GigaScience, 0, 2018, 1–0
doi: 10.1093/gigascience/giy026
Advance Access Publication Date: 0 2018
Commentary

COMMENTARY

The global catalogue of microorganisms 10K typestrain sequencing project: closing the genomic gaps
for the validly published prokaryotic and fungi species
Linhuan Wu1,2,3 , Kevin McCluskey4,5 , Philippe Desmeth4,6 ,Shuangjiang Liu2,4 , Sugawara Hideaki7 , Ye Yin8 , Ohkuma Moriya9 ,Takashi Itoh9 , Cha Young Kim10 , Jung-Sook Lee10 , Yuguang Zhou11 ,Hiroko Kawasaki12 , Manzour Hernando Hazbón13 , Vincent Robert14 ,Teun Boekhout14,15,16 , Nelson Lima17 , Lyudmila Evtushenko18 ,Kyria Boundy-Mills4,19 , Boyke Bunk20 , Edward R. B. Moore21 ,Lily Eurwilaichitr4,22 , Supawadee Ingsriswang22 , Heena Shah23 , Su Yao24 ,Tao Jin8 , Jinqun Huang8 , Wenyu Shi1 , Qinglan Sun1 , Guomei Fan1 , Wei Li1 ,Xian Li1 , İpek Kurtböke 4,25, * and Juncai Ma 1,2,3,4, *1

Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing
100101, China, 2 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of
Sciences, Beijing 100101, China, 3 WFCC-MIRCEN World Data Center for Microorganisms, Beijing 100101,
China, 4 World Federation of Culture Collections (WFCC) , 5 Fungal Genetics Stock Center, Kansas State
University, Manhattan, KS 66506, USA, 6 Belgian Coordinated Collections of Micro-organisms Program, Belgian
Science Policy Office, Brussels 231 1050, Belgium, 7 National Institute of Genetics, Yata, Mishima 411-8540,
Japan, 8 BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China, 9 Japan Collection of Microorganisms/Microbe
Division, RIKEN BioResource Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan, 10 Korean Collection forType Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup-si,
Jeollabuk-do, 56212, Republic of Korea, 11 China General Microbiological Culture Collection Center, Institute ofMicrobiology, Chinese Academy of Sciences, Beijing10010, China, 12 NITE Biological Resource Center, National
Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan, 13 American
Type Culture Collection, 10801 University Boulevard, Manassas, VA 20110, USA, 14 Westerdijk Fungal
Biodiversity Institue, Utrecht 3534CT, Netherlands, 15 Institute of Biodiversity and Ecosystem Dynamics,
University of Amsterdam, Spui 21 1012 WX Amsterdam, Netherlands, 16 Shanghai Key Laboratory of Molecular
Medical Mycology, Shanghai Institute of Mycology, Shanghai Changzheng Hospital, Shanghai 200003, China,
17
Micoteca da Universidade do Minho, Biological Engineering Centre, 4710-057 Braga, Portugal, 18 All-Russian

Received: 4 March 2018; Revised: 14 March 2018; Accepted: 16 March 2018
C The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons

Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium,provided the original work is properly cited.

12Collection of Microorganisms, GK Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS,
Pushchino, Moscow Region 142290, Russia, 19 Phaff Yeast Culture Collection, Food Science and Technology
Department, University of California Davis, 1 Shields Avenue, Davis, CA 95616–8598, USA, 20 Leibniz-Institute
DSMZ – German Collection of Microorganisms and Cell Cultures, D-38124 Braunschweig, Germany, 21 Culture
Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, SE-41346
Gothenburg, Sweden, 22 Bioresources Technology Unit, Thailand Bioresource Research Center, National Center
for Genetic Engineering and Biotechnology, Bangkok National Science and Technology Development Agency,
113, Thailand, 23 National Collection of Type Cultures, Public Health England, Porton Down, Salisbury, Wiltshire
SP4 0JG, UK, 24 China Center of Industrial Culture Collection, Beijing 100015, China and 25 Faculty of Science,
Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4558,
Australia*Correspondence address. Ipek Kurtböke, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast Locked Bag 4,
Maroochydore DC QLD 4558, Australia. Tel: +61 07 5430 2819; E-mail: IKurtbok@usc.edu.au http://orcid.org/0000-0003-2056-2484; Juncai Ma, NO.1
Beichen West Road, Chaoyang District, Beijing 100101, China. Tel: +86 10 64807422; E-mail: ma@im.ac.cn http://orcid.org/0000-0001-6382-8014

