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Core Facility for Germ-free Research

Explore the microbiota at the Core Facility for Germ-free Research and at the GF Satellite Unit.

Types of bacterial environments

Germ-free (GF) mice are derived and raised in an environment devoid of resident bacterial flora (microbiota). At Karolinska Institutet, GF models are housed at the Core Facility for Germ-free Research (CFGR). Hands-on, user-friendly procedures may be carried out at the recently established GF Satellite unit.

Recent publications

VijayKumar Patra, Karin Wagner, Velmurugesan Arulampalam, Peter Wolf.

iScience. 2019 Apr 26;15:211-222. doi: 10.1016/j.isci.2019.04.026

Petursdottir DH, Nordlander S, Qazi KR, Carvalho-Queiroz C, Ahmed Osman O, Hell E, Björkander S, Haileselassie Y, Navis M, Kokkinou E, Lio IZL, Hennemann J, Brodin B, Huseby DL, Nilsson C, Hughes D, Udekwu KI, Sverremark-Ekström E.

Front Immunol. 2017 Dec 1;8:1699. doi: 10.3389/fimmu.2017.01699. eCollection 2017

Schrumpf E, Kummen M, Valestrand L, Greiner TU, Holm K, Arulampalam V, Reims HM, Baines J, Bäckhed F, Karlsen TH, Blumberg RS, Hov JR, Melum E.

J Hepatol. 2017 Feb;66(2):382-389. doi: 10.1016/j.jhep.2016.09.020. Epub 2016 Oct 5.

Arentsen T, Qian Y, Gkotzis S, Femenia T, Wang T, Udekwu K, Forssberg H, Diaz Heijtz R.

Mol Psychiatry. 2017 Feb;22(2):257-266. doi: 10.1038/mp.2016.182. Epub 2016 Nov 15.

Montagner A, Korecka A, Polizzi A, Lippi Y, Blum Y, Canlet C, Tremblay-Franco M, Gautier-Stein A, Burcelin R, Yen YC, Je HS, Al-Asmakh M, Mithieux G, Arulampalam V, Lagarrigue S, Guillou H, Pettersson S, Wahli W.

Sci Rep. 2016 Feb 16;6:20127. doi: 10.1038/srep20127

GF Satellite Unit: Handle your own GF mice

To provide the infrastructure for a world-class research facility, Karolinska Institutet Mouse Models (KIMM) and CFGR have begun to test, adapt and implement a number of measures which will advance technical interfaces and provide user participation. The first of these would be to create a satellite facility which will exclusively be used to maintain animals in isocages earmarked for specific experiments.

Our goal is to integrate a number of existing research platforms at KIMM, Solna in order to aid and expand microbiota research at the satellite unit. This will include interfacing with behavioural and metabolic research facilities in the premises.

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Why embark on using germfree models?

Humans carry approximately 1.5 to 2 kg of microbes (microbiota) in their gut, which have an impact on long term health and a variety of physiological parameters. The last decade has seen much groundbreaking research that has linked microbiota variability to a multitude of physiological and pathological signatures in humans. Many disease pathologies involve the interplay between the human body, the external environment and the complex communities of microorganisms residing on many surfaces of our body.

Germfree mice are a crucial and currently the only model to validate and understand the systemic biological functions of the microbiota. These mice provide a blank canvas onto which different sources of microbiota may be "painted" to observe and delineate specific and differential functions of the microbiota. CFGR provides a highly specialised platform for an ever growing research niche in academia and in the biotech and pharmaceutical industries.

The facility

Presently CFGR has the capacity to operate double tiered, flexible isolator units (up to 28 isolators). Every isolator is a self-sufficient unit, and can hold up to 30 animals in Mac2 and Mac2L cages. However, for ease of daily work routines and to accommodate newborn pups in breeding colonies, isolators are not kept fully stocked. In cases of short-term experimental procedures, 30 mice per isolator is acceptable.

Presently we mainly have C57BL/6 and NMRI, the most common strains requested by researchers at this facility. Other strains can be taken in, through Caesarian-section GF derivation upon request (see timeline below). CFGR also has a fully equipped laboratory, where simple experimental procedures can be performed. In addition, a satellite unit is being established (see above).

What can we offer?

Consolidated in 2003, CFGR has many years of experience in providing gnotobiotic research services. Apart from derivation of germfree mice the facility also provides in-tent technical services (see table below). Any procedures where you can autoclave or aerosol-sterilise instruments and use sterilized solutions can be carried out in an isolator. Automation of behavioural and metabolic observations is being planned at the satellite unit.

Additionally, the staff at CFGR will undertake monocolonization and conventionalization procedures upon request. Tents may also be hired by customers for different periods of time and the mice within monitored. All experiments adhere to strict ethical requirement and CFGR will help in obtaining the necessary ethical permits from the Swedish authorities.

All scientists must have a valid ethical approval, appropriate for either the core facility or the satellite unit, coordinated through CFGR. For non-Swedish-speaking researchers from abroad we will apply on their behalf.

    Services available:

    • Writing of ethics applications
    • Derivation of germfree mice
    • Organ, tissue and biofluid collection
    • Gavaging of microbial suspensions, nutrients, drugs etc
    • Ear marking, tail biopsy, typing
    • Weighing and simple parametric measurements
    • Injections: i.p; s.c; i.v and intradermally (with special permit)
    • Sedation and simple behavioral monitoring using IR-camera
    • Various colonization procedures: human flora, monocolonization, cocktails, infections etc
    • GF crosses and breeding protocols
    • Isolator rental for procedures using specialised instruments or long term experiments
    Timeline for germfree derivation

    Timeline for derivation

    CFGR: A brief history

    Since the 1950's, Karolinska Institutet has maintained a unique platform for the handling and derivation of gnotobiotic models kept under germ-free (GF) conditions. Established by the late Professor Bengt Gustafsson, the current CFGR unit functions as a core facility for KI and provides GF models to academic researchers as well as to the biotech and pharmaceutical industries. This facility is one of a handful in Scandinavia, and the number of similar facilities throughout the world is still very low.

    Staff and organisation

    At present we have two full time technicians and a part-time scientific coordinator who together with the staff at the GF Satellite Unit will help researchers with planning experiments and providing timely delivery of mice and services to customers. The staff will also maintain and monitor all ethical and experimental regulations.

    We constantly aim to expand the range and expertise of technical, methodological and experimental possibilities within CFGR. The staff at CFGR are always ready to discuss experimental procedures and approaches with facility users.

    CFGR, housed at Astrid Fagraeus laboratory, is part of Karolinska Institutet Mouse Models and managed by Comparative Medicine.


    Please contact us for a price list for our services.

    Contact us

    For additional information, up-to-date quotes, experimental planning etc you are welcome to contact us at: