . . . . . . . . . ..................................................................................... 5
Administration of the SeqCode. . . . . . . . . ..................................................................................... 6
Conclusions . . . . . ........................................................................................................ 6
Acknowledgements . . . . . . . . . . . . . . . . . . ..................................................................................... 6
Appendix A. Supplementary material. . ..................................................................................... 7
References . . . . . . ........................................................................................................ 7
Introduction
Genomics has profoundly influenced prokaryotic systematics
over the last fifteen years. Led by Nikos Kyrpides and Tanja Woyke
at the U.S. Department of Energy’s Joint Genome Institute, in col-
laboration with Hans-Peter Klenk and later Markus Gӧker at the
DSMZ, the systematic sequencing of microbial genomes began
with the Genomic Encyclopedia of Bacteria and Archaea (GEBA)
project [24,66]. It was joined in 2018 by the World Data Centre
for Microorganisms at the Chinese Academy of Sciences in Beijing
in a project called GCM2.0, led by Juncai Ma and Linhuan Wu [67].
These large-scale genome sequencing projects targeted type
strains, the taxonomic reference material of prokaryotic species,
and together have sequenced over 4,000 type strains to date. In
parallel, most prokaryotic systematics journals now require or
strongly recommend that genome sequences be included in
descriptions of new species [5]. As a result of these and other
efforts, the genome sequences of >14,500 of the approximately
18,000 type strains are now available (https://gctype.wdcm.org/).
The remaining as-yet-unsequenced type strains were mostly
described prior to the advent of widespread genome sequencing
and include fastidious prokaryotes from a wide variety of habitats.
The availability of inexpensive genome sequencing has also led
to a key role for genomics in the establishment of modern species
definitions. Previously, DNA:DNA hybridization was the consensus
method to delineate and distinguish prokaryotic species [60].
However, this method was difficult to execute and prone to exper-
imental error [51]. Genome sequence similarity was shown to cor-
relate with DNA:DNA hybridization values [13] but is more precise,
repeatable, and less prone to experimental error, leading to the
development of genomic methods, such as Average Nucleotide
Identity (ANI) [23,42,49] and digital DNA:DNA hybridization
(dDDH) [27]. These in silico techniques have allowed the broad
application of sequence similarity and improved the fidelity of
prokaryotic species delineation. As a result, genome comparisons
are now central to prokaryotic species descriptions and provide
greater resolution than 16S rRNA gene-based comparisons, which
have long been widely used.
In parallel with culture-based genomics, high throughput
sequencing has increasingly been applied to microbial communi-
ties (metagenomics) [48], culminating in the ability to obtain com-
plete and nearly complete bacterial and archaeal genomes directly
from environmental sequence data, so called metagenome-
assembled genomes (MAGs) [4,35,54]. However, since most MAGs
are still draft assemblies of environmental contigs, and each contig
is often a mixture of sequences from sympatric strains, the fidelity
of such genomes has been questioned [28,58]. Continuing
improvements in both laboratory and bioinformatic approaches,
including the use of long-read sequencing, suggest that MAG qual-
ity can often, but not always, be on par with that of isolate gen-
omes and will likely soon be on par in all cases when long-read
sequencing becomes more accessible and reliable [30]. The cost-
effective generation of MAGs has resulted in sequences of tens of
thousands of genomes across dozens of ecosystems, which has
substantially increased our understanding of prokaryotic diversity
[46].
Apart from using genome sequences for the delineation of spe-
cies, the availability of genomes representing higher taxonomic
groups [24], as well as intra-species diversity, has changed the
classification of Bacteria and Archaea in a profound way. Genomic
data have not only been used to address the systematics and evo-
lution of specific genera [3,8,12,53,69] but also several higher taxa
[14,18]. Genome sequences have also been used to develop a stan-
dardized bacterial and archaeal classification based on phyloge-
netic analyses and sequence divergence [45,50], as is currently
reflected in the Genome Taxonomy Database (GTDB) [46,50]. The
incorporation of nearly 260,000 genomes, including >53,000 MAGs
has significantly improved the state of knowledge of the phylogeny
and classification of Bacteria and Archaea [46].