Abstract
Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher thecharacteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questionsof nature and human life. However, large gaps remain in the available genomic sequencing information published forbacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms(GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes.
Hence, the GCM aims to promote research by deep-mining genomic data.
Keywords: phylogenomics; taxonomy; biodiversity; whole-genome sequencing; type strains; bacteria; Archaea; fungi

Introduction
Microorganisms are the most abundant organisms on Earth. The
total diversity of prokaryotes may comprise up to 109 species [1].
For prokaryotic species, only new names published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM)
as an original article or in the “Validation Lists” are consideredvalid. As of the end of 2017, 15,081 valid prokaryotic species andsubspecies were published compared to 12,981 at the end of December 2015 [2]. The number of publications increased by 1,088
in 2016 and by 1,012 in 2017. The most commonly accepted estimate of the number of existing fungal species is 2.27 million, as
hypothesized by Hawksworth [3], while the number of species
reported in the Dictionary of Fungi is only about 100,000.
The taxonomy of microorganisms, including their classification, identification, and nomenclature, has developed frommorphological and metabolic characterization to incorporate
numerical taxonomy based on phenetic analyses, chemotaxonomy, and finally polyphasic approaches that combine phenotypic, chemotaxonomic, genotypic, and genomic information. The IJSEM recently announced that since January 2018,
authors of new taxa descriptions have been asked to provide
genome sequence data with descriptions of novel taxa with theirmanuscript submissions [4]. As such, the taxonomy of microorganisms has entered the genomics era. A genomic “gold standard” for consistent microbial species definitions is urgently
needed. To meet this end, a fundamental step is to sequence thetype strains of validly published prokaryotic and fungal species.
In addition to the microorganisms that can be isolated andmaintained in situ, the vast majority of microorganisms cannot
yet be cultivated and thus are relatively poorly studied. Cultureindependent approaches have been developed to investigate thecompositions and functions of environmental and human mi-

crobiomes. However, accurate taxonomic and functional predictions based on metagenomic data are dependent on the availability of high-quality reference genomic data [5]. Therefore, sequencing the genomes of type strains of recognized microbial
species will provide a taxonomic context for metagenomic data
analysis, which is commonly comprised of short and incompletesequences from complex environmental communities.
Microorganisms possess extensive genomic and metabolic
diversity, which makes them ideal biotechnological tools. Decoding the full genomes of the type strains of various species
in order to provide reference genomes will thus enable genes tobe associated with functions, such as metabolic activity, virulence, antibiotic production or resistance, biomass deconstruction, cellulose agricultural nitrogen fixation, and the liberationof environmental phosphorus. Access to microbial genomic sequences will significantly contribute to future studies in microbial biology, ecology, and biochemistry and these will, in turn,accelerate the discovery of new natural products and drugs [5].

The Current Status of the Strain Sequencing
Project
Descriptions of prokaryotic species are based on living cultures,and one representative strain is designated as the nomenclatural “type.” The IJSEM and the International Committee on Systematics of Prokaryotes require that the type strains of new
species be deposited in at least two recognized collections in
two countries. The type strains of 15,081 prokaryotic species arewidely preserved in more than 130 culture collections. In mycology the trend is similar, although hitherto a fungal type specimen must be metabolically inactive.
Presently, the selection of strains for whole-genome sequencing is based predominantly on medical, ecological, or in-Wu et al.

