All-Russian Collection of Microorganisms (VKM):

Current state-of-art, plans and expectations

Alexey A. Leontievsky

GCM 2.0 type strain sequencing project workshop 2018 November 21-22

All-Russian Collection of Microorganisms (VKM)

•1958 – VKM established in the Institute of Microbiology, Moscow

•1964 – the first catalogue was published

•1980 – VKM was re-allocated to Pushchino, Moscow region

VKM is the department at G.K. Skryabin Institute of Biochemistry

and Physiology of Microorganisms Russian Academy of Sciences

(IBPM RAS)

«Center for the collection, maintenance, study and dispatch of

microorganisms and associated information for scientific,

educational and industrial organizations»

•1987 – VKM recognized as an International Depository Authority (IDA) under

the Budapest Treaty for the deposit of microorganisms for patent purposes

•Membership in WFCC and ECCO

- VKM is the largest among the microbiological collections in Russia

- Over 21000 strains of bacteria, archaea, filamentous fungi

and yeasts are currently maintained in the collection

- The VKM on-line catalog includes over 7,500 strains

(more than 750 genera and 3,300 species)

- Strains originate from various ecosystems of different geography,

including Arctic and Antarctica

Coming in from the cold

A “cool” VKM sub-collection includes over 2000 strains

The age of permafrost

sediments was estimated to

reach up to 3 million years

The strains mainly originate from

- permafrost soil

- ancient plant seeds found in

permafrost

- frozen volcano ashes

- non-frozen sodium-chloride

water brines (cryopegs)

located in permafrost

sediments of marine origin

Banger Oasis

Progress

Russkaya

Novolazarevskaya

Leningragskay

Druzhnaya

Mirny

The sampling places

in Antarctica

Nearly 1100 strains

of the “cool” VKM sub-collection are filamentous fungi

(73 genera and 186 species)

Majority of the strains belong to the genera Penicillium, Geomyces and Cladosporium,

many species of which possess high adaptive capabilities and some grow at -2 °C, at high salt concentration (20%) and under low oxygen tension

Taxa Genera Species Strains Strains identified at the species level

Ascomycota 69 179 925 883

Basidiomycota 3 3 13 8

Mucoromycota 1 4 8 8

Total 73 186 1067 899

Ascomycota

Basidiomycota

Mycelia sterilia (white)

Mycelia sterilia (dark)

168 fungal strains from the cold (polar) regions with no species identification

Cell wall glycopolymers in actinobacteria

> 600 strains have been studied

> 100 novel structures of glycopolymers have been found

The taxonomic specificity of polymers have been shown

Teichoic acids [– Polyol–P–Polyol–P– ]

Sugar 1-phosphate polymers [– Sug–P–Sug–P– ]

Teichuronic acids [– Sug–SugA– ]

Teichulosonic acids [ –Sug–Kdn–Sug–Kdn– ]

Polysaccharides (PS) [ –Sug–Sug– ]

VKM, Zelinsky Institute of Organic Chemistry RAS, and

Faculty of Biology, Lomonosov Moscow State University.

→2)-α-D-Manp-(1→3)-α-D-Rhap-(1→

→2)-α-D-Manp-(1→3)-α-D-Rhap-(1→

3)

↑

β-D-Xylp-(1

→2)-α-D-Manp-(1→3)-α-D-Rhap-(1→

3)

↑

β-D-Manp-(1

Rhamnomannans in different Rathayibacter species

→3)-α-D-Manp-(1→2)-α-D-Rhap-(1→

→3)-α-D-Manp-(1→2)-α-D-Rhap-(1→

3)

↑

β-D-Xylp-(1

→3)-α-D-Manp-(1→2)-α-D-Rhap-(1→

3)

↑

β-D-Xylp-(1

2)

↑

β-D-Xylp-(1

2)

↑

α-D-Glcp-(1

4,6)

↑

Pyr

Sugars of teichuronic acids in Rathayibacter spp.

β-D-GlcpA/GalpA β-D-Galp β-D-Glcp β-D-Manp L-Rhamp-(1-

Yeasts mycocins (killer toxins)

•Over 1000 strains have been

tested

•Grouping of yeast strains on

the basis of sensitivity to

mycocins correlates with their

clustering based on the DNA

sequences.

•Make it possible to reveal

heterogeneity of the yeast

species.

•Many strains with antifungal

activities against plant

pathogenic fungi have been

found

STEROIDs (Greek, stereos = solids)

Steroid medicines are now ranked among the most marketed products of pharmaceutical

industry (second after antibiotics)

Steroids have originated hundreds millions years ago.

They are regarded as chemical fossils and often used

as geochemical markers in the sediment maturity

estimation in petroleum geochemistry

Key Pharmaceutical Indications

for Steroid Drugs

Antiinflammation: Asthma, Arthritis, Crohn‘s Disease, Colitis, etc. Female Health: Contraception, Endometriosis, Hormone Replacement Therapy, etc. Male health: Prostate Hyperplasia, Anabolics, etc. Oncology: Brain Cancer, Prostate Cancer, Breast Cancer, etc. Heart Health: Hypertension, Heart Failure, Diuretics, etc. Healthy Digestion: Obesity, Hepatocirrhosis, Bile gallstones,

Cholecystitis, etc.

