NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource.

National collection of type cultures bacterial genomes genome assemblies pacific bioscience long reads

Journal

Microbial genomics
ISSN: 2057-5858
Titre abrégé: Microb Genom
Pays: England
ID NLM: 101671820

Informations de publication

Date de publication:
05 2023
Historique:
medline: 18 5 2023
pubmed: 17 5 2023
entrez: 17 5 2023
Statut: ppublish

Résumé

The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains - many of medical, scientific and veterinary importance - available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains. Here, at the beginning of the collection's second century, we introduce the resulting NCTC3000 sequence read datasets, genome assemblies and annotations as a unique, historically and scientifically relevant resource for the benefit of the international bacterial research community.

Identifiants

pubmed: 37194944
doi: 10.1099/mgen.0.000976
pmc: PMC10272881
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 101503/Z/13/Z
Pays : United Kingdom

Références

Genome Med. 2015 Sep 28;7:97
pubmed: 26411565
Proc Biol Sci. 2019 Apr 10;286(1900):20182025
pubmed: 30966987
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Genome Res. 2017 May;27(5):722-736
pubmed: 28298431
Genome Biol. 2015 Dec 29;16:294
pubmed: 26714481
BMC Bioinformatics. 2011 Sep 30;12:385
pubmed: 21961884
Microb Genom. 2022 Aug;8(8):
pubmed: 35960642
Nat Methods. 2013 Jun;10(6):563-9
pubmed: 23644548
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
BMC Genomics. 2022 May 11;23(Suppl 4):361
pubmed: 35546658
Bioinformatics. 2013 Oct 1;29(19):2487-9
pubmed: 23842809
Lancet. 2014 Nov 8;384(9955):1691-7
pubmed: 25441199
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Nat Commun. 2018 Jul 13;9(1):2703
pubmed: 30006589
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500

Auteurs

Jo Dicks (J)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Mohammed-Abbas Fazal (MA)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Karen Oliver (K)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

Nicholas E Grayson (NE)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Present address: Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK, OX3 9DU, UK.

Jake D Turnbull (JD)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Evangeline Bane (E)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Edward Burnett (E)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Ana Deheer-Graham (A)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Nancy Holroyd (N)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

Dorota Kaushal (D)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Jacqueline Keane (J)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

Gemma Langridge (G)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Present address: Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.

Jane Lomax (J)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

Hannah McGregor (H)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Steve Picton (S)

Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA.

Michael Quail (M)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

Deepak Singh (D)

Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA.

Alan Tracey (A)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

Jonas Korlach (J)

Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA, USA.

Julie E Russell (JE)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Sarah Alexander (S)

Culture Collections, UK Health Security Agency, 61 Colindale Avenue, London, NW9 5EQ, UK.

Julian Parkhill (J)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.

Articles similaires

Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing
Populus Soil Microbiology Soil Microbiota Fungi
Aerosols Humans Decontamination Air Microbiology Masks

Classifications MeSH