dustrial importance, which often leads to bias in assessing phylogenetic relationships. There are several ongoing phylogeneticbased microbial sequencing projects. The Genomic Encyclopedia of Bacteria and Archaea (GEBA), led by the US Departmentof Energy Joint Genome Institute (US DOE JGI), has pioneered
the partnership between culture collections and sequencing
projects. The GEBA project published 1,003 whole-genome sequences of type strains in 2017 as the outcome of its first stage[7]. GEBA started the new stage of the project in 2015, which has
a focus on the genomes of soil, plant-associated, and newly described type strains [8].
Similarly, the US DOE JGI, in collaboration with international
research teams, conducted a 5-year project to sequence 1,000
fungal genomes from across the Fungal Tree of Life [9]. The overall plan is to fill in gaps in the Fungal Tree of Life by sequencing
at least two reference genomes from the more than 500 recognized families of fungi.
Many type strains of microbial species remain unsequenced.
Hence, the World Federation of Culture Collections (WFCC) andthe World Data Centre for Microorganisms (WDCM) have initiated an international community-led project to sequence thefull genomes of microbial type strains to support continued scientific discovery and biotechnological utilization. Considering
the wide distribution of type strains, cooperation across theglobal culture collection community is essential for success.

Emerging Enhancements of Culture Collectionin the Genomic Era
Efforts made by culture collection curators to explore the diversity of microorganisms and to harness their genes, properties,
and products remain insufficient. While type collections are notalways large or diverse, the genome sequencing efforts of the
Global Catalogue of Microorganisms (GCM) will increase accessto resources in smaller collections.
The WDCM is the data center of the WFCC and the Microbial Resources Centers Network. The WDCM is working on facilitating the application of cutting-edge information technology
to improve the interoperability of microbial data, promote access and use of data, and coordinate international cooperation
among culture collections, scientists, and other user communities. The first stage of the GCM project, started in 2012, focusedon sharing strain catalogue data from culture collections [10].
The proposed type strain sequencing project is the continuationof the GCM project as its second stage, GCM 2.0.

Project Development and Current Progress
The project was first announced during the 14th International
Culture Collections Conference, held in Singapore in July 2017
in conjunction with the International Union of Microbiological Societies conferences. Following that, in October 2017, a
launch ceremony was held in Beijing, China, at which representatives from the following culture collections were present:
the American Type Culture Collection (ATCC), Belgian Coordinated Collections of Microorganisms (BCCM), Biological Resource Center, Japan National Institute of Technology and Evaluation (NBRC), Culture Collection of the University of Gothenburg(CCUG), China General Microbiological Culture Collection Center (CGMCC), Fungal Genetics Stock Center (Kansas State University, USA) (FGSC), Japan Collection of Microorganisms (JCM), Korean Collection for Type Cultures (KCTC), Leibniz-Institut DSMZDeutsche Sammlung von Mikroorganismen und Zellkulturen

