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BCCM/GeneCorner Plasmid Collection

 

The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe.

Embedding

BCCM/GeneCorner is embedded in the Department of Biomedical Molecular Biology (DBMB, Ghent University) and the VIB-UGent Center for Inflammation Research (IRC, VIB), which together form the host laboratory for BCCM/GeneCorner. 

The BCCM/GeneCorner activities are continuously supported by the research activities of its host laboratory, which focus on molecular and cellular mechanisms that are at the origin of chronic inflammation, autoimmune diseases, infectious diseases and cancer. These mechanisms are mainly studied in cellular and animal model systems by using the most advanced methods of molecular biology, cell biology and immunology. Expression plasmids for human and mouse genes are frequently generated and extensively used, offering an ideal environment for BCCM/GeneCorner. Research of the host laboratory is multidisciplinary with molecular biologists, immunologists, cell biologists, and bioinformaticians collaborating with clinicians. It is the ambition of the host laboratory to translate basic research into innovative ways for diagnosis and therapy of human diseases.

Click here for a list of publications of the host laboratory.

BCCM/GeneCorner has already performed a number of research projects to improve plasmid DNA storage and to enlarge its scope of basic vectors and genes in view of the needs of the academic and industrial communities, and is continuously interested in project-based scientific collaborations on these issues.

 

Scope of the biological material

The BCCM/GeneCorner Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance.

The focus is on the collection of recombinant plasmids that can replicate in a microbial host strain, with main interest for:

  • empty cloning plasmids useful for recombinant (over)expression of proteins of interest in bacteria, yeast, fungi, insect cells, plant and animal cells;
  • (expression) plasmids carrying specific protein-coding genes and derivatives from a wide range of organisms (human, mouse, various bacterial species, ...);
  • expression plasmids with specific non-coding genes such as shRNA and miRNA;
  • plasmids for mouse genetic engineering, allowing the generation of transgenic mice.

BCCM/GeneCorner also accepts natural and genetically modified animal or human cell lines, including hybridomas, as well as other genetic material, in the safe deposit and patent deposit collections.

 

Quality

BCCM/GeneCorner is ISO 9001:2015 certified for accession, control, preservation, storage and supply of biological material and related information in the frame of public deposits, safe deposits and patent deposits.

 

Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development (Borrell et al. 2019)

In 2019, BCCM/ITM had the honor to welcome a new interesting subcollection into its public repository, known by mycobacteriologists as the “Mycobacterium tuberculosis complex (MTBC) clinical strains reference set” from the Borrell et al. (2019) publication.

This “MTBC clinical strains reference set” comprises 20 clinical strains covering 7 known human-adapted MTBC lineages (L1-L7) (Fig 1). Together with the newly described lineage 8 strain ITM 500961 (described by Ngabonziza et al. (2020) as the sole known viable L8 strain available so far) also available at BCCM/ITM, this reference set offers researchers the perfect opportunity to go beyond one single MTBC lineage and explore the phenotypic impact of MTBC diversity.

 

Why the need for such a reference set?

Members of the MTBC can cause tuberculosis (TB) in humans and various other mammals. The human-adapted strains comprise eight phylogenetic lineages that differ in their geographical distribution (Comas et al. 2013; Firdessa et al. 2013; Ngabonziza et al. 2020). There is growing evidence that this phylogeographic diversity modulates the outcome of TB infection and disease (Borrell et al. 2019).

As described by Borrell et al. (2019), for decades, TB research and development has mainly focused on the two canonical MTBC laboratory strains H37Rv and Erdman, together with the more recently used clinical strain CDC1551. These three strains all belong to MTBC Lineage 4 (Gagneux & Small 2007), and therefore do not represent the broader MTBC variability. Moreover, since their original isolation, these laboratory strains have been passaged countless times in various laboratories. This continuous passaging cycle can possibly lead to adaptation to laboratory conditions (Ioerger et al. 2010).

Borrell et al. (2019) emphasize that relying on only a few laboratory-adapted strains can thus be misleading as the study results might not paint the full picture and might not be directly transferrable to clinical settings where patients are infected with a diverse array of strains, including drug-resistant variants.

TB research and development would therefore benefit from validation in more genetic backgrounds, by incorporating the MTBC phylogenetic diversity. To facilitate this, Borrell et al. (2019) have assembled a set of 20 genetically well-characterized clinical strains representative of the known phylogenetic diversity of TB, comprising the first seven discovered human-adapted MTBC lineages.

 

What do you mean with well-characterized strains?