The extensive use of genomic data in taxonomy and the stabil-
ity and insight it has provided has led microbiologists to propose
better integration of genomic data into formal systems to name
and classify taxa, including those without representative pure cul-
tures. Various proposals were made to incorporate DNA sequence
data into formal systems of nomenclature. Hedlund et al. [15]
and Konstantinidis and Rossello-Mora [20] proposed revision of
the Candidatus concept from the International Code of Nomencla-
ture of Prokaryotes (ICNP) to incorporate SAGs and MAGs regard-
less of the ability to visualize these organisms in natural
samples. Whitman [61,62] further proposed revision of the ICNP
to incorporate high-quality genome sequences as nomenclatural
types. That proposal would have paved the way for validation of
Candidatus names and improved the stability of their nomenclature
[64].
In 2017, Konstantinidis et al. [21] articulated the need for a
stable system for naming uncultivated microbes and for the first
time proposed the possibility of a separate nomenclatural system
based on high-quality MAGs and SAGs. The following year, Hed-
lund and Reysenbach obtained funding from the US National
Science Foundation’s Systematic and Biodiversity Science Cluster
to develop a strategy for Microbial Systematics for the Next Decade.
Several online meetings and in-person workshops in October 2018
and April 2019 resulted in the publication of a Consensus State-
ment [34] endorsed by 120 prominent microbiologists from
around the globe. The first goal (‘Plan A’) was the ratification of
Whitman’s proposal [62] by the ICNP to allow DNA sequences as
nomenclatural types, whilst the alternative goal (‘Plan B’) was a
separate code based on genome sequences as types, as proposed
earlier [21]. In anticipation of using genome sequences as type, cri-
teria for selecting type genomes have been proposed [6,21]. After
debating ‘Plan A’ in an e-mail discussion forum, the International
Committee on Systematics of Prokaryotes (ICSP) rejected the pro-
posal by Whitman [62] that DNA could serve as types under the
ICNP [57]. In response, ‘Plan B’ was initiated. The first draft of the
Code of Nomenclature of Prokaryotes Described from Sequence
Data (SeqCode) was prepared in the summer of 2020 and discussed
at a series of international online workshops held during February
2021 under the banner of the International Society for Microbial
Ecology (ISME), which engaged 848 registrants from 42 countries.
The focus of the workshops was to communicate ‘Plan B’ and
gather stakeholder feedback on important issues, which were
incorporated into revisions of the draft SeqCode (https://www.
W.B. Whitman, M. Chuvochina, B.P. Hedlund et al. Systematic and Applied Microbiology 45 (2022) 126305
2
isme-microbes.org/seqcode-workshops). As a result of this process,
the first edition of the SeqCode has now been published [16].
Below we review some of the context and considerations
underpinning the design and proposed operation of the SeqCode,
particularly in relation to lessons learned from the workings of
the ICNP.
Some general principles of biological nomenclature
Naming is an essential component of scientific investigations,
including those in biology. Without the ability to assign precise
and unambiguous names, it is impossible to communicate effec-
tively. For instance, prior to the implementation of the ICNP and
formation of the Approved Lists [55],Mycobacterium tuberculosis,
the causative agent of tuberculosis, had at least nine scientific
names [2]. Not only did the multiple names make following the lit-
erature difficult, but the exact meanings of the names were uncer-
tain, which caused confusion and was perilous in a medical/
veterinary microbiology context. Precise naming is also critical
for the meaningful implementation of large databases and for
large-scale analyses made possible by computing. Without a single,
relatively stable name, databases require frequent curation, which
becomes increasingly difficult as their content grows. Thus, a pre-
cise naming system is needed for the effective application of mod-
ern bioinformatics tools.
In biology, most codes of nomenclature have been designed to
create precise names by establishing identifiers that have a one-
to-one correspondence with natural entities [65]. Their goals are
often described in sections entitled ‘‘General considerations” or
‘‘Principles”. Chief among their goals is to ensure that each entity
has only a single, unique formal name in a particular taxonomic
context or ‘position’. This goal is challenging because naming pro-
ceeds concurrently with biodiversity discovery, which occurs inde-
pendently by investigators all over the world. Investigators often
have different taxonomic opinions and philosophies, and naming
must accommodate these differences. Nomenclatural codes seek
to knit these divergent efforts into a single, shareable, robust
nomenclature.
