Publications by authors named "Victoria Shcherbakova"

14 Publications

  • Page 1 of 1

gen. nov., sp. nov. isolated from human faeces.

Int J Syst Evol Microbiol 2020 Feb;70(2):1210-1216

Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia.

A strain of obligately anaerobic, spore-forming, Gram-positive rods was isolated from child faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole genome sequencing revealed the strain to represent a member of the family distant from described species and genera. The strain was moderately saccharolytic with mannose as the preferred substrate and produced lactic acid, acetic acid and H as the end products. The major cellular long-chain fatty acids were C and C aldehyde. The genomic DNA G+C content was 52.3 mol%. On the basis of chemotaxonomic and genomic properties it was concluded that the strain represents a novel species in a new genus within the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is ASD2818 (=VKM B-3268=JCM 33295).
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http://dx.doi.org/10.1099/ijsem.0.003900DOI Listing
February 2020

Prevotella rara sp. nov., isolated from human faeces.

Int J Syst Evol Microbiol 2018 Dec 19;68(12):3818-3825. Epub 2018 Oct 19.

1​Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia.

A strain of obligately anaerobic, Gram-stain-negative rods was isolated from human faeces and characterized both phenotypically and genotypically. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed the strain to represent a member of the genus Prevotella, distant from the species with validly published names, with the closest relationship to Prevotella oryzae. The strain was moderately saccharolytic and proteolytic. The predominant menaquinones were MK-13 and MK-12. The major cellular long-chain fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 45.7 mol%. On the basis of chemotaxonomic and genotypic properties, it was concluded that the strain represent a novel species within the genus Prevotella, for which the name Prevotellarara sp. nov. is proposed. The type strain of Prevotellarara is 109 (=VKM B-2992=DSM 105141).
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http://dx.doi.org/10.1099/ijsem.0.003066DOI Listing
December 2018

Methanogens in the Antarctic Dry Valley permafrost.

FEMS Microbiol Ecol 2018 08;94(8)

Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, 142290, Russia.

Polar permafrost is at the forefront of climate change, yet only a few studies have enriched the native methane-producing microbes that might provide positive feedbacks to climate change. Samples Ant1 and Ant2, collected in Antarctic Miers Valley from permafrost sediments, with and without biogenic methane, respectively, were evaluated for methanogenic activity and presence of methanogens. After a one-year incubation of both samples under anaerobic conditions, methane production was observed only at room temperature in microcosm Ant1 with CO2/H2 (20/80) as carbon and energy sources and was monitored during the subsequent 10 years. The concentration of methane in the headspace of microcosm Ant1 changed from 0.8% to a maximum of 45%. Archaeal 16S rRNA genes from microcosm Ant1 were related to psychrotolerant Methanosarcina lacustris. Repeated efforts at achieving a pure culture of this organism were unsuccessful. Metagenomic reads obtained for the methane-producing microcosm Ant1 were assembled and resulted in a 99.84% complete genome affiliated with the genus Methanosarcina. The metagenome assembled genome contained cold-adapted enzymes and pathways suggesting that the novel uncultured Methanosarcina sp. Ant1 is adapted to sub-freezing conditions in permafrost. This is the first methanogen genome reported from the 15 000 years old permafrost of the Antarctic Dry Valleys.
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http://dx.doi.org/10.1093/femsec/fiy109DOI Listing
August 2018

Draft Genome Sequence of Antarctic Methanogen Enriched from Dry Valley Permafrost.

Genome Announc 2016 Dec 8;4(6). Epub 2016 Dec 8.

Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA

A genomic reconstruction belonging to the genus Methanosarcina was assembled from metagenomic data from a methane-producing enrichment of Antarctic permafrost. This is the first methanogen genome reported from permafrost of the Dry Valleys and can help shed light on future climate-affected methane dynamics.
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http://dx.doi.org/10.1128/genomeA.01362-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146446PMC
December 2016

Peptococcus simiae sp. nov., isolated from rhesus macaque faeces and emended description of the genus Peptococcus.

Int J Syst Evol Microbiol 2016 Dec 9;66(12):5187-5191. Epub 2016 Sep 9.

Animal Science Department, Biomedical Primate Research Center, P.O. Box 3306, 2280 GH Rijswijk, The Netherlands.