Borrell et al. (2019) used their global collection of MTBC clinical strains (and their associated phylogenomic data) to select a subset suitable as reference strains for future research.

This subset was characterized by performing whole-genome sequencing, spoligotyping and phenotypic drug-susceptibility testing for the main anti-TB drugs.

Moreover, the whole-genome sequencing (Illumina HiSeq 2500) data are freely available via the project accession number: PRJEB27802 on

ENA (https://www.ebi.ac.uk/ena/browser/view/PRJEB27802)

NCBI (https://www.ncbi.nlm.nih.gov/bioproject/PRJEB27802)

 

How can we avoid laboratory adaptation?

By having a joint agreement to avoid passaging these strains extensively between laboratories through repeated subculturing. This is why having a central “biobank” that assures the quality, purity and authenticity of the strains is of such great added value.

By ordering these strains from the Mycobacterial culture bank of the Belgian Coordinated Collections of Microorganisms (BCCM/ITM), you are ensured that the original properties of the strains are preserved.

 

Want to know more about the strain details?

Check the article of Borrell et al. 2019 or take a look at the strain info mentioned in our online catalogue on the BCCM website https://bccm.belspo.be/catalogues/catalogue-search?collection=ITM

You can use the strain numbers mentioned in Table 1 to facilitate your search through the online catalogue and/or to mention in your request letter.

 

BCCM/ITM Accession Nr (LIMS)

BCCM/ITM Culture Nr

Original ID

Place of Birth

Lineage

ITM 500941

2018-00082

N0157

Philippines

L1

ITM 500942

2018-00083

N0072

India

L1

ITM 500944

2018-00085

N0145

China

L2

ITM 500945

2018-00087

N0031

China

L2

ITM 500946

2018-00088

N0155

China

L2

ITM 500947

2018-00089

N0004

India

L3

ITM 500948

2018-00090

N1274

Afghanistan

L3

ITM 500949

2018-00091

N0054

Ethiopia

L3

ITM 500950

2018-00092

N1216

Ghana

L4

ITM 500951

2018-00093

N0136

USA

L4

ITM 500952

2018-00094

N1283

Germany

L4

ITM 500953

2018-00095

N1176

Ghana

L5

ITM 500954

2018-00096

N1272

Ghana

L5

ITM 500955

2018-00097

N1268

Sierra Leone

L5

ITM 500956

2018-00098

N1201

Ghana

L6

ITM 500957

2018-00099

N0091

Gambia

L6

ITM 500958

2018-00100

N1202

Ghana

L6

ITM 500959

2018-00101

N3913

Ethiopia

L7

ITM 500960

2018-00102

N0069

China

L1

ITM 500976

2018-03241

N0052

China

L2

Table 1: Strain IDs from the MTBC Clinical strains reference set accompanied by their new BCCM/ITM accession numbers from the LIMS. Note: Strain N0052, mentioned in Borrell et al. 2019 as ITM-2018-02241 is now ITM-2018-03241 (ITM 500976).

 

How to order this MTBC clinical strains reference set?

Interested in using this MTBC clinical strains reference set for your research? Please send an e-mail to bccm.itm@itg.be  and we will kindly help you further with the order procedure!

 

Fig 1 Maximum Likelihood topology of the 20 reference strains (open circles) plus 236 genomes representative of MTBC global diversity. © 2019 Borrell et al.

Branch lengths are proportional to nucleotide substitutions and the topology is rooted with Mycobacterium canettii. Bootstrap values for clades corresponding to main MTBC lineages are shown. Grey circles indicate the phylogenetic placement of laboratory Mtuberculosis strains commonly used. “A” stands for animal MTBC.

 

 

References:

Borrell, S., Trauner, A., Brites, D., Rigouts, L., Loiseau, C., Coscolla, M., Niemann, S., De Jong, B., Yeboah-Manu, D., Kato-Maeda, M., Feldmann, J., Reinhard, M., Beisel, C., & Gagneux, S. (2019). “Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development.” PloS one 14(3), e0214088.

Comas, I., et al. (2013). "Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans." Nature Genetics 45: 1176-1182.      

Firdessa, R., et al. (2013). "Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia." Emerg Infect Dis 19: 460-463.

Gagneux, S. & Small, P.M. (2007). “Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development.” Lancet Infect Dis. 7(5):328-37.

Ioerger, T.R., et al. (2010). “Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories.” J Bacteriol.192(14):3645-53.

Ngabonziza, J.C.S.,  et al. (2020). “A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region.” Nat Commun 11, 2917.

