Laboratories IKBFU

Bioprospekting and Metagenomics of Ecosystems

General information

Lab of microbial genomics was established in 2013 to develop fruitful research area of genomics of extremophilic microbes in collaboration with FRC “Biotechnology” RAS. Since then lab developed wide collaboration network including Moscow State University; University of Bangor (Wales, UK); Institute of Coastal and Marine Environments (Messina, Sicily); Institute of Physical Chemistry (Moscow, Russia); Novosibirsk State University (Russia), Atlas Biomedical Group (Moscow, Russia) and other research and biotech centers worldwide. Lab works closely with classical microbiological labs to develop projects and generate experimental plan. We then use next-generation sequencing technologies to generate big biological datasets which are then analyzed by different methods of bioinformatics. We work with both classical microbiological isolates (pure cultures) and environmental samples “as is” – metagenomics. Metagenomic approach allows us to study non-culturable fraction of microbial communities which cannot be studied by classical cultivation techniques.

Obtained data is used both for fundamental studies of microbial diversity, metabolism and evolution and bioinformatic identification of new enzymes and small molecules which can be used in biotechnological industry to develop and optimize processes of biological conversion.

Equipment

To conduct analysis of genomes and metagenomes lab use the following equipment of SLS IKBFU:

  1. MiSeq High-throughput Sequencing System (Illumina) – will be used to sequence genomes and metagenomes. MiSeq system is capable of producing long reads (300+300 bp) which makes it best for genome sequencing of pure cultures. Also MiSeq allows to obtain high amount of single reads per run (approximately 25 million) so it is perfect benchtop system for metagenomic analysis

  2. Ion Torrent PGM High-throughput Sequencing System (Life Technologies) will be used as alternative sequencing platform due to several reasons. Firstly, the MiSeq sequence-specific error profile differs from one of Ion Torrent, therefore the combination of two approaches will allow to significantly reduce error level in final sequence. Secondly, length of reads (400 bp) and low price of a run makes Ion Torrent suitable for preliminary metagenomic analysis of complex microbial population using amplicone sequencing of hypervariable sites of 16S RNA genes

  3. The 96-capillary DNA Analyzer ABI 3730 XL (Life Technologies) is essential for final steps of de novo sequencing of new microbial strains and routine verification of molecular cloning results.

  4. Automatic system for hydrodynamic fragmentation Hydroshear Plus (Digilab) provides shearing DNA into large fragments, which makes it indispensible for preparation of long-insert genomic DNA library for whole genome sequencing and also for fosmid library preparation.

  5. Sonication device for DNA fragmentation Bioruptor (Diagenode) will be used for fragmentation of DNA into small fragments in standard fragment library preparation protocol for whole genome and metagenome sequencing

Furthermore, the research group has all additional equipment necessary for standard molecular-biological methods (such as cloning, PCR, RT-PCR) including gel electrophoresis cameras, gel documentation system (GelDoc, Bio-Rad Laboratories), centrifuges, thermostats, vacuum concentrator, amplificators (Veriti, Life Technologies and С100, Bio-Rad), amplificators with real-time signal detection (CFX-96, Bio-Rad Laboratories), fluorimeter Qubit (Life Technologies) and other standard laboratory equipment.

Research Team

Lab head -  Mikhail Yakimov, PhD, visiting professor

National Research Council, Rome

Areas of research: Microbial Ecology, DNA, RNA.

Stepan Toshchakov, PhD

graduated in 2006 from Moscow State University (molecular genetics), made his PhD theses presentation in 2009 in Institute of Gene Biology RAS (Moscow, Russia) studying long-distance chromosome interactions in Drosophila. In 2010-2012 worked as field application scientist specialized in next generation sequencing at Life Technologies corporation. Joined IKBFU in 2012.

Michail Yakimov, PhD, visiting professor;

Professor Yakimov leads the lab of Marine Molecular Microbiology and Biotechnology at Institute of Coastal and Marine Environments (Messina, Sicily). Specialized mainly in marine microbiology he is author of more than 160 publications in internationally recognized journals. Since 2016 within a framework of 5top100 project joined SLS IKBFU to develop multidisciplinary microbiological research and biotech application

Aleksei Korzhenkov, junior scientist;

Graduated in 2011 from IKBFU (chemistry). Works in lab of microbial genomics from very beginning. Aleksey is responsible for bioinformatics going in the lab. Delivers course of basic bioinformatics for 3d year students

Margarita Goeva, PhD student

Graduated in 2015 from IKBFU (bioengineering&bioinformatics). Rita is specialized in molecular biology (wetlab) and tries cultivation experiments.