A study of the faecal microbiome in three healthy female rhesus macaques revealed the presence of a novel obligately anaerobic, chemoorganoheterotrophic, non-sporing, coccoid, non-motile, Gram-stain-positive bacterial species. Three strains of this species, designated as M108T, M916-1/1, and M919-2/1, were non-haemolytic, H2S-positive, catalase-positive, bile- and NaCl-sensitive and required peptone for growth. Strains also were asaccharolytic, able to utilize sulfite, thiosulfate and elemental sulfur as electron acceptors, and produced acetic and butyric acids as metabolic end-products. Strain M108T is characterized by the prevalence of C14 : 0, C16 : 0 and C18 : 1ω9cis dimethyl acetal among the cellular fatty acids, and the presence of MK-10 menaquinone. The DNA G+C content was found to be 51 mol%. Phylogenetic analysis of partial 16S rRNA gene sequences of strains M108T, M916-1/1 and M919-2/1 placed these strains into the genus Peptococcus (family Peptococcaceae). On the basis of phenotypic and genotypic properties we conclude that these strains represent a novel bacterial species for which the name Peptococcus simiae sp. nov. is proposed. The type strain is M108T (=DSM 100347T=VKM B-2932T).
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http://dx.doi.org/10.1099/ijsem.0.001494DOI Listing
December 2016

Archaeal communities of Arctic methane-containing permafrost.

FEMS Microbiol Ecol 2016 10 15;92(10). Epub 2016 Jun 15.

Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya str. 2, Pushchino Moscow region, 142290, Russian Federation.

In the present study, we used culture-independent methods to investigate the diversity of methanogenic archaea and their distribution in five permafrost samples collected from a borehole in the Kolyma River Lowland (north-east of Russia). Total DNA was extracted from methane-containing permafrost samples of different age and amplified by PCR. The resulting DNA fragments were cloned. Phylogenetic analysis of the sequences showed the presence of archaea in all studied samples; 60%-95% of sequences belonged to the Euryarchaeota. Methanogenic archaea were novel representatives of Methanosarcinales, Methanomicrobiales, Methanobacteriales and Methanocellales orders. Bathyarchaeota (Miscellaneous Crenarchaeota Group) representatives were found among nonmethanogenic archaea in all the samples studied. The Thaumarchaeota representatives were not found in the upper sample, whereas Woesearchaeota (formerly DHVEG-6) were found in the three deepest samples. Unexpectedly, the greatest diversity of archaea was observed at a depth of 22.3 m, probably due to the availability of the labile organic carbon and/or due to the migration of the microbial cells during the freezing front towards the bottom.
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http://dx.doi.org/10.1093/femsec/fiw135DOI Listing
October 2016

Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces.

Int J Syst Evol Microbiol 2016 Aug 6;66(8):3041-3049. Epub 2016 May 6.

Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia.

Two novel strains of Gram-stain-negative, rod-shaped, obligately anaerobic, non-spore-forming, non-motile bacteria were isolated from the faeces of healthy human subjects. The strains, designated as 585-1T and 668, were characterized by mesophilic fermentative metabolism, production of d-lactic acid, succinic acid and acetic acid as end products of d-glucose fermentation, prevalence of C18 : 1ω9, C18 : 1ω9 aldehyde, C16 : 0 and C16 : 1ω7c fatty acids, presence of glycine, glutamic acid, lysine, alanine and aspartic acid in the petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4-56.6 mol%. The complete 16S rRNA gene sequences of the two strains shared 91.7/91.6 % similarity with Anaerofilum pentosovorans FaeT, 91.3/91.2 % with Gemmiger formicilis ATCC 27749T and 88.9/88.8 % with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a novel species in a new genus within the family Ruminococcaceae, for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain of Ruthenibacterium lactatiformans is 585-1T (=DSM 100348T=VKM B-2901T).
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http://dx.doi.org/10.1099/ijsem.0.001143DOI Listing
August 2016

Alistipes inops sp. nov. and Coprobacter secundus sp. nov., isolated from human faeces.

Int J Syst Evol Microbiol 2015 Dec;65(12):4580-4588

Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow 117997, Russia.

Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism.The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C15 : 0 fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 (in a 1 : 1 ratio) and the predominant menaquinone was MK-11.The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627T and 177T placed these bacteria in the genera Alistipes(family Rikenellaceae) and Coprobacter (family Porphyromonadaceae), respectively.On the basis of the phenotypic and genotypic properties of strains 627T and 177T, we conclude that these strains from human faeces represent two novel bacterial species, for which the names Alistipes inops sp. nov. (type strain 627T5DSM 28863T5VKM B-2859T) and Coprobacter secundus sp. nov. (type strain 177T=DSM 28864T=VKM B-2857T) are proposed.
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http://dx.doi.org/10.1099/ijsem.0.000617DOI Listing
December 2015

Desulfonatronum zhilinae sp. nov., a novel haloalkaliphilic sulfate-reducing bacterium from soda Lake Alginskoe, Trans-Baikal Region, Russia.

Extremophiles 2015 May 5;19(3):673-80. Epub 2015 Apr 5.

Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Moscow Region, Russia,

A novel haloalkaliphilic sulfate-reducing bacterium, designated Al915-01(T), was isolated from benthic sediments of the Lake Alginskoe, a soda lake located in the Trans-Baikal Region, Russia. Cells of the strain were Gram-stain negative, motile, non-spore-forming vibrion (0.4-0.5 × 1.2-2.3 µm). Strain Al915-01(T) grew in the pH range from 8.0 to 10.5 (optimum pH 9.0) and required NaCl for growth (5-100 g l(-1) NaCl, optimum 40 g l(-1)). The bacterium grew at 10-40 °C (optimally at 36 °C) and used lactate, formate and pyruvate as electron donors in the presence of sulfate. It was able to reduce sulfate, sulfite, thiosulfate and nitrate with lactate as an electron donor. The isolate was able to grow lithoheterotrophically with sulfate and molecular hydrogen if acetate was added as a carbon source. The predominant fatty acids were anteisoC15:0, isoC17:1, C18:1ω7 and C16:1ω7. The G+C content in the DNA was 58.3 ± 1 mol %. Analysis of the 16S rRNA gene sequence showed that the new bacterium belongs to the genus Desulfonatronum. The closest relatives were Desulfonatronum buryatense Ki5(T) (99.9 % similarity) and Desulfonatronum lacustre Z-7951(T) (99.2 % similarity). On the basis of the genotypic, phenotypic and phylogenetic characteristics, the isolate is proposed as a representative of a novel species Desulfonatronum zhilinae with the type strain Al915-01(T) (=VKM B-2744(T) = DSM 26338(T)).
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http://dx.doi.org/10.1007/s00792-015-0747-0DOI Listing
May 2015

New sulfate-reducing bacteria isolated from Buryatian alkaline brackish lakes: description of Desulfonatronum buryatense sp. nov.

Extremophiles 2013 Sep 24;17(5):851-9. Epub 2013 Jul 24.

Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospect Nauki 5, Pushchino, Moscow, 142290, Russia.

New strains of sulfate-reducing bacteria were isolated from two alkaline brackish lakes located in the Siberian region of Russia, namely in the Southern Transbaikalia, Buriatia. The article presents data describing morphology, physiology, and biochemical characteristics of the isolated strains. These strains Ki4, Ki5, and Su2 were mesophilic and alkaliphilic with optimal growth at pH 8.9, 9.4, and 10.0, respectively. All isolated strains utilized lactate, formate, and ethanol in the presence of sulfate for growth and sulfidogenesis accompanied with formation of acetate and CO2. Strains Ki5 and Su2 were able to reduce Fe(III). The DNA G + C content in strains Ki4, Ki5 and Su2 was 56.3, 48.8 and 59.6 mol%, respectively. According to phylogenetic analysis of 16S rRNA sequences, the new strains were clustered within the genus Desulfonatronum, and the closest relative D. lacustre Z-7951(T) (=DSM 10312(T)) showed 99.3-99.6 % similarity. DNA-DNA relatedness values of the strains Ki4, Ki5, and Su2 with D. lacustre Z-7951(T) were 89, 53, and 79 %, respectively. Polyphasic taxonomy data suggest that strain Ki5(T) is representative of the proposed novel species Desulfonatronum buryatense sp. nov.
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http://dx.doi.org/10.1007/s00792-013-0567-zDOI Listing
September 2013

Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces.

Int J Syst Evol Microbiol 2013 Nov 14;63(Pt 11):4181-4188. Epub 2013 Jun 14.

Department of Microbiology and Virology, Russian National Research Medical University, Moscow 117997, Russia.

