User Service : Service offers | MIRRI - Microbial Resource Research Infrastructure: better managed resources

This webpage is maintained for historical reasons only and some of its contents might have become obsolete.
Please visit MIRRI's new webpage at www.mirri.org

Microbiological Services

This site provides an overview of services provided by collections participating in MIRRI.

Please note that MIRRI is not responsible for the content of external pages or their timeliness.

Consultancy, training and contract research

	Prokaryotes	Yeasts	Filamentous fungi	other types of resources
Consultancy (taxonomy, handling and preservation of strains)	BCCM, CABI, CBS, CCIM, CECT, CIRM, CRBIP, DSMZ, HAMBI, IEGM, MSCL, NCAIM, PCM, VKM	BCCM, CABI, CBS, CCIM, CCY, CECT, CIRM, DBVPG, DSMZ, MSCL, MUT, NCAIM, NCYC, PYCC, VKM	BCCM, CABI, CBS, CCIM, CCF, CECT, CIRM, DSMZ, HAMBI, ITEM, MSCL, MUM, MUT, NCAIM, VKM	BCCM, DSMZ
Consultancy (topics related to the collection's expertise)	BCCM, CABI, CCIM, CECT, CIRM, CRBIP, DSMZ, IEGM, UMCC, VKM	BCCM, CABI, CCIM, CECT, DSMZ, NCYC, PYCC, UMCC	BCCM, CABI, CCIM, CECT, DSMZ, MUM, MUT, VKM	BCCM
Contract Research (content depends on the provider)	BCCM, CBS, CCIM, CIRM, CRBIP, DSMZ, MSCL, UMCC, VKM	CBS, CCIM, CIRM, MSCL, NCYC, UMCC, VKM	CBS, CCIM, CIRM, HAMBI, MSCL, MUT, VKM
Training courses (content depends on the provider)	BCCM, CABI, CCIM, CECT, CIRM, CRBIP, DSMZ, IEGM, UMCC, VKM	BCCM, CABI, CBS, CCIM, CECT, DBVPG, DSMZ, NCYC, PYCC, UMCC	BCCM, CABI, CBS, CCIM, CECT, DSMZ, MUM, MUT	BCCM, DSMZ

Data management

CC/mBRC	service details
BCCM/LMG	StrainInfo - StrainInfo integrates via the application of the Nuckles and Nodes approach, scattered data on strain information (various catalogues of mBRCs), sequence data (Genbank, EMBL), taxonomic information (LPS, NCBI) and literature. It allows the user to find on fly via the StrainPasport information page i) relevant strain information ii) contact points of mBRC’s iii) reliable 16S sequences etc. The MCL (microbial Common Language) offers a format that allows regular updating semi automatically.
CBS	MycoBank - MycoBank is owned by the International Mycological Association and is an on-line database aimed as a service to the mycological and scientific community by documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations.
CECT	Yeast-id - The yeast-id is a tool for quick and cheap yeasts identification based on restriction analysis of the region that includes the gene codifying 5,8S rRNA and the transcribed intergenic regions ITS (5,8S-ITS). Browsing by species name and searching patterns by the length of the DNA fragments obtained in the restriction analysis is possible. Links to MycoBank data of the species will be also available in the next version that will be available before the end of 2015.
CIRM	YeastIP - YeastIP is a comprehensive gene database which contains the major barcodes of all the species of the subphylum Saccharomycotina and tools to establish the identification of yeasts to the species level and their phylogenetic relationships.
DSMZ	BacDive - The Bacterial Diversity Metadatabase focuses providing organism-linked information covering the multifarious aspects of bacterial biodiversity. The BacDive portal offers information on taxonomic classification, morphology, physiology, cultivation, origin and natural habitat for more than 50,000 bacterial and archeal strains. Where available, links are given to access the respective biological resources and the associated sequence data via the INSDC accession numbers for genomes and 16S rRNA. In addition to the advanced search functionallities of the web portal access, BacDive offers data retrieval via a web service api or individual compilations of data sets that can be exported to CSV spreadsheet files. The integration of new data is a central objective of BacDive and is a continuous process. Proposals for the integration of relevant collection descriptions especially by the data owner are highly encouraged.
DSMZ	Prokaryotic Nomenclature up-to-date (PNU) - PNU is a compilation of all names of Bacteria and Archaea which have been validly published according to the Bacteriological Code since 1. Jan. 1980, and nomenclatural changes which have been validly published since. It will be updated with the publication of each new issue of the Int. J. Syst. Evol. Microbiol. (IJSEM). Prokaryotic Nomenclature is published by the Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. We offer an alphabetical search option of prokaryotic names. Alternatively, you may go to Downloads and select one of the lists in PDF or Excel format. Additionally, content can be retrieved in machine readable XML and JSON format by the PNU web service (http://bacdive.dsmz.de/api/pnu/).
DSMZ	Genome-To-Genome Distance Calculator (GGDC) - The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). The web service hosted at DSMZ offers state-of-the-art methods for inferring whole-genome distances which are well able to mimic DDH. Values calculated with GGDC yield a better correlation with wet-lab DDH values than alternative approaches such as "ANI". These distance functions can also cope with heavily reduced genomes and repetitive sequence regions. Some of them are also very robust against missing fractions of genomic information (due to incomplete genome sequencing). Thus, this web service can be used for genome-based species delineation. As of 2014 the GGDC also delineates subspecies.
VKM	FungalDC - FungalDC (Fungal Diversity in Culture Collections) assembles data on fungal diversity held in 264 registered culture collections (WDCM) as well as in individual laboratories around the world (according to available catalogues in electronic or paper formats or list of strains). It provides current information about a fungal species by linking to the particular species/strain page in such sources as: Index Fungorum, MycoBank, GenBank or StrainInfo. FungalDC provides an opportunity to readily compare the fungal species diversity available from culture collections and GenBank, to locate the culture collections where representatives of particular species and/or particular strains (including ex-type and authentic samples) are maintained, and to reveal species either omitted from the aforementioned information sources or perhaps absent as living culture.

