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Protocols

WDCM specifications

Information


Unique identifier OMICS_21376
Name WDCM
Alternative name World Data Centre for Microorganisms
Restrictions to use Academic or non-commercial use
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Juncai Ma

Publication for World Data Centre for Microorganisms

WDCM citations

 (8)
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Draft Genome Sequence of Agrococcus baldri Strain Marseille P2731

2017
Genome Announc
PMCID: 5347231
PMID: 28280011
DOI: 10.1128/genomeA.00015-17
call_split See protocol

[…] r genes larger than 5,000 nucleotides. No gene coding for resistance to antibiotics was identified.Strain Marseille-P2731 was deposited in the Collection de Souches de l’Unité des Rickettsies (CSUR) (WDCM 875) under number P2731 and in the DSMZ under number DSM 103061. […]

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High Quality Draft Genome Sequence of Bacillus amyloliquefaciens Strain 629, an Endophyte from Theobroma cacao

2015
Genome Announc
PMCID: 4653783
PMID: 26586881
DOI: 10.1128/genomeA.01325-15
call_split See protocol

[…] in is deposited in the Biological Institute Culture Collection of Phytopathogenic Bacteria (IBSBF) (Campinas, São Paulo, Brazil) under accession no. IBSBF-3106. This collection is registered with the World Data Centre for Microorganisms collection under no. WDCM-110.Genomic DNA from isolate 629 was extracted and sequenced using the Ion Torrent PGM platform (Life Technologies) 318 chip. A total of […]

library_books

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

2014
Stand Genomic Sci
PMCID: 4334874
PMID: 25780495
DOI: 10.1186/1944-3277-9-2

[…] lture collections until the early 1920s, the original type cultures of E. coli got lost (just like those of the early isolates of other bacterial species). Strain U5/41T (= DSM 30083T = ATCC 11775T = WDCM 00090T) was isolated by Fritz Kauffmann at the State Serum Institute Copenhagen, Denmark in 1941 [], from the urine of a patient with cystitis, and was accepted as neotype of E. coli in 1963 []. […]

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Diversity of culturable bacteria including Pantoea in wild mosquito Aedes albopictus

2013
BMC Microbiol
PMCID: 3617993
PMID: 23537168
DOI: 10.1186/1471-2180-13-70
call_split See protocol

[…] es in GenBank using the BLASTn program in the National Center for Biotechnology Information (http://blast.ncbi.nlm.nih.gov/Blast.cgi). The Ribosomal Database Project II Chimera Check was used (http://wdcm.nig.ac.jp/RDP/html/analyses.html) to discard any chimeric sequences.Phylogenetic analyses were performed on a set of Pantoea sequences. Sequences of 16S rRNA genes from Pantoea isolates from mosq […]

library_books

Meeting Report: Hackathon Workshop on Darwin Core and MIxS Standards Alignment (February 2012)

2012
Stand Genomic Sci
PMCID: 3570805
PMID: 23451295
DOI: 10.4056/sigs.3166513

[…] and expand out from there to include others. Initiate formal contacts with SILVA, MG-RAST and Moorea Biocode.Re-connect the WFCC database, now moved from Japan to China, to GBIF network. Now that the WDCM is developing the WFCC Global Catalogue of Microorganisms (GCM), much more data from WFCC culture collections will be available to GBIF.Deliver Japanese translation of DwC properties to GBIF.Deli […]

library_books

Bacteria in Crude Oil Survived Autoclaving and Stimulated Differentially by Exogenous Bacteria

2012
PLoS One
PMCID: 3444520
PMID: 23028421
DOI: 10.1371/journal.pone.0040842

[…] described , . Representative clones from each group were randomly picked and sequenced. All the sequences were checked with the CHECK-CHIMERA program in the Ribosomal Database Project (RDP-II, http://wdcm.nig.ac.jp/RDP/html/analyses.html) . Phylogenetic trees were then constructed using the neighbor-joining algorithm with the Jukes–Cantor correction factor in ARB . Tree topology was also evaluated […]

Citations

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WDCM institution(s)
Network information center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Pharmaceutical Science, Jiangnan University, Wuxi, Jiangsu, China; Belgian Coordinated Collections of Micro-organisms Programme, Belgian Science Policy Office, Brussels, Belgium; National Institute of Genetics, Yata, Mishima, Japan; Fungal Genetics Stock Center, University of Missouri- Kansas City, MO, USA; CABI, Bakeham Lane, Egham, Surrey, UK; All-Russian Collection of Microorganisms, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, Moscow region, Russia; Micoteca da Universidade do Minho, Universidade do Minho Braga, Portugal; Japan Collection of Microorganisms/ Microbe Divion, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan; Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, Utrecht, Utrecht, Netherlands; China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Scientific Data Center, Computer Network Information Center, Chinese Academy of Sciences, Beijing, China; Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology, Bangkok, Thailand
WDCM funding source(s)
Supported by the National High Technology Research and Development Program of China [2014AA021501, 2014AA021503, 2015AA020108]; International S&T Cooperation Program of China (ISTCP) [2015DFG32550]; Bureau of Science & Technology for Development of Chinese Academy of Sciences (Strategic bio-resources information center) and Field Cloud Project of Chinese Academy of Sciences [XXH12503-05-01].

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