To accomplish this goal, nomenclatural codes must deal with
four fundamental components of naming. The first is the hypothe-
sis that there exists a biological entity deserving of a name. From
the viewpoint of a taxonomist, the biological entity is defined as
a taxon. Like other codes, the ICNP is purposely ambiguous regard-
ing the nature of these entities and defines them as ‘‘any group of
organisms treated as a named group in a formal taxonomy” (Gen-
eral Consideration 7(3)) [44]. This ambiguity is necessary because
codes must be useable by investigators with very different taxo-
nomic philosophies. However, the ICNP does exclude certain
things, such as fossils, which are named under other codes.
The second component is evidence for the taxon, which is the
nomenclatural type (or just ‘type’) under most codes. Types have
three essential functions. First, they prove the existence of the
taxon. Second, they provide a reference standard for comparison
with a new specimen to determine whether it belongs to the
same or a different taxon. As a consequence of the latter, the third
function of types is their role in the application of names. Pres-
ence of a type in a taxon demands that its name be based upon
the name of the type. Exclusion of all known types from a taxon
warrants the creation of a new name. The system of types ensures
the precise meaning of the names [17]. For instance, a specimen
named Mycobacterium tuberculosis must be included in a taxon
that encompasses the type of the species to warrant the same
name.
There are two fundamentally different kinds of types. Firstly,
the types for species and subspecies are the experimental evidence
for the taxon and in prokaryotic biology have historically been
strains or, in some cases prior to 1 January 2001, detailed descrip-
tions, preserved (non-viable) specimens or illustrations [26,43].In
the SeqCode, this kind of type is a genome sequence. Secondly, the
types for genera and higher taxa are their subordinate taxa (for
example, a genus has a type species and a family has a type genus).
As a consequence, every taxon is associated with some experimen-
tal evidence of its existence, either directly as for species and sub-
species or indirectly as for taxa above the rank of species. Likewise,
the precise meaning of each name is derived from the knowledge
that the taxon includes a particular type.
The third component is the name itself, which is arguably the
least important component. Although Linnaean tradition favours
binomial names formed from Latin and Greek, in principle the
name could be formed from any source and even arbitrarily [39].
Latinization of names was understandable when naming was pri-
marily a European activity and Latin was a common component
of their scientists’ education [65]. It is less justified in the modern
global context, and the International Code of Virus Classification
and Nomenclature has recently been emended to permit names
that are not Latin binomials (https://talk.ictvonline.org/informa-
tion/w/ictv-information/383/ictv-code).
Ideally, names should be understandable and easy to form. In
practice, latinization of names often requires extensive curation
by experts and lacks scalability. Thus, while it is not difficult to cre-
ate a few names during a research project, generating large num-
bers of names is time-consuming, tedious, and prone to
grammatical error. Fortunately, there are a number of ways to
increase the scalability of naming even within the ICNP. Pallen
et al. [41] recently created the ‘Great Automatic Nomenclator’ or
GAN, which can combinatorically generate large numbers of names
from a small number of Latin roots. This approach may be general-
ized and improved in the near future and eliminate the problem of
scalability while providing even more options for creating linguis-
tically correct names. An alternative is to create a system of simpli-
fied latinization with relaxed rules to simplify the naming process
for the research community and decrease the burden on curators.
Some biological codes of nomenclature have also relaxed the rules
for naming so that strict adherence to Latin is not required. A more
complete discussion of the process of creating names is given by
Pallen [39].
Fourthly, a code should describe a process or system that allows
names to be added as new data or new perspectives are acquired.
This process resembles an algorithm, which is a simple set of rules
that enables solving of complex problems. By systematically com-
bining the discoveries from a large pool of investigators, a consen-
sus nomenclature can be achieved even in the absence of a unified
classification. The algorithm must allow for creation of new names
as taxa are discovered or when the classification of existing taxa
change. The process of union, transfer, and division of taxa must
be straightforward so that it is easily understood and readily
adopted; and when conflicts arise, there must be means to objec-
tively resolve them.