Deposit

	Prokaryotes	Yeasts	Filamentous fungi	other types of resources
Patent Deposit	BCCM, CABI, CBS, CCIM, CECT, DSMZ, MSCL, NCAIM, NCTC, PCM, VKM	BCCM, CABI, CBS, CCIM, CCY, CECT, DBVPG, DSMZ, MSCL, NCAIM, NCYC, PYCC, VKM	BCCM, CABI, CBS, CCIM, CECT, DSMZ, MSCL, NCAIM, VKM	BCCM, DSMZ
Public Deposit	BCCM, CABI, CBS, CCIM, CECT, CIRM, CRBIP, DSMZ, HAMBI, MSCL, NCAIM, NCTC, PCM, UMCC, VKM	BCCM, CABI, CBS, CCIM, CCY, CECT, CIRM, DBVPG, DSMZ, HAMBI, MSCL, MUT, NCAIM, NCYC, PYCC, UMCC, VKM	BCCM, CABI, CBS, CCIM, CCF, CECT, CIRM, DSMZ, HAMBI, ITEM, MSCL, MUM, MUT, NCAIM, VKM	BCCM, DSMZ
Safe Deposit	BCCM, CABI, CBS, CCIM, CECT, CIRM, DSMZ, HAMBI, MSCL, NCAIM, NCTC, PCM, UMCC, VKM	BCCM, CABI, CBS, CCY, CCIM, CECT, CIRM, DBVPG, DSMZ, HAMBI, MSCL, MUT, NCAIM, NCYC, PYCC, UMCC, VKM	BCCM, CABI, CBS, CCIM, CCF, CECT, CIRM, DSMZ, HAMBI, ITEM, MSCL, MUM, MUT, NCAIM, VKM	BCCM, DSMZ

