METHODS
Wu and Ma, Int J Syst Evol Microbiol
DOI 10.1099/ijsem.0.003276

The Global Catalogue of Microorganisms (GCM) 10K type strain
sequencing project: providing services to taxonomists forstandard genome sequencing and annotation
Linhuan Wu1,2 and Juncai Ma1,2,*

Abstract
The World Federation of Culture Collections and the World Data Center for Microorganisms (WDCM) initiated an international
community-led project to sequence and annotate newly described prokaryotic taxa. This sequencing project aims tocooperate with international culture collections and the International Journal of Systematic and Evolutionary Microbiology andcontribute to the expansion of whole genome sequencing databases for type strains. It will provide global microbial
taxonomists with free standard genome sequencing and annotation services. Taxonomists are encouraged to contact the
WDCM and participant culture collections to submit a type strain sequencing proposal.

INTRODUCTION
Since the late nineteenth century, the taxonomy of microorganisms has evolved from classical phenotypic methods
to polyphasic approaches. However, the current widely used
genotypic criteria, including DNA G+C content, DNA–DNA hybridization (DDH), 16S rRNA and other housekeeping gene sequence nucleotide similarity analyses, havevarious limitations [1].
Results obtained from genomic DDH experiments and thesequence analysis of small-subunit rRNA are widely usedand have come to be recognized as the so-called, ‘gold standard’ for species delineation. In prokaryotic taxonomy,
strains with DDH values greater than 70 % similarity understandardized conditions are generally considered to belong
to the same species [2]. However, this method is rather personnel-consuming and does not allow the construction of
cumulative databases [3].
The various domains of the rRNA gene serve as usefulmarkers in prokaryotic taxonomy and biodiversity assessments, due to its ubiquitous presence and conserved properties. However, this gene is highly conserved and often notable to provide discrimination among species within thesame genus, whereas multiple-gene and whole-genomederived approaches often provide the required resolution[4]. Since 1987, well before genome sequencing ofprokaryotes was commonplace, the search for an ideal taxonomy recognized that the complete deoxyribonucleic acid
(DNA) sequence would be the reference standard to determine phylogeny [5].
The rapid development of next-generation sequencing technology has made high-throughput sequencing a key tool formany microbiology laboratories. Average nucleotide identity and average amino acid identity, as well as core- andpan-genome cluster analyses-based approaches have been
demonstrated to be robust measurements of genomic relatedness between organisms and accurate approaches for a
genome-based taxonomy. [6–8].
As a result, the International Journal of Systematic and Evolutionary Microbiology (IJSEM) announced that, as of January
2018, authors of new bacterial and archaeal taxa descriptions are requested to provide genome sequence data with
their description of novel taxa (including novel species) [9],which means that genomic data should be made available atthe time of publication.
For many decades, culture collections around the world
have taken responsibilities for isolation, identification, distribution and long-term preservation of microbial resources
to document and preserve, ex situ, Earth’s microbial diversity and to provide reference materials to support researchand biotechnology. There are currently approximately

Author affiliations: 1Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China;
2
WFCC-MIRCEN World Data Center for microorganisms, WDCM, Beijing 100101, PR China.
*Correspondence: Juncai Ma, ma@im.ac.cn
Keywords: type strain; genome sequencing; culture collections; prokaryote.
Abbreviations: AAI, average amino acid identity; ANI, average nucleotide identity; DDH, DNA-DNA hybridization (DDH); DNA, deoxyribonucleic acid;
GCM, global catalogue of microorganisms; GEBA, genomic encyclopedia of bacteria and archaea; GOLD, genomes online database; IJSEM, International Journal of Systematic and Evolutionary Microbiology; NGS, next-generation sequencing; SOPs, standard operating procedures; USDOE JGI,US Department of Energy Joint Genome Institute; WDCM, World data center for microorganisms; WFCC, World federation of culture collections.
003276 ã 2019 IUMS

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Wu and Ma, Int J Syst Evol Microbiol

Fig. 1. Workflow of the new type strain sequencing. 1, Taxonomists deposit the strains, to be proposed as type strains, in culture collections in at least two different countries (at least one culture collection listed in Table 1) and obtain receiving numbers (a preassigned number by culture collections before formally accepting the type strain deposition) for the strains. 2, Using the receiving
number (declaring that the strains have been deposited in culture collections), taxonomists register with the WDCM Global Catalogueof Microorganisms project for candidate type strain sequencing and send DNA samples to the WDCM. 3, the WDCM sends the sequencing results to the taxonomists within 2 months (including assembly, G+C content, OGRI, N50 and annotation results required by the
IJSEM). 4, The taxonomists inform the WDCM of the culture collection accession numbers when they receive formal certificates fromthe respective culture collections. 5, The WDCM substitutes the receiving numbers for the culture collection strain accession numbers
and links these numbers with genome sequence data. 6, Taxonomists request the WDCM to publish the raw data and annotation data
within the NCBI/EMBL/DDBJ/GCM. 7, Taxonomists submit the manuscript to the IJSEM with the genome sequence accession number.
8, If the paper is not published in the IJSEM (including without submission to journal, withdrawal by the authors or rejection by the editors), sequencing data will be published in the NCBI/EMBL/DDBJ/GCM databases 24 months after sequencing.

2 693 000 microbial strains available from the 746 collections in 76 countries and regions referring to the CCINFO andSTRAIN database of the World Data Center for Microorganisms (WDCM)[10]. The Genomes OnLine Database (GOLD)[11] maintains an open, public genome database of 16 112
bacterial and archaeal type strains covering more than 6000
species. Comparing with the more than 15 000 species
described in the IJSEM with validly published names, additional efforts to continue sequencing type strains are necessary to fill in the gap.
Addressing the gap in genome data, the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project led by the US
Department of Energy Joint Genome Institute (US DOE
JGI) has published the outcomes of its first stage: 56 wholegenome sequences at year 2009 [12] and 1 003 [13] at year
2017, for a total of 1059 type strain whole-genome sequences. The newly started third-stage of the GEBA focuses on the
genomes of soil, plant-associated and newly described typestrains [14].