BCCM/ULC collection: Home to several reference (or ‘type’) strains of novel cyanobacterial taxa

A reference or ‘type’ strain in the cyanobacterial taxonomy is an isolate, which was used to describe a novel genus or a species, and which will serve as a reference to assign new isolates to this novel genus or species. The ULC Cyanobacterial collection harbors now several strains, which are the references of newly described taxa reflecting the diversity and the rich ecological background, which is represented in the collection.

This diverse set of reference strains includes the ones for the species Plectolyngbya hodgsonii, Shackletoniella antarctica, Timaviella circinata and T. karstica, Cephalothrix komarekiana and Parakomarekiella sesnandensis. Plectolyngbya hodgsonii (ULC009T) is a false-branching cyanobacterium with thin trichomes, which are sometimes arranged in bundles of multiple trichomes in one polysaccharidic sheath. The genus is endemic in Antarctic continental lakes (Taton et al., 2011). ULC037T is the reference of Shackletoniella antarctica and has a polar distribution. It occurs in flowing waters or builds thick benthic mats in lakes, where it forms short and long thin filaments with thin sheaths (Strunecky et al., 2020). The species Timaviella circinata and T. karstica (ULC401T, ULC402T) were isolated from the ‘Lampenflora’ of the Giant Cave in Italy. The filaments are red-brownish and have trichomes with false branching, which are slightly constricted at the cross wall and which are surrounded by a multilayered colorless sheath (Sciuto et al. 2017). By using a multifaceted approach, the genus Cephalothrix komarekiana (ULC718T) could be distinguished from other members of the polyphyletic genus Phormidium. This genus consists of cylindrical and straight trichomes in a firm sheath that are slightly attenuated and bent at the end. It was isolated from an alkaline lake in the Brazilian Pantanal wetlands (da Silva Malone et al., 2017). Parakomarekiella sesnandensis (ULC591T) was isolated from the biodeteriorated walls of the Old Cathedral of Coimbra (UNESCO World Heritage Site), and is morphologically and phylogenetically close to Komarekiella, but was placed in a separated genus-level clade (Soares et al., 2020).

 

                              

Cephalothrix komarekiana (ULC718T)                 

 

Furthermore to our knowledge, the ULC collection harbors the only cultivated representative of the genus Snowella sp., ULC335, which commonly occurs in temperate lakes. This strain was isolated from a bloom sample taken during the BelSPO project B-BLOOMS2 from Lake Falemprise in the Eau d'Heure lake complex in Belgium.  

Recently, the BLCC (Berthold-Laughinghouse Culture Collection) deposited multiple strains with several novel taxa from marine, freshwater and terrestrial ecosystems in Florida, a subtropical to tropical climate region. The goal of these isolations carried out during several projects was to describe and characterize novel cyanobacteria from different ecosystems. For the marine strains, an additional aim was to study their production of bioactive compounds in collaboration with researchers in medicinal chemistry from the Smithsonian Institute.

The diversity of cyanobacteria in coastal sediments and mats is huge and still largely unexplored. Therefore, many deposits originate from coastal areas like the newly described genera and species Johannesbaptistia floridana sp. nov. (ULC590T) isolated as epipelic from benthic coastal substrata (Berthold et al., 2020), Neolyngbya biscaynensis sp. nov. (ULC530T) and Affixifilum floridanum gen. nov., sp. nov. (ULC525T) coming from marine benthic cyanobacterial mats (Lefler et al. 2021), and Leptochromothrix gen. nov. (ULC597T), Ophiophycus gen. nov. (ULC599T) and Vermifilum gen. nov. (ULC454T) purified from benthic mats of mangrove forests (Berthold et al., 2021).

 

                        

Johannesbaptistia floridana (ULC590T)                     Vermifilum ionodolium (ULC454T)             

 

During a study that investigated the identity of nuisance
Cyanobacteria occurring in greenhouses and developed new algaecides against those, several isolates were described as novel species, including Iningainema tapete sp. nov. (ULC575T), which is capable of producing two isoforms of nodularin in high quantities and therefore forming a threat to the food production in greenhouses (Berthold et al., 2021) as well as the novel species Brasilonema fioreae sp. nov. (ULC548T), B. santannae sp. nov. (ULC544T) and B. wernerae sp. nov. (ULC573T) (Barbosa et al. 2021).

These rather unexplored ecosystems of benthic coastal areas and greenhouses in tropical areas are a potential source of novel secondary compounds. Indeed, it has been shown that strains of Neolyngbya and Brasilonema are able to produce compounds with antibiotic and antifungal properties (Sanz et al., 2015; Caires et al. 2018).