Identification, molecular typing and phylogenetic/community analysis

	Prokaryotes	Yeasts	Filamentous fungi	other types of resources
AFLP	BCCM	BCCM, CCIM	BCCM, ITEM	BCCM
Identification from pure cultures	BCCM, CABI, CBS, CCIM, CECT, CIRM, CRBIP, DSMZ, IEGM, MSCL, NCAIM, PCM, UMCC, VKM	BCCM, CABI, CBS, CCIM, CCY, CECT, CIRM, DBVPG, DSMZ, MUT, NCAIM, NCYC, PYCC, UMCC, VKM	BCCM, CABI, CBS, CCIM, CCF, CECT, CIRM, DSMZ, HAMBI, ITEM, MUM, MUT, NCAIM, VKM	BCCM, DSMZ
Inter-LTR		CIRM
Microsatellites	CECT, CIRM, UMCC	CECT, CIRM, UMCC	CECT, MUT	BRC Toxo, DSMZ
MLST	CIRM, CRBIP, UMCC	CIRM, UMCC
PCR-DGGE	BCCM, UMCC	BCCM, UMCC	BCCM	BCCM
PFGE	BCCM, CIRM, UMCC	BCCM, CIRM, UMCC	BCCM	BCCM
Phylogenetic analysis based on other genes	BCCM, CCIM, CIRM	CCIM, CIRM, DSMZ, NCYC	CCF, CCIM, CIRM, DSMZ, MUT
Phylogenetic analysis based on rRNA genes	BCCM, CCIM, CIRM, CRBIP, DSMZ, CECT, VKM	CCIM, CECT, CIRM, DSMZ, NCYC, VKM	CCF, CCIM, CECT, CIRM, DSMZ, MUT
Plasmid profile analysis	BCCM	BCCM	BCCM	BCCM
RAPD	BCCM, CECT, CIRM, UMCC	BCCM, CCIM, CECT, NCYC, PYCC, UMCC	BCCM, CECT, MUT	BCCM
RFLP (genomic, mt-RFLP, ARDRA …)	CABI, CCIM, CECT, CIRM, UMCC	CABI, CCIM, CECT, CIRM, UMCC	CABI, CECT
Ribotyping	CCIM, CECT, DSMZ	CCIM, CECT	CECT
TTGE	CIRM

Isolation, preservation and cultivation

	Prokaryotes	Yeasts	Filamentous fungi	other types of resources
Freeze-drying	BCCM, CBS, CCIM, CCUG, CECT, CIRM, CRBIP, DSMZ, HAMBI, VKM	CBS, CCIM, CCUG, CECT, DSMZ, DBVPG, MUT, NCYC, VKM	CBS, CCF, CCIM, CCUG, CECT, DSMZ, MUM, MUT, VKM	BRC Toxo
Isolation and purification of strains	BCCM, CBS, CIRM, CRBIP, HAMBI, IEGM, MSCL, UMCC, VKM	BCCM, CBS, CCY, CECT, CIRM, DBVPG, MSCL, NCYC, PYCC, UMCC, VKM	BCCM, CBS, CCF, CECT, CIRM, HAMBI, MSCL, MUT, VKM	BCCM, BRC Toxo
Microbial counting	BCCM, UMCC	DBVPG, UMCC
Optimisation of cultivation/fermentation	BCCM, CMII, PCM, UMCC, VKM	CCIM, CMII, NCYC, UMCC, VKM	CMII, VKM
Optimisation of preservation conditions	BCCM, CCIM, CMII, CRBIP, IEGM, UMCC	CCIM, CMII, NCYC, UMCC	CCIM, CMII, MUT	BRC Toxo
Propagation of bacteriophages	DSMZ			DSMZ, PCM
Revitalisation of lyophilised material	BCCM, CCIM, CRBIP	CCIM, DBVPG, MUT, NCYC	, MUT