The principle of priority is a key element of this process. This
principle states that the earliest validly published name for a taxon
is the correct name for the taxon. This principle ensures the stabil-
ity of names and that, in a given taxonomic position, each taxon
has only one correct name. At the rank of species and subspecies,
names are directly associated with a nomenclatural type, so the
earliest name that includes a particular type has priority over
any subsequent name and cannot be changed. For instance, if a
species is moved to another genus, its species epithet remains
the same even though the genus name changes. If a species is uni-
ted with another species, the earliest validly published name
remains the correct name. If a species is divided, the taxon that
retains the type must retain the original name.
W.B. Whitman, M. Chuvochina, B.P. Hedlund et al. Systematic and Applied Microbiology 45 (2022) 126305
3
Because the nomenclature is binomial, a genus name and the
epithet of its type species have to be proposed at the same time
and, thus, have the same date of priority. Any genus that includes
that type species must have the earliest validly published genus
name of that species. Likewise, if a taxonomist unites two genera,
the type species of the resulting merged taxon will be the one with
the earliest, validly published name. If a genus is divided, the name
must be retained by the taxon that retains the type species.
Most nomenclatural codes attempt to be philosophically neutral
on the great issues in taxonomy. Principle 1(4) of the ICNP states:
‘‘Nothing in this Code may be construed to restrict the freedom of
taxonomic thought or action” [44]. However, in practice, absolute
neutrality is not possible [52]. For instance, both the ICNP and the
SeqCode are designed to create names for a hierarchical classifica-
tion, and thus both assume that a hierarchy is both desirable and
reflective of nature. Likewise, they also assume that entities called
‘species’ exist in prokaryotic biology. Implicit in these assumptions
is that every species belongs to a genus, and every genus belongs to
one of each of the higher ranks used in this hierarchy, i.e. family,
order, class, and phylum. Even if these founding assumptions are
incorrect, it is still possible to create a useful nomenclature.
Nomenclatural codes also strive to be independent of taxo-
nomic philosophy. This is necessary because perspectives change
with discoveries and the application of new techniques. As an
example, prior to the mid-1980s, prokaryotic taxonomy was lar-
gely determinative and did not necessarily seek to identify natural
relationships among taxa described at the higher taxonomic ranks.
Consequently, the ICNP placed great importance on the identifica-
tion of diagnostic properties of the lower taxa. With the develop-
ment of robust methods to determine genetic relationships,
prokaryotic taxonomy transitioned to a phylogenetic approach,
resulting in major changes in the nomenclature of individual taxa
[10,11,60]. The ICNP provided the framework that guided this pro-
cess, and many of the names created under the determinative tax-
onomy survived the transition to a phylogenetic taxonomy.
Comparison of the ICNP and the SeqCode
The SeqCode was developed over the last two years to allow the
naming of prokaryotes based on their genome sequences as
nomenclatural types. Thus, it will allow the naming of the enor-
mous uncultivated biodiversity discovered through the aid of
metagenomic sequencing and single-cell genomics as well as fas-
tidious prokaryotes that cannot reasonably be maintained and dis-
tributed by culture collections [34]. However, the SeqCode will
accomplish other things as well: (i) The naming rules will be lar-
gely consistent with those of the ICNP [44], and it is hoped that
the nomenclatures formed under both codes will eventually be
merged. (ii) The ICNP is difficult to read, and some parts are contra-
dictory. The SeqCode strives to resolve ambiguities without contra-
dicting the nomenclature developed under the ICNP. (iii) By being
more plainly written, less apt to alternative interpretations and
easier to understand, it will reduce controversy and confusion.
(iv) The SeqCode will provide an online system for registration
and curation of names. (v) The SeqCode will provide means to gen-
erate names with priority for taxa that can presently only be
named under the ICNP with the provisional Candidatus status.
Major differences between the SeqCode and ICNP are summa-
rized in Table 1. In addition, a detailed comparison of the two codes
is provided in the Supplementary Material.