A novel obligately anaerobic, non-spore-forming, rod-shaped, non-motile Gram-reaction-negative bacterium was isolated from infant faeces. The strain, designated NSB1(T), was able to grow on rich media at 30-37 °C, in the presence of up to 2 % (w/v) Oxgall and 2 % (w/v) NaCl. Cells of strain NSB1(T) produced catalase, but not urease and indole. Aesculin was not hydrolysed. The strain was able to utilize d-glucose, lactose, maltose, mannose and raffinose as electron donors. When grown on d-glucose, the main metabolic end products were propionic and acetic acids, with a minor product being succinic acid. The major cellular fatty acids, iso-C15 : 0 and anteiso-C15 : 0, were present at a 1 : 1 molar ratio. The major menaquinone was MK-11. The DNA G+C content was found to be 38.5 mol%. According to 16S rRNA gene sequence analysis strain NSB1(T) is a member of the family Porphyromonadaceae, phylum Bacteroidetes. The closest relatives of the strain were Barnesiella viscericola (88.2 % identity) and Barnesiella intestinihominis (87.4 % identity). On the basis of phenotypic and genotypic properties of strain NSB1(T) we conclude that this strain represent a novel species in a new genus within the family of Porphyromonadaceae for which the name Coprobacter fastidiosus gen. nov., sp. nov. is proposed. The type strain of the species is NSB1(T) ( = DSM 26242(T), = VKM B-2743(T)).
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http://dx.doi.org/10.1099/ijs.0.052126-0DOI Listing
November 2013

Structure of the O-specific polysaccharide from the lipopolysaccharide of Psychrobacter cryohalolentis K5(T) containing a 2,3,4-triacetamido-2,3,4-trideoxy-L-arabinose moiety.

J Nat Prod 2012 Dec 29;75(12):2236-40. Epub 2012 Nov 29.

Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia.

A novel constituent of bacterial polysaccharides, 2,3,4-triacetamido-2,3,4-trideoxy-L-arabinose, was found in the O-specific polysaccharide from the lipopolysaccharide of Psychrobacter cryohalolentis K5(T) and identified by 1D and 2D (1)H and (13)C NMR studies of the polysaccharide and a disaccharide obtained by solvolysis of the polysaccharide with triflic acid. The following structure of the branched polysaccharide was established by sugar analysis, triflic acid solvolysis, Smith degradation, and 2D NMR spectroscopy.
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http://dx.doi.org/10.1021/np300484mDOI Listing
December 2012

Structure of an acidic polysaccharide isolated from Psychrobacter maritimus 3pS containing a bacillosamine derivative.

Carbohydr Res 2012 Oct 21;359:7-10. Epub 2012 Jul 21.

Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia.

An acidic polysaccharide was obtained from Psychrobacter maritimus 3pS isolated from a Siberian cryopeg sample (Kolyma lowland). The following structure of the tetrasaccharide repeating unit of the polysaccharide was established by sugar analysis along with (1)H and (13)C NMR spectroscopy: →2)-α-L-Rhap-(1→4)-α-D-GalpNAcA-(1→3)-α-D-QuipNAc4NHb-(1→3)-β-D-QuipNAc4NHb-(1→ where D-GalNAcA indicates 2-acetamido-2-deoxy-D-galacturonic acid and d-QuiNAc4NHb indicates 2-acetamido-2,4,6-trideoxy-4-[(S)-3-hydroxybutanoyl]amino-D-glucose.
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http://dx.doi.org/10.1016/j.carres.2012.07.007DOI Listing
October 2012

Structure of the O-polysaccharide chain of the lipopolysaccharide of Psychrobacter muricolla 2pS(T) isolated from overcooled water brines within permafrost.

Carbohydr Res 2012 Feb 6;349:78-81. Epub 2011 Dec 6.

Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia.

Psychrotrophic bacteria of the genus Psychrobacter have not been studied in respect to lipopolysaccharide structure. In this work, we determined the structure of the O-specific polysaccharide of the lipopolysaccharide of Psychrobacter muricolla 2pS(T) isolated from overcooled (-9°C) water brines within permafrost. The polysaccharide was found to be acidic due to the presence of an amide of 2-acetamido-2-deoxy-l-guluronic acid with glycine (l-GulNAcA6Gly), which has not been hitherto found in nature. The following structure of the disaccharide repeating unit of the polysaccharide was established using composition analysis along with 1D and 2D (1)H and (13)C NMR spectroscopy: →4)-α-l-GulpNAcA6Gly-(1→3)-β-d-GlcpNAc-(1→
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http://dx.doi.org/10.1016/j.carres.2011.11.027DOI Listing
February 2012
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