Eugen Lunev, PhD student

Graduated in 2017 from IKBFU (neurobiology), but joined microbiology answering the call of the heart. Works on expression of biotechnologically-relevant proteins and NGS library preparation.

Nazar Samarov, junior scientist;

Graduated in 2010 from IKBFU (biology). When not asleep works with NGS wetlab techniques.

Undergrads:

  1. Alina Tepliuk (bioengineering&bioinformatics), 3d year;

  2. Olga Zakharova (bioengineering&bioinformatics), 3rd year;

  3. Dmitry Kazerov (biology), magister 1st year

  4. Andrey Dudun (bioengineering&bioinformatics), 5th year

  5. Ekaterina Aksartova (chemistry), magister 1st year

  6. Bogdan Efimenko (bioengineering&bioinformatics), 1st year

  7. Maria Vassilieva (bioengineering&bioinformatics), 4th year

  8. Marina Polyakova (bioengineering&bioinformatics), 4th year

Publications

1. Kompantseva EI, Kublanov IV, Perevalova AA, Chernyh NA, Toshchakov SV, Litti YV, Antipov AN, Bonch-Osmolovskaya EA, Miroshnichenko ML. Calorithrix insularis gen. nov., sp. nov., a novel representative of the phylum Calditrichaeota. Int J Syst Evol Microbiol. 2016 Dec 16.

DOI: 10.1099/ijsem.0.001744.

https://www.ncbi.nlm.nih.gov/pubmed/27983475

Impact Factor: 2.80

2. Frolov EN, Kublanov IV, Toshchakov SV, Samarov NI, Novikov AA, Lebedinsky AV, BonchOsmolovskaya EA, Chernyh NA. Thermodesulfobium acidiphilum sp. nov., a new thermoacidophilic sulfate-reducing chemoautotrophic bacterium from a Kamchatkan thermal site. Int J Syst Evol Microbiol. 2016

DOI: 10.1099/ijsem.0.001745

https://www.ncbi.nlm.nih.gov/pubmed/27995866

Impact Factor: 2.80

3. AV Teplyuk, NI Samarov, AA Korzhenkov, MO Ul’yanova, MA Goeva, IV Kublanov, TA Kanapatskii, NV Pimenov, SV Toshchakov. Analysis of chitinase diversity in the Baltic Sea bottom sediments. Microbiology (Russia). 2017

Impact Factor: 0.80

4. Podosokorskaya OA, Merkel AY, Gavrilov SN, Fedoseev I, Heerden Ev, Cason ED, Novikov AA, Kolganova TV, Korzhenkov AA, Bonch-Osmolovskaya EA, Kublanov IV. Tepidibacillus infernus sp. nov., a moderately thermophilic, selenate- and arsenate-respiring hydrolytic bacterium isolated from a gold mine, and emended description of the genus Tepidibacillus. Int J Syst Evol Microbiol. 2016

DOI: 10.1099/ijsem.0.001166.

https://www.ncbi.nlm.nih.gov/pubmed/27216447

Impact Factor: 2.80

5. Ivanova, A.A., Kulichevskaya, I.S., Merkel, A.Y., Toshchakov, S.V., Dedysh, S.N. High diversity of planctomycetes in soils of two lichen-dominated sub-arctic ecosystems of Northwestern Siberia. Frontiers in Microbiology. 2016; 7: 2065.

DOI: 10.3389/fmicb.2016.02065

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5177623/

Impact Factor: 3.94

6. Sorokin DY, Messina E, Smedile F, Roman P4, Damsté JS, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Kublanov IV, Samarov NI, Toshchakov SV, La Cono V, Yakimov MM. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME Journal. 2016.203. [Epub ahead of print]

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2016203a.html

Impact Factor: 9.328

7. Messina E, Sorokin DY, Kublanov IV, Toshchakov S, Lopatina A, Arcadi E, Smedile F, La Spada G, La Cono V, Yakimov MM. Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee.

Stand Genomic Sci. 2016 May 13;11:35

https://www.ncbi.nlm.nih.gov/pubmed/27182430

Impact Factor: 1.88

8. Kochetkova TV, Kublanov IV, Toshchakov SV, Osburn MR, Novikov AA, Bonch-Osmolovskaya EA, Perevalova AA. Thermogladius calderae gen. nov., sp. nov., an anaerobic, hyperthermophilic crenarchaeote from a Kamchatka hot spring. Int J Syst Evol Microbiol. 2016 Jan 21. Volume 66, Issue 3, Pages 1407-1412

http://www.ncbi.nlm.nih.gov/pubmed/26801582

Impact Factor: 2.80

9. Toshchakov SV, Korzhenkov AA; Samarov NI; Mazunin IO, Mozhey OI; Shmyr IS; Derbikova KS; Taranov EA; Dominova IN; Bonch-Osmolovskaya EA, Patrushev MV, Podosokorskaya OA, Kublanov IV.

Complete genome sequence of and proposal of Thermofilum uzonense sp. nov. a novel hyperthermophilic crenarchaeon and emended description of the genus Thermofilum.

Stand Genomic Sci. 2015 Dec 9;10:122.

http://www.ncbi.nlm.nih.gov/pubmed/26664700

Impact Factor: 3.17

10. Sorokin DY, Toshchakov SV, Kolganova TV and Kublanov IV. Halo(natrono)archaea isolated from hypersaline lakes utilize cellulose and chitin as growth substrates. Front. Microbiol. 2015. 6:942

http://journal.frontiersin.org/article/10.3389/fmicb.2015.00942/full

Impact Factor: 3.94

11. Placido A, Hai T, Ferrer M, Chernikova TN, Distaso M, Armstrong D, Yakunin AF, Toshchakov SV, Yakimov MM, Kublanov IV, Golyshina OV, Pesole G, Ceci LR, Golyshin PN. Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase. Appl Microbiol Biotechnol. 2015 Aug 13.

http://link.springer.com/article/10.1007/s00253-015-6873-x/fulltext.html

Impact Factor: 3.81

12. Stepan V Toshchakov, Ilya V Kublanov, Enzo Messina, Michail M Yakimov, Peter N Golyshin. Genomic Analysis of Pure Cultures and Communities. Hydrocarbon and Lipid Microbiology Protocols (Springer Protocols Handbooks), 08/2015 pp 1-21.

http://link.springer.com/protocol/10.1007/8623_2015_126

13. Merkel AY, Korneeva VA, Tarnovetskii I Yu, Bryukhanov AL, Chasovnikov VK, Taranov EA, Toshchakov SV, Pimenov NV. Structure of the archaeal community in the Black Sea photic zone. Microbiology. 2015 (Jul-Aug); 84(4):570-576.

http://link.springer.com/article/10.1134/S0026261715040128

Impact Factor: 0.71

14. Kovaleva OL, Merkel AY, Novikov AA, Baslerov RV, Toshchakov SV, Bonch-Osmolovskaya EA. Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov. Int J Syst Evol Microbiol. 2015 Feb;65(Pt 2):549-55

http://www.ncbi.nlm.nih.gov/pubmed/25404483

Impact Factor: 2.80

15. Gasanov NB, Toshchakov SV, Georgiev PG, Maksimenko OG. The Use of Transcription Terminators to Generate Transgenic Lines of Chinese Hamster Ovary Cells (CHO) with Stable and High Level of Reporter Gene Expression. Acta Naturae. 2015 Jul-Sep;7(3):74-80.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610167/

Impact Factor: 1.00

16. Podosokorskaya OA, Bonch-Osmolovskaya EA, Godfroy A, Gavrilov SN, Beskorovaynaya DA, Sokolova TG, Kolganova TV, Toshchakov SV, Kublanov IV. Thermosipho activus sp. nov., a thermophilic, anaerobic, hydrolytic bacterium isolated from a deep-sea sample. Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3307-13.

http://www.ncbi.nlm.nih.gov/pubmed/24994778

Impact Factor: 2.80

17. Podosokorskaya OA, Bonch-Osmolovskaya EA, Beskorovaynyy AV, Toshchakov SV, Kolganova TV, Kublanov IV. Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium. Int J Syst Evol Microbiol. 2014 Aug;64(Pt 8):2657-61.

http://www.ncbi.nlm.nih.gov/pubmed/24827706

Impact Factor: 2.80

18. Dominova IN, Kublanov IV, Podosokorskaya OA, Derbikova KS, Patrushev MV, Toshchakov SV.

Complete Genomic Sequence of "Thermofilum adornatus" Strain 1910bT, a Hyperthermophilic Anaerobic Organotrophic Crenarchaeon. Genome Announc. 2013 Sep 12;1(5). pii: e00726-13. doi: 10.1128/genomeA.00726-13.

http://www.ncbi.nlm.nih.gov/pubmed/24029764

19. Dominova IN, Sorokin DY, Kublanov IV, Patrushev MV, Toshchakov SV Complete Genome Sequence of Salinarchaeum sp. Strain HArcht-Bsk1T, Isolated from Hypersaline Lake Baskunchak, Russia. Genome Announc. 2013, Jul-Aug; 1(4): e00505-13

http://www.ncbi.nlm.nih.gov/pubmed/23868130