In accomplishing these goals, the SeqCode is evolutionary and
not revolutionary. It adds no new ideas to the canon of biological
naming. For instance, the most controversial aspect of this code is
that it does not require physical evidence for the taxon in the form
of viable cultures. However, neither did the 1990 International Code
of Nomenclature of Bacteria [26], which allowed detailed descrip-
tions and illustrations to serve as nomenclatural types until January
2001 [44]. Similarly, the International Code of Virus Classification
and Nomenclature (https://talk.ictvonline.org/information/w/ictv-
information/383/ictv-code) does not require deposition of physical
samples, and none of the other codes requires living samples. The
goals of the SeqCode are practical and not philosophical, and it
seeks to make naming easy and yet clearly regulated. Ease is an
important virtue for nomenclatural codes because it encourages
wide use. The diversity of prokaryotes is enormous and far exceeds
the capacity of contributors to any specialized discipline to fully
understand. Hence it is hoped that the SeqCode will encourage par-
ticipation by those working in diverse disciplines.
Nomenclatural types
In addition to providing guidelines for naming, nomenclatural
codes also provide standards for the evidence that can be consid-
ered as type. While recognized standards are necessary to prevent
Table 1
Comparison of the SeqCode and ICNP.
Category ICNP SeqCode Comments
Type Viable culture DNA sequence and viable culture The SeqCode recognizes ICNP names with
priority
Criteria of authenticity Viable culture representing type is
deposited in two culture collections
in different countries.
Sequence representing type is deposited in an INSDC
database and accession number is cited in effective
publication and online Registry.
Registration of names Publication in IJSEM or Validation
Lists
Online SeqCode Registry SeqCode registration requires an effective
publication
Compatibility of names
with databases
None, requires manual curation Database structure of registration system avoids a
need of third parties and allows easy access, search
and retrieval of information.
Governing body International Committee on the
Systematics of Prokaryotes (ICNP)
Committee on the Systematics of Prokaryotes
Described from Sequence Data (CSPSDS)
Number of taxonomic ranks
above genus
9 4 SeqCode does not recognize many rarely
utilized taxonomic ranks
Type for taxonomic ranks
above genus
Genus except class, which is order Genus for all higher taxa
Priority for taxonomic ranks
above genus
Depends on date the name is
validly published
Depends on the date the type genus is validly
published
Number of rules 65 50 Omission of rules related to unused taxa
and names prior to the Approved List
allowed reduction of SeqCode
Start date 1947 January 1, 2022
W.B. Whitman, M. Chuvochina, B.P. Hedlund et al. Systematic and Applied Microbiology 45 (2022) 126305
4
the creation of imprecise names and other abuses, they necessarily
restrict the freedom of taxonomic thought. For instance, since
2001, Rule 30 of the ICNP has required deposition of viable type
strains into two service collections [7,25,31,44]. The deposition of
axenic cultures is a restrictive methodological standard and pre-
vents the expansion of nomenclature to the large numbers of
uncultured prokaryotes identified by metagenomic sequencing.
Many fastidious prokaryotes are also excluded because service col-
lections lack the facilities to cultivate them. Lastly, some organisms
are excluded by international laws preventing the export of biolog-
ical material from their countries, which include several recog-
nized biodiversity hotspots [57]. Although these organisms may
be readily culturable, at the present they cannot be freely dis-
tributed through culture collections and so are disbarred from for-
mal, valid naming. The restrictive nature of the ICNP is discordant
with the more inclusive nature of all other codes of nomenclature,
and by restricting names to a small range of the full diversity of
Archaea and Bacteria, it fails to serve the greater microbiology
research community [43].
Candidatus names were proposed to ameliorate some of the
consequences of Rule 30 and are described in an appendix of the
ICNP [32,33,40]. The Candidatus provisional category was intended
for taxa known originally by 16S rRNA gene data and other data,
principally morphology, ecology, or physiology, but has since been
co-opted to include MAGs and SAGs [20] as well as pure cultures
which could not be deposited in culture collections. Although over
a thousand Candidatus names were proposed before 2019 [37,38],
these names lack priority and other protections offered by the leg-
islative section of the ICNP. Therefore, Candidatus names fail to
accomplish the major goals of nomenclatural codes and have not
replaced many of the alphanumeric identifiers widely used for dec-
ades for many uncultured taxa. Most of these alphanumeric codes
are imprecisely defined and many suffer from a high degree of syn-
onymy, lack any concept of rank, and are difficult to remember
because they are memorized and recalled as strings of words, let-
ters, and numbers rather than a single word for a formal taxonomic
name, which strains memory and easy recall [22,29,43].