These reference strains as well as other cyanoabacterial strains can be ordered at the ULC collection via the online portal: https://bccm.belspo.be/shopping-cart. If you have questions, please do not hesitate to contact us under bccm.ulc@uliege.be.

T indicates that the strain is the reference (or ‘type’) strain of the species

 

References:

Barbosa, M., Berthold, D.E., Lefler, F.W., and Laughinghouse IV, H.D. (2021). Diversity of the genus Brasilonema (Nostocales, Cyanobacteria) in plant nurseries of central Florida (USA) with the description of three new species: B. fioreae sp. nov., B. santannae sp. nov. and B. wernerae sp. nov. Fottea 21, 82-99. doi: 10.5507/fot.2020.019

Berthold, D.E., Lefler, F.W., Huang, I-S., Abdulla, H.A.N., Zimba, P., and Laughinghouse IV, H.D. (2021). Iningainema tapete sp. nov. (Scytonemataceae, Cyanobacteria) from greenhouses in central Florida (USA) produces two types of nodularin with biosynthetic potential for microcystin-LR and anabaenopeptins. Harmful Algae 101: 101969. doi: 10.1016/j.hal.2020.101969

Berthold, D.E., Lefler, F.W., and Laughinghouse IV, H.D. (2021). Untangling filamentous marine cyanobacterial diversity from the coast of South Florida with the description of Vermifilaceae fam. nov. and three new genera: Leptochromothrix gen. nov., Ophiophycus gen. nov., and Vermifilum gen. nov. Mol. Phylogenet. Evol. In press. doi:10.1016/j.ympev.2020.107010

Berthold, D.E., Lefler, F.W., Werner, V.R., and Laughinghouse IV, H.D. (2020). Johannesbaptistia floridana sp. nov. (Chroococcales, Cyanobacteria), a novel marine cyanobacterium from coastal South Florida (USA). Fottea 20:152-159. doi: 10.5507/fot.2020.008.

Caires, T.A., da Silva, A.M.S., Vasconcelos, V.M., Affe, H.M.J., de Souza Neta, L.C., Boness, H.V.M., Sant'Anna, C.L., and Nunes J.M.C. (2018). Biotechnological potential of Neolyngbya (Cyanobacteria), a new marine benthic filamentous genus from Brazil. Algal Res. 36. 1-9. doi: 10.1016/j.algal.2018.10.001.

Da Silva Malone, C.F., Rigonato, J., Laughinghouse, H.D., Schmidt, É.C., Bouzon, Z.L., Wilmotte, A., Fiore, M.F., Sant'Anna, C.L. (2015). Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses. Int. J. Syst. Evol. Microbiol. 65, 2993-3007. doi: 10.1099/ijs.0.000369. 

Lefler, F. W., Berthold, D. E., and Laughinghouse, D.A. (2021). The occurrence of Affixifilum gen. nov. and Neolyngbya (Oscillatoriaceae) in South Florida (USA), with the description of A. floridanum sp. nov. and N. biscaynensis sp. nov. J. Phyco. doi: 10.1111/jpy.13065.

Sanz, M., Andreote, A.P.D., Fiore, M.F., Dörr, F.A. and Pinto, E. (2015). Structural characterization of new peptide variants produced by Cyanobacteria from the Brazilian Atlantic coastal forest using liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry. Mar. Drugs 13, 3892-3919. doi:10.3390/md13063892

Sciuto, K., Moschin, E., and Moro, I. (2017). Cryptic cyanobacterial diversity in the giant cave (Trieste, Italy): The new genus  Timaviella (Leptolyngbyaceae). Cryptogamie Algol 38, 285-323.

Soares, F., Ramos, R., Trovão, J., Cardoso, S.M., Tiago, I., and Portugal, A. (2020). Parakomarekiella sesnandensis gen. et sp. nov. (Nostocales, Cyanobacteria) isolated from the Old Cathedral of Coimbra, Portugal (UNESCO World Heritage Site). Eur. J. Phycol. doi: 10.1080/09670262.2020.1817568

Strunecky, O., Raabova, L., Bernardova, A., Ivanova, A.P., Semanova, A., Crossley, J., and Kaftan, D. (2020). Diversity of cyanobacteria at the Alaska North Slope with description of two new genera: Gibliniella and Shackletoniella. FEMS Microbiol. Ecol. 96:fiz189. doi: 10.1093/femsec/fiz189

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