Phenotypic and molecular characterization

	Prokaryotes	Yeasts	Filamentous fungi	other types of resources
Analysis of cell wall sugars	DSMZ, IEGM, VKM	VKM	VKM	DSMZ
Analysis of peptidoglycan structure	CRBIP, DSMZ, IEGM, VKM	VKM	VKM	DSMZ
Analysis of polysaccharide degrading enzymes			CBS
Analysis of the cellular fatty acid composition	BCCM, CCUG, CECT, DSMZ, VKM	BCCM, CCUG, CECT, VKM	BCCM, CCUG, CECT, VKM	BCCM, DSMZ
Analysis of the cellular polar lipid composition	DSMZ, IEGM, VKM	VKM	VKM	DSMZ
Analysis of volatile metabolites	VKM	CCIM, VKM	VKM
Analysis of ligninolytic enzymes			CBS, HAMBI, MUT
Analysis of mycolic acids	DSMZ, VKM	VKM	VKM	DSMZ
Analysis of respiratory quinones	DSMZ, VKM	VKM	VKM	DSMZ
Biochemical tests (classical or miniaturized i.e. API, Biolog ...)	BCCM, CCIM, CCUG, CECT, DSMZ, UMCC, VKM	BCCM, CCIM, CCUG, CCY, CECT, DBVPG, DSMZ, UMCC, PYCC, VKM	BCCM, CCUG, CECT, DSMZ, MUT, VKM	BCCM, DSMZ
Determination of mol% G+C content of DNA	BCCM, CECT, DSMZ, VKM	BCCM, CECT, DSMZ	BCCM, CECT, DSMZ	BCCM, DSMZ
Determination of ploidy		CIRM
DNA - DNA hybridization	BCCM, CECT, DSMZ, VKM	BCCM, CECT, VKM	BCCM, CECT, VKM	BCCM, DSMZ
Immunochemical analysis	IEGM
MALDI-TOF	CCUG, CECT, CRBIP, DSMZ, PCM, VKM	CCUG, CECT, DSMZ, VKM	CCUG, CECT, DSMZ, VKM	DSMZ
NGS from pure cultures	CRBIP
Sequence analysis of housekeeping genes	BCCM, CCUG, CECT, CIRM, VKM	BCCM, CCUG, CECT, CIRM, PYCC	BCCM, CCF, CCUG, CECT	BCCM
Sequence analysis of rRNA genes (small and/or large subunit)	BCCM, CCUG, CECT, CIRM, DSMZ, IEGM, UMCC, VKM	BCCM, CCUG, CECT, CIRM, DBVPG, DSMZ, NCYC, PYCC, UMCC, VKM	BCCM, CCF, CCUG, CECT, CIRM, DSMZ, VKM	BCCM, DSMZ
Sequence analysis of virulence genes	CIRM		CIRM

Screening, tests and bioassays

	Prokaryotes	Yeasts	Filamentous fungi	other types of resources
Analysis of adhesive activity	IEGM
Analysis of biosurfactant-producing activity	IEGM		MUT
Analysis of hydrocarbon-oxidizing activity	IEGM
Antimicrobial bioassays	BCCM, CIRM, CRBIP, DSMZ, IEGM, MSCL	BCCM, DSMZ, MSCL	BCCM, DSMZ	BCCM, DSMZ
Bacteriophage titer service	PCM
Characterisation of bioproducts (analytical, pharmaceutical)	CMII, HAMBI	CMII	CMII, MUT
Characterisation of technology abilities	CCIM, CIRM	CCIM	CIRM, MUT
Detection of human pathogenic viruses and other cell culture contaminating viruses in human cell cultures				DSMZ
Material resistance testing	BCCM	BCCM	BCCM, VKM
Mycoplasma detection and eradication from cell cultures				DSMZ
Plant Virus Analysis (Diagnosis, disease clinic, resistance screening)				DSMZ
Quality control and sterility testing of raw materials and products	CABI	CABI, NCYC	CABI
Screening (targets depend on the provider)	BCCM, CIRM, CRBIP, IEGM, UMCC, VKM	CIRM, CCY, DBVPG, NCYC, PYCC, UMCC	CIRM, VKM
Supply of control DNAs for mycoplasma PCR testing				DSMZ
Verification of microorganisms associated with novel products	CABI, CCIM	CABI, CCIM, NCYC	CABI, CCIM, MUT
Viability of Active Dry Yeasts testing		CIRM, NCYC

Miscellaneous

	Prokaryotes	Yeasts	Filamentous fungi
Construction of hybrids		CIRM, UMCC
DNA extraction	BCCM, CBS, CECT, CIRM, CRBIP, DSMZ, UMCC, VKM	CBS, CCIM, CECT, DBVPG, DSMZ, UMCC	CBS http://www.ibprs.pl/english-version, CECT, DSMZ, HAMBI, MUT
Down-streaming processing	CMII	CMII	CMII
Mycotoxin analysis			CBS, CCIM, MUM
Provision of inactivated strains (phytopathogenic bacteria)	CIRM

Note: No guarantee for completeness of listed services.

If you need a certain service not listed above please contact us or the relevant mBRC.

MIRRIMicrobial Resource Research Infrastructure