Timofey Skvortsov

Queen's University Belfast | QUB · School of Pharmacy

Lough Neagh is the largest and the most economically important lake in Ireland. It is also one of the most nutrient rich amongst the world's major lakes. In this study, 16S rRNA analysis of total metagenomic DNA from the water column of Lough Neagh has revealed a high proportion of Cyanobacteria and low levels of Actinobacteria, Acidobacteria, Chlo...

This review is devoted to the state-of-the-art strategies for the in vivo whole-transcriptome analysis of intracellular pathogens. The methods for the initial enrichment with bacterial RNA are discussed in detail, including the hybridization-based approaches, as well as the methods for cDNA synthesis taking into account the specific features of pro...

Dormant Mycobacterium tuberculosis bacilli are believed to play an important role in latent tuberculosis infection. Previously, we have demonstrated that cultivation of M. tuberculosis in K + -deficient medium resulted in generation of dormant cells. These bacilli were non-culturable on solid media (a key feature of dormant M. tuberculosis in vivo)...

The ongoing antimicrobial resistance crisis has incentivised research into alternative antibacterial and antibiofilm agents. One of them is plasma-activated water (PAW), which is produced by exposing water to a cold plasma discharge. This process generates a diverse array of reactive oxygen and nitrogen species (ROS/RNS) with antimicrobial properti...

Multidrug efflux pumps have been found to play a crucial role in drug resistance in bacteria and eukaryotes. In this study, we investigated the presence of functional multidrug and toxic compound extrusion (MATE) efflux pumps, inferred from whole genome sequencing, in the halophilic archaeon Halorubrum amylolyticum CSM52 using Hoechst 33342 dye acc...

Background: Robust methods to track pathogens support public health surveillance. Both wastewater (WW) and individual whole genome sequencing (WGS) are used to assess viral variant diversity and spread. However, their relative performance and the information provided by each approach have not been sufficiently quantified. Therefore, we conducted a...

Aims This study aimed to develop a new bioinformatic approach for the identification of novel antimicrobial peptides (AMPs), which did not depend on sequence similarity to known AMPs held within databases, but on structural mimicry of another antimicrobial compound, in this case an ultrashort, synthetic, cationic lipopeptide (C12-OOWW-NH2). Method...

Multidrug efflux pumps have been found to play a crucial role in drug resistance in bacteria and eukaryotes. In this study, we investigated the presence of functional multidrug and toxic compound extrusion (MATE) efflux pumps, inferred from whole genome sequencing, in the halophilic archaeon Halorubrum saccharovorum CSM52 using Hoechst 33342 dye ac...

Biofilm production plays a clinically significant role in the pathogenicity of many bacteria, limiting our ability to apply antimicrobial agents and contributing in particular to the pathogenesis of chronic infections. Bacteriophage depolymerases, leveraged by these viruses to circumvent biofilm mediated resistance, represent a potentially powerful...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an unprecedented impact on the people of Ireland as waves of infection spread across the island during the global coronavirus disease 2019 (COVID-19) pandemic. Viral whole-genome sequencing (WGS) has provided insights into SARS-CoV-2 molecular mechanisms of pathogenicity and evolu...

Cold atmospheric-pressure plasma (CAP) has emerged as a potential alternative or adjuvant to conventional antibiotics for the treatment of bacterial infections, including those caused by antibiotic-resistant pathogens. The potential of sub-lethal CAP exposures to synergise conventional antimicrobials for the eradication of Pseudomonas aeruginosa bi...

Biofilm production plays a clinically significant role in the pathogenicity of many bacteria, limiting our ability to apply antimicrobial agents and contributing in particular to the pathogenesis of chronic infections. Bacteriophage depolymerases, leveraged by these viruses to circumvent biofilm mediated resistance, represent a potentially powerful...

Background Gut microbiomes are crucial for host nutrition due to their feed energy-harvesting capacity. In the rumen microbiome Butyrivibrio and Pseudobutyrivibrio dominate and play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified (Butyrivibrio fibrisolvens, B. hungatei, B. proteoclasticus, Pseud...

Background The COVID-19 pandemic has highlighted the importance of whole genome sequencing (WGS) of SARS-CoV-2 to inform public health policy. By enabling definition of lineages it facilitates tracking of the global spread of the virus. The evolution of new variants can be monitored and knowledge of specific mutations provides insights into the mec...

Regulatory small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. Various stresses such as hypoxia and nutrient starvation cause a reduction in the metabolic activity of Mycobacterium smegmatis, leading to entry into dormancy. We investigated the functional role of F6, a small RNA of M. smegmatis...

The adherence of Proteus mirabilis to the surface of urinary catheters leads to colonization and eventual blockage of the catheter lumen by unique crystalline biofilms produced by these opportunistic pathogens, making P. mirabilis one of the leading causes of catheter-associated urinary tract infections. The Proteus biofilms reduce efficiency of an...

Butyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified ( Butyrivibrio fibrisolvens , Butyrivibrio hungatei , Butyrivibrio proteoclasticus , Pseudobutyrivibrio ruminis and Pseu...

Introduction: The COVID-19 pandemic has highlighted the importance of whole genome sequencing (WGS) of SARS-CoV-2 to inform public health policy. By enabling definition of lineages it facilitates tracking of the global spread of the virus. The evolution of new variants can be monitored and knowledge of specific mutations provides insights into the...

Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. Some of these halophiles may have been preserved over geological timescales within hypersaline fluid inclusions, but ingresses of water and/or anthropogenic activities can lead to the formation of alt...

Clathrate hydrates are nonstoichiometric crystalline inclusion compounds. Water acts as a "host lattice" and traps small guest molecules in stable cavities. One example, methane hydrates, are especially prevalent in situ at the seafloor. Although microorganism-produced proteins and polypeptides, including marine methylotroph porin proteins, can acc...

Background Butyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting energy from the diet. Within these genera, 5 rumen species have been classified (B. fibrisolvens, B. hungatei, B. proteoclasticus, P. ruminis and P. xylanivorans); nonetheless, the phylo...

Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotyp...

In clathrate hydrates, a water host lattice encages small guest molecules in cavities. Methane hydrates are the most widespread in-situ clathrate in the permafrost and continental-shelf ocean regions, constituting a significant energy resource, and prompting recent marine-hydrate gas-production trials. Despite exciting engineering advances and a fe...

Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approac...

In clathrate hydrates, a water host lattice encages small guest molecules in cavities. Methane hydrates are the most widespread in-situ clathrate in the permafrost and continental-shelf ocean regions, constituting a significant energy resource, and prompting recent marine-hydrate gas-production trials. Despite exciting engineering advances and a fe...

Pseudomonas aeruginