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Guidelines for management and use of the scientific collection

Guidelines for management and use

of the scientific collection

Human Microbiota Biobank

at Department of Microbiology, University of Tartu

1. General

Human Microbiota Biobank (HUMB) is a scientific collection that contains microbe strains of human origin (including microbiota bacteria and opportunistic pathogens), samples of human microbiota and the extracted DNA samples. The biobank was established to support and promote research work on collecting, processing and preserving the information about the human microbes and their communities, as well as development of probiotics.

The collection is guided by the suggestions of the international organisations of the corresponding fields (ECCO ? European Culture Collections’ Organizations, WFCC ? World Federation of Culture Collections, CABRI ? Common Access to Biological Resources and Information, OECD Best Practice Guidelines for Biological Resource Centre), suggestions of Nagoya Protocol and legislations of University of Tartu.

The collection is registered at WDCM (World Data Centre for Microorganisms) as WFCC Estonian Human Microbiota Biobank (collection no. WDCM 977, acronym HUMB).

Information about the collection is accessible on the Estonian Electronic Microbial dataBase (EEMB) website in English ( and Estonian (

On the basis of the collection, research work is done and formal education is given. The collection is openly available for the scientists working at Department of Microbiology, University of Tartu, as well as other scientists who need it for research or teaching purposes according to agreement of collection managers. The catalogue of the collection is openly accessible on the collection website.

2. Structure and management of biobank

The collection is formed of collected, bought and donated microbe strains and microbiota samples as well as information stored in the digital database.

The purpose of collecting and preserving the collection is to ensure its accessibility for research work, probiotic development and teaching purposes.

When submitting new strains to the collection, a contract is signed with the person submitting the strains. This contract must contain information about the amount of strains submitted, the project during which the materials were collected, financial source, workers involved and the region from which the material was collected. These contracts are signed and archived.

Management of the collection is done with the help of electronic database developed on the basis of dbForge Studio for MySQL Professional. The database includes several information about the preserved material, including the data about preservation (form, date, location, next check-up), heritage (nation, material, donator), identification (methods, results), determined properties, clinical and animal trials, publications (patents, papers, dissertations).

The collection database is stored digitally in a couple of copies that are located in different computers. Printouts of the database are done periodically.

Updates of the collection (information about new material or new information for existing material) are uploaded into the digital database steadily. The updates are managed by the collection administrator who collects necessary information from other staff, researchers and students.

Each preserved item has an unique ID-code which consists on the collection acronym and a number combination.

It is mandatory to document the geographical region of origin, the date of submitting the strain and the person who submitted the strain to the collection (EU Regulation No 511/2014).

It is mandatory to document the material, clinical information about the donor, geographical region, date of submission to the collection and the person adding the material for all microbiota preservatives.

The head and administrator of the collection are responsible for proper usage of the collection and database.

The collection is located at the Department of Microbiology, University of Tartu (Ravila 19, Tartu 50411, Estonia).

3. Storage and viability control of the samples

The preservatives (microbe strains, microbiota samples, extracted DNAs) are stored at -80°C in multiple parallels in multiple freezers. Isolated strains are preserved inside sterile cryovials in SKIM-milk medium or in special chemically treated cryosolutions in cryovials. Part of the strains are lyophilised and stored at +4°C.

Viability check of the strains is performed in 3-5 years depending on the species.

The terms of preservation (temperature, running maintenance of the freezers) are controlled by the staff responsible for the collection.

The collection is preserved in locked refrigerators. The collection is accessible only to the assigned person, in absence of those persons only to an assigned substitute. No third party has access to the collection.

Freezers are equipped with fault detection systems. In case of a malfunction, a message automatically is sent to the person assigned to the collection.

In case of danger to the storage rooms, actions are in compliance with the university security rules.

Samples are handled and utilized according to the “Regulations for handling infectious material” legislation (in force since 31.10.2013 nr. 119, RTL 2003, 115, 1831).

Biological materials are assigned a code and preserved according to the regulations of the Council of the European Union (Recommendation Rec(2006)4 of the Committee of Ministers of member states on research on biological materials of human origin).


4. Use and availability of biobank

The strains and other materials preserved in the collection as well as the information about them are accessible for academic research (noncommercial purposes) within the institution.

The microbe strains are available for other institutions of University of Tartu as well as other parts according to MTA (material transfer agreement) for academic research (noncommercial purposes). These contracts are archived. This cooperation results in shared publications, dissertations and patents.

Use of strains for commercial purposes by third parties are regulated in agreements concluded between University of Tartu and the user.

The collection catalogue is publicly accessible:


University of Tartu 

 © 2013-2021 by University of Tartu, Estonia.

Version 09.11.2021