The World Federation of Culture Collections (WFCC) [15]and the WDCM have initiated an international communityled project towards genome sequencing and data annotationof microbial type strains, the Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project. This
project will include all bacterial and archaeal 80 type strains
with validly published species names, as well as selected reference fungal type strains frequently used for functional or
phylogenetic studies.
This project proposes to cooperate with international culturecollections and the IJSEM to include type strains of proposednovel species into this project. It will provide global taxonomists with a standard genome sequencing and annotation service. When taxonomists deposit the proposed type strains of
newly described species to one of the culture collections(Table 1) that is cooperating with the WDCM for new typestrain sequencing, the depositors could arrange to receive
genomic sequencing and full annotation by the WDCM as freeservices. A proposed procedure could be as shown in Fig. 1.

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Wu and Ma, Int J Syst Evol Microbiol

Table 1. Culture collections cooperating with the WDCM for new type strain sequencing
Acronym*

Full name/institution

Country

Homepage

1

ATCC

American Type Culture Collection

USA

www.atcc.org/

2

BCRC

www.bcrc.firdi.org.tw

3

CAIM

ChineseTaipei
MexicoCzech

http://sci.muni.cz/ccm/index.html

4CCM

Bioresource Collection and Research Center/Food Industry Research and Development InstituteCollection of Aquatic Important Microorganisms/ CIAD/Mazatlan Unit for
Aquaculture and Environmental Management
Czech Collection of Microorganisms/ Masaryk University

5

CCUG

Culture Collection University of Gothenburg

Swedenwww.ccug.se

6

CECT

Spanish Type Culture Collection / University of Valencia

Spainwww.cect.org

7

CGMCC

China General Microbiological Culture Collection Center

China

www.cgmcc.net

8

CICC

China Center of Industrial Culture Collection

Chinawww.china-cicc.org

Francehttps://catalogue-crbip.pasteur.fr

New Zealand

www.landcareresearch.co.nz/
resources/collections/icmp
http://jcm.brc.riken.jp/

www.ciad.mx/caim

9

CIP

Collection de l’Institut Pasteur

10

ICMP

International Collection of Microorganisms from Plants

11

JCM

12

KCTC

http://kctc.kribb.re.kr

13

KMM

Republic of
Korea
RussiaJapan

www.nite.go.jp/en/nbrc/index.html

Hungary

http://ncaim.uni-corvinus.hu/

UKwww.phe-culturecollections.org.uk/

ThailandNot available

Thailandwww.tbrcnetwork.org

14

NBRC

Japan Collection of Microorganisms/
RIKEN BioResource Center
Korean Collection for Type Cultures, Korea Research Institute of Bioscience andBiotechnology
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian
Academy of Sciences
Biological Resource Center/National Institute of Technology and Evaluation

15

NCAIM

National Collection of Agricultural and Industrial Microorganisms

16

NCTC

National Collection of Type Cultures

17

PCU

18

TBRC

19

TISTR

Pharmaceutical Sciences Chulalongkorn University
Culture Collection/ Chulalongkorn University
Thailand Bioresource Research Center/National Center for Genetic Engineering andBiotechnology
TISTR Culture Collection/Bangkok MIRCEN

20

VKM

All-Russian Collection of Microorganisms

Japan

Not available

ThailandRussianFederation

www.tistr.or.th/tistr_culture
http://www.vkm.ru/*The abbreviations of culture collections are listed in alphabetical order.

The WDCM has established standard operating proceduresfor DNA extraction, sample submission, sequencing anddata processing to ensure that all genetic resources and associated metadata of type strains are comparable, properly
maintained, recorded and stored. One of the aims of thisproject is to make sequencing data available to the scientificcommunity. If taxonomists choose not to submit an article,
the sequence data will be published in the public databases
24 months after sequencing is completed. The details of the
GCM 10K type strains sequencing project is described in
the previous project announcement [16].
Since microbial taxonomy is based upon comparisons of living type cultures, the preservation of type strains, not only
including the viable, pure and well-characterized strains,
but also the curated and comprehensive metadata associatedwith each strain, are essential for follow-up studies. As aresult, a comprehensive description of taxonomic information will be recommended for new strain sequencing
registration.
This effort will contribute to establish a high-quality complete genome sequence database and, hence, to form agenome-based prokaryotic taxonomic framework as thenew ‘gold standard’. The resulting knowledge and tools generated through this project will not only directly facilitate
identification of micro-organisms, but also improve ourabilities to predict new gene complexes as well as the functional existence of microbial communities.
Funding information
This work was supported by the National key Research Program of
China(GrantNos.
2017YFD0400302,
2016YFC1200801,
2016YFC0901702); the Key Research Program of the Chinese Academy of Sciences (Grant No. KFZD-SW-219); the 13th Five-year Informatization Plan of Chinese Academy of Sciences (Grant Nos.
XXH13506, XXH13505).
Acknowledgements
We would like to thank the participant collections who have made thecooperation possible. We would like to thank the WFCC Executive Boardfor supports, especially İpek Kurtböke (WFCC President), Kevin McCluskey (WFCC Vice-President) and Philippe Desmeth (WFCC Past-President)
for support. We would like to thank Martha E. Trujillo and Fred A.
Rainey for suggestions to the cooperation and the article. We would
like to thank the former director of the WDCM, Hideaki Sugawara, who
gives continuous support to the WDCM.
Conflicts of interest
The authors declare that they have no conflicts of interest.

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