The major difference between the SeqCode and the ICNP is that
the SeqCode allows DNA sequences, primarily genome sequences to
serve as types. Genome sequences satisfy all the criteria necessary
for types [61]. They prove the evidence of the existence of taxa and
allow ready comparisons to the types of other taxa. Moreover, they
offer many practical advantages over type strains [22,43]. They are
suitable for both uncultivated and cultivated taxa. They are inex-
pensive to store and easy to share. They create a permanent record,
whereas culture collections require regular maintenance, and the
viability of archival material is uncertain. A mechanism is also pro-
posed to create minimum standards to ensure data quality of the
SeqCode. The minimum standards are themselves outside the code
to allow for flexibility as experimental methods change. Thus, the
SeqCode also requires a working group to review and approve min-
imum standards. Previously proposed standards for isolate gen-
omes, MAGs and SAGs served as guides for these standards
[1,5,6,9,21]. In addition, less restrictive minimum standards could
be proposed by taxonomists with expertise in specific taxa. For
instance, it may not be possible at the present time to generate gen-
ome sequences for certain obligate endosymbionts. If experts famil-
iar with these organisms have experimentally validated alternative,
sequence-based procedures such as multilocus sequence analyses,
they will be acceptable types under the SeqCode.
Priority of higher taxa
Elements of the ICNP are poorly suited for a phylogenetic clas-
sification. When most of the backbone of the ICNP was written in
the second half of the last century, the extent of prokaryotic diver-
sity was greatly underestimated. Many genera were not assigned
to higher taxonomic ranks, and class was the highest recognized
rank. The Approved Lists from 1980 contained only seven named
classes and 58 names in total above the rank of family [55]. More-
over, there was no standardization in the formation of class names.
At that time, the ICNP heavily emphasized naming species and gen-
era, and rules for naming the higher taxonomic ranks were rarely
discussed and remained ambiguous. In contrast, today there are
more than five hundred validly published names of taxa above
the rank of family [47]. More than a hundred classes have been
named, and the rank of phylum has become widely used even
though it has only recently been incorporated into the ICNP. As a
consequence of the ambiguities in the ICNP regarding higher taxa,
many of these names were not created in a standard manner,
resulting in contradictions in the nomenclature.
With the exception of classes, the types of the higher taxonomic
ranks in the ICNP are genera, and the genus names serve as the
roots of their names. Although the genus with the earliest name
may be chosen as the type of a family or order, the ICNP does
not provide clear direction in this regard and the fact that the type
of a class is one of the contained orders introduces a discontinuity
into the system. Moreover, the priority of the names of higher taxa
depends on the date of validation of the name. Since naming higher
taxa was not a common practice prior to Garrity et al. [11], these
rules created the potential for instability and confusion. For
instance, it has been argued that a validly published family name
has priority even when its type genus is illegitimate [59,63].It
has also led to the creation of confusing names. For instance, under
the ICNP, if the genera Alcaligenes Approved Lists 1980 and
Burkholderia Yabuuchi et al. 1993 are united in the same family,
the family is named Alcaligenaceae De Ley et al. 1986 and not
Burkholderiaceae Garrity et al. 2006 because of the priority of Alcali-
genaceae De Ley et al. 1986. However, because an order ‘‘Alcalige-
nales” has never been validly published, the family is classified in
the order Burkholderiales Garrity et al. 2006.