3(DSMZ), Micoteca da Universidade do Minho (Portugal) (MUM),
Thailand Bioresource Research Center (TBRC), and Westerdijk
Fungal Biodiversity Institute (CBS). The meeting representatives
held detailed discussions on the organization and operational
procedures of the GCM 2.0 project. Some culture collections (e.g.,
All-Russian Collection of Microorganisms [VKM], China Centerof Industrial Culture Collection [CICC], Phaff Yeast Culture Collection [University of California Davis, USA;(UCD-FST], Thailand
Institute of Scientific and Technological Research Culture Collection [TISTR], and UK National Collection of Type Cultures[NCTC]) did not have a representative present at the launch ceremony but expressed their willingness to join the collaboration.
It is expected that the project will be completed within
5 years, including a pilot stage in the first year. GCM 2.0 includes two core subprojects, sequencing 10,000 bacterial and archaeal type strains and sequencing fungal type strains. It will
also embrace several satellite projects on specific scientific targets. GCM 2.0 is coordinated by a steering committee and fiveinterlinked working groups: Bacteria Selection, Fungi Selection,
Standard Operational Procedures, Databases, and Intellectual
Property Rights and Legal Issues.
The project has established standard operational proceduresfor DNA extraction, sample submission, sequencing, and dataprocessing to ensure that all genetic resources, data, and metadata associated with type strains are appropriately obtained,recorded, and stored. A project proposed by the WDCM, “AWI
20170: Specification on Data Integration and Publication in Microbial Resource Centers,” which would meet International Organization for Standardization standards, is under development. The raw data and annotation results generated from thisproject will be published on the GCM portal. Following norms established for genome projects coming from the Bermuda Principles and Fort Lauderdale agreement, the resulting genomic data
will also be made freely available in public databases, including
those maintained by the National Center for Biotechnology Information, the European Molecular Biology Laboratory, and the
DNA Data Bank of Japan, after completion of data analysis andannotation and ensurance that the data has met a set of quality
criteria.
All validly published bacterial and archaeal type strains, aswell as selected reference fungal type strains that are frequently
used for functional or phylogenetic studies, will be on the listof candidates for sequencing. Each strain has documentation
issued by the providing culture collection, which ensures thepurity and identity of the type strain. BGI-Shenzhen will support the microbial genome sequencing and assist with the data
analysis for this project. Sampling works for the pilot stage havebeen initiated. The project has established a global network tocollect approximately 800 candidate type strain samples from
American, British, Belgian, Chinese, Dutch, Japanese, Korean,
Portuguese, Russian, Swedish, and Thai collections. Althoughextracted DNA samples are much preferred, it is also acceptable
to send cultured cell samples of the strains. Importantly, under
the terms of Nagoya Protocol, GCM 2.0 will respect the accessand benefit-sharing regulations of all countries.
The GCM type strain sequencing project encourages all culture collections to participate in this international collaborative
project. Interested parties should be willing to provide DNA fortype strains held in their collections. All microbiologists and institutions from related fields are welcome to submit subprojects
for genomic data-related research questions. Brief proposals, including questions to be addressed and type strains to be sequenced and analyzed, should be emailed to Dr Juncai Ma at
ma@im.ac.cn. Once a proposal is granted as a subproject, the4scientist(s) will be asked to lead the full genome analysis andjointly publish the generated outcomes.

Conclusion
As a collaborative network of international culture collections,
GCM 2.0 will contribute to a genome-based microbial taxonomic framework, establishing high-quality complete genome
sequences as the new gold standard. The resulting knowledge
and tools generated through this project will not only directly
facilitate the identification of microorganisms but will also improve our ability to predict new gene complexes and theirfunctions from microbial communities. Thus, our knowledge ofthe hitherto undiscovered microbial diversity will be expanded,
which may lead to the sustainable utilization of microbial resources for human benefit.

Abbreviations
GEBA, Genomic Encyclopedia of Bacteria and Archaea; GCM,
Global Catalogue of Microorganisms; IJSEM, International Journalof Systematic and Evolutionary Microbiology; US DOE JGI, Uniteed
States Department of Energy Joint Genome Institute; WDCM,
World Data Centre for Microorganisms; WFCC, World Federationof Culture Collections.

Conflict of interest
The authors declare that they have no competing interests.

Funding
This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant
XDA19050301), the Bureau of International Cooperation of theChinese Academy of Sciences (grants 153211KYSB20160029
and 153211KYSB20150010), the National Key Research Program of China(grants 2017YFC1201202, 2016YFC1201303, and2016YFC0901702), the 13th Five-year Informatization Plan of
the Chinese Academy of Sciences(grant XXH13506), and the
National Science Foundation for Young Scientists of China(grant
31701157).

Author contributions
L.H.W. drafted the original manuscript with detailed input
from other authors. All authors participated in the GCM typestrain sequencing project and have read and approved the final
manuscript.

Acknowledgements
The authors thank the WFCC Executive Board for its support andalso acknowledge the members, partners, and advisors of the
GCM type strain sequencing project who have made this collaboration possible. We thank Takashi Gojobori from King Abdullah University of Science and Technology; Guoping Zhao from
Shanghai Institutes for Biological Sciences, Chinese Academyof Sciences; Xuewei Xu from the State Oceanic Administration,
China; Xiaoyang Zhi from Yunnan University, China; and Hua
Xiang and Lei Cai from the Institute of Microbiology, Chinese
Academy of Sciences, for their insightful suggestions.

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