• Cholesterol, plant sterols • Neurosteroids • Vitamin D3 • Mineralocorticoids • Bile acids • Adrenocorticoids • Sex hormones • Plant hormones • Ecdysteroids (moulting hormones), others…

Steroids are widely used in agriculture and veterinary; their control is of importance for

ecobiotechnology and other fields

Estrone Estriol Cortisone Betamethasone

Hydrocortisone Cortisone Prednisone Prednisolone (P) 6-methyl-P Exemestane

Drospirenone, and others

3-TR Dexamethasone Betamethasone Triamcinolone acetamide

Progesterone and derivatives

Testosterone (Ts) Methyl-Ts Boldenone Canrenone Spirolactone

Actinobacteria modification of phytosterols for synthesis of Active Pharmaceutical Ingredients (APIs)

Steroid modifications by actinobacteria

Bioprocesses for steroid production

Androstenedione (AD)

Androstadienedione (ADD)

9a-hydroxyAD

Exemestane (6a-methyl ADD)

Testosterone

Dehydroepiandrosterone (DHEA)

Androst-1,4,9-trienedione

6α-Methyl prednisolone

7α,15α-Dihydroxyprasterone

Hydrocortisone

6α-F,11β-hydroxy,16α-methyl deoxycorticosterone

Testolactone / testololactone

Ursodeoxycholic acid

Ursocholic acid

…. and others

Novelty, industrial importance

Original strains and «know-how» at the

different production stages

Some bioprocesses has been

implemented at the semi-industrial level

(2,000 L bioreactors)

Self-contained technological schemes

Re-usable materials…

Screening of about 1000

bacterial and fungal strains

resulted in development of

over 20 bioprocesses!

1000 • Bioinformatics analysis

950 • PCR amplification

800 • Cloning into host cell

700 • Plates expression test

400-600 • Fermentation in the flasks

400-600 • Purification

500 • Characterisation: рН, Т, susbtrates

1-2 • Selection of 1-2 hit enzymes

HTS-technology of enzyme preparations obtaining

Microbial culture collections

in Comecon subnetwork

1989-1992

Participating countries: Bulgaria, Czech, Germany, Mongolia, USSR, Vietnam

Participating repubics of USSR: Armenia, Azerbaijan, Byelorussia, Estonia, Georgia, Kazakhstan, Latvia, Lithuania, Russia, Ukraine, Uzbekistan

Participating Russian microbial culture collections: VKM, VKPM, IEGM, LE(BIN), KMM, VIZR, INA, INMI, IPR, IBPRM, KBP_MSU, KM_MSU (and five more microbial culture collections)

Currently VKM participates in:

• Microbiological communities: ECCO, WFCC

• Infrastructure MIRRI

with culture collections: BCCM, including DCG, GeneCorner, IHEM, ITM, LMG, MUCL, ULC (Belgium), CIRM-Inra, Institut Pasteur (France), ATHUBA, ATHUM, UOA-HCPF, ACA-DC, BPIC (Greece), MSCL, University of Latvia (Latvia), Westerdijk Fungal Biodiversity Institute - KNAW (Netherlands), IAFB-KKP, PCM, KPD (Poland), Pt-mBRCN, including ACOI, LEGE-CC, MUM, PYCC, UCCCB (Portugal), BEA, CECT (Spain)

• Project EOSC-Life with infrastructures:

Elixir, EMBL, BBMRI-ERIC, EATRIS-ERIC, ECRIN, EMBRC-ERIC, FORSCHUNGSZENTRUM JULICH GMBH, ERINHA, FORSCHUNGSVERBUND BERLIN EV, INFRAFRONTIER GMBH, INSTRUCT-ERIC, UNIVERSITA' DEGLI STUDI DI MILANO-BICOCCA INSTRUCT-ERIC, MIRRI, CHARITE - UNIVERSITAETSMEDIZIN BERLIN, ALBERT-LUDWIGS-UNIVERSITAET FREIBURG, THE CHANCELLOR, SORBONNE UNIVERSITE, INSERM, UNIVERSITA DEGLI STUDI DI TORINO, UNIVERSITY OF DUNDEE, ABO AKADEMI, FRAUNHOFER GESELLSCHAFT ZUR FOERDERUNG DER ANGEWANDTEN FORSCHUNG E.V.

and a big list of additional members.

• IT construction systems: FAIR EG, Digital Objects.

FAIR EG – FAIR MIRRI comparison

FAIR SYSTEMS TO MAKE

FAIR ACTION PLAN RECS PARTIALLY

PRESENTED IN MIRRI PLANS

1, 3, 7, 18, 20, 28, 34

FAIR ACTION PLAN RECS NOT PRESENTED IN MIRRI AT ALL

2, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 23, 24, 25, 26, 27,

29, 30, 31, 32, 33

VKM obligations in EOSC-Life

• VKM makes interconnection between

(1) the system of biological databases of EOSC-Life partners

and

(2) the system of strains in European microbial culture

collections (CC).

• In preliminary step most of the databases available on Internet

were inspected (Biosharing, MetaBase, ELIXIR Data Resources,

in ExPASy, NAR and in majority of other sources).

• Databases were characterised by 16 parameters. Using the

database's interconnection system constructed in this research,

the data integration level indicators were calculated.

• With these indicators, the minimum number of integration

contracts sufficient for desirable level of interconnection with

biological databases was discovered. The current effort is to bring

the latest databases study, necessary quality level, connection to the latest EOSC data structures, and FAIRness.

Towards the genomic center

- Efforts to organize a center for genomic research at the Institute

- The group of genomics and bioinformatics has been established

- More than 50 genomes have been sequenced by now

(The sequencing was performed mainly in the «centers

of collective use» in Russia and in the framework of

realization of international projects).

- Approval of a large-scale program in the field of genomic research

in Russia (2018)

- Collaboration with WDCM within the framework of GCM 2.0 project

Thank for your

attention!