In the SeqCode, the priority of the names of higher taxa depends
on the priority of the genus name. The rationale is that, in a hierar-
chical classification, the creation of a new genus implies the poten-
tial for a new family, order, class, and phylum even if they are not
named at the time. By using the earliest named genus as the type,
future unions of genera are unlikely to change the name, thus
ensuring the stability of the names of higher taxa. Moreover, if
higher taxa are united, the name would be chosen from the one
whose genus name had priority. If a higher taxon is divided, the
branch that includes the type would retain the name. The newly
recognized branch would acquire a name based upon the taxa
immediately below it in rank. An entirely new higher taxon could
only occur upon discovery of a novel genus. Importantly, the Seq-
Code accepts all names validly published under the ICNP before
January 1, 2022. As a consequence, this rule has no effect on the
names of higher taxa validly published before that date, and it only
affects the names of higher taxa proposed after that date. For
instance, any order that included the genus Burkholderia would
be named Burkholderiales in both the ICNP and the SeqCode.
Simplification of the code
The ICNP distinguishes five categories of names: legitimate, ille-
gitimate, effectively published, validly published, and correct.
Legitimate names are formed according to the rules of the code,
including being validly published. In the ICNP, validly published
means registered either in the Approved Lists or by subsequent
publication in the IJSEM or its Validation Lists. All legitimate names
must be validly published. While in principle all validly published
W.B. Whitman, M. Chuvochina, B.P. Hedlund et al. Systematic and Applied Microbiology 45 (2022) 126305
5
names should be legitimate, this is not always the case. Sometimes
names become illegitimate due to breach of the principle of prior-
ity when applied to merged taxa or changes in the rules of the
Code. Lastly, correct names must be legitimate but are also those
to be used in a particular classification. These distinctions are also
used in the SeqCode. However, unlike the ICNP, the SeqCode uses
an online registration system, the SeqCode Registry. In this system,
the registration is completed by the authors of new names, prefer-
ably prior to publication. The names will then be reviewed and
approved by the list curators. Upon completion of an entry with
effective publication and type sequence details, the names will
become validly published. This system ensures priority of names
based on valid publication through the SeqCode Registry and not
based on the date of publication in journals, which equalizes the
opportunities of publishing names in any journal and do not favor
one over others. Moreover, the SeqCode Registry makes provisions
for names undergoing the proposal process, which are not yet
validly published, reserving these names for up to a year to avoid
synonymy with future publications. It also allows correction of
names early in the validation process, which will decrease confu-
sion and instability.
The goal of the SeqCode Registry is just to provide a list of names
that are connected with metadata and compliant with the data
standards and orthography of the SeqCode, and it is outside the
mandate of nomenclature committees to dictate taxonomic princi-
ples to the user community. Nevertheless, recommendations for
good practices for naming uncultivated taxa have been proposed
by Chuvochina et al. [6]. Similarly, there are only minimal require-
ments for validation of names in the ICNP. As a consequence, the
SeqCode will not prevent publications of papers with thousands
of computer-generated names with little associated information
should such papers be effectively published. However, we feel that
such naming is of little value and should be discouraged. While
thresholds based upon sequence similarities have proven to be
invaluable tools, they are also well known to be unreliable as the
sole criterion for taxon circumscription. Moreover, replacing
alphanumeric labels with Latin names in the absence of further
analyses misrepresents the state of knowledge of a taxon and leads
to the proliferation of confusing names. In general, taxa should only
be named when there is something to say about them.
Nevertheless, this concern is balanced by the consideration that
providing names or labels are important steps that facilitate com-
munication about taxa when they are further studied. While in an
ideal situation naming would be concurrent with detailed descrip-
tions, these two steps can be performed by different parties or the
same party at different times. In either case, naming helps track
knowledge as it is added and can serve as the starting rather than
the end point of the search for understanding.
The SeqCode proposes two other major departures from the ICNP.
The ICNP currently recognizes thirteen taxonomic ranks, while the
SeqCode is restricted to seven canonical ranks: subspecies, species,
genus, family, order, class, and phylum. The ranks of subgenus, sub-
tribe, tribe, subfamily, suborder, and subclass, which are recognized
in the ICNP, are not included in the SeqCode. These ranks are rarely
used in the modern literature, and their conceptual and experimen-
tal bases are ambiguous [36]. Secondly, many of the Rules of the ICNP
deal with naming prior to adoption of the Approved Lists and Valida-
tion Lists. Now that all the current names are incorporated into these
Lists, these Rules are no longer necessary.
Administration of the SeqCode
The SeqCode also proposes the creation of two administrative
bodies to facilitate its implementation. The Committee on the Sys-
tematics of Prokaryotes Described from Sequence Data (colloqui-
ally,the SeqCode Committee) will be responsible for the content
of the code and administering the infrastructure required for main-
tenance of the SeqCode Registry. Its functions are similar to those
of the ICSP. The SeqCode Committee will also oversee the election
of a SeqCode Reconciliation Commission with the authority to
resolve disputes regarding the interpretations of the rules and to
grant exceptions in unusual circumstances. Its functions are simi-
lar to those of the Judicial Commission of the ICSP. As noted above,
a working group will be maintained to advise on appropriate stan-
dards and quality control of sequence data. Oversight and organi-
zational support for these will be provided by ISME.
Conclusions
By creating the SeqCode, our intention is to produce a practical
solution to the nomenclature of the huge number of taxa currently
excluded from formal naming by the specific insistence in the ICNP
that types must be viable cultures. We hope that this will provide a
service to the wider community working on prokaryotic diversity
and that, in due course, this will allow the formal nomenclature
of all taxa to be brought under a unified framework.
The SeqCode is not intended to discourage isolation and collec-
tion of strains, and investigators are strongly encouraged to deposit
strains into culture collections whenever feasible to promote
resource sharing and reproducibility. The study of living cultures
is essential to progress in prokaryotic biology and obtaining a full
understanding of life on Earth. Currently, it is not possible to infer
the complete potential of Archaea and Bacteria from their genome
sequences, and strains remain important tools for fully under-
standing their pathogenicity, biotechnological applications, physi-
ology, ecology, lifestyle, and other properties of great practical
and theoretical importance. For these reasons, strains will retain
their value even when they are not nomenclatural types. This prin-
ciple is well illustrated by the recent isolation and characterization
of Prometheoarchaeum syntrophicum by Imachi et al. [19]. This
archaeon possesses the signature features of the Asgard archaea.
Described initially from MAGs, these deep sea microorganisms
are likely descendants of the ancestors of the archaeal component
of the first eukaryotes [56,68], and the availability of a representa-
tive culture provides key insights into the evolution of the first
eukaryotes [19]. Moreover, naming uncultivated microorganisms
facilitates all subsequent investigations whatever their scope and
nature. Importantly, it allows the creation of classifications unify-
ing cultured and uncultured taxa, identifying key taxa for environ-
mental and other processes, and encourages the isolation and
characterization of representative uncultivated taxa. In this man-
ner, the SeqCode will encourage cultivation of species of prokary-
otes known now only from their genome sequences. Of great
importance, it will foster the development of synergies between
the microbial disciplines of molecular biology, biochemistry, phys-
iology, systematics, environmental science and ecology. Already
evident, the benefits of this emergent understanding will continue
to have enormous consequences on the study of life.
Acknowledgements
Funding was provided by the US National Science Foundation
(DEB 1841658 and EAR 1516680), the US National Institute of Gen-
eral Medical Sciences (P20 GM103440) from the National Institutes
of Health, the Spanish Ministry of Science, Innovation and Univer-
sities (PID2021-126114NB-C42), the Australian Research Council
(FL150100038), the Deutsche Forschungsgemeinschaft (DFG, Ger-
man Research Foundation, SFB 1439/1 2021 – 426547801) also
supported with European Regional Development Funds (FEDER),
and the International Society for Microbial Ecology (ISME). We also
W.B. Whitman, M. Chuvochina, B.P. Hedlund et al. Systematic and Applied Microbiology 45 (2022) 126305
6
thank all participants in the SeqCode workshops, especially guest
speakers who graciously shared their expertise: Jongsik Chun,
Nicole Dubilier, Emiley Eloe-Fadrosh, Chris Lane, Juncai Ma,
Edward Moore, Aharon Oren, Jörg Overmann, Susanne Renner, Vin-
cent Robert, Conrad Schoch, Scott Tinghe, Linhuan Wu, and Arvind
Varsani.
Appendix A. Supplementary material
Supplementary data to this article can be found online at
https://doi.org/10.1016/j.syapm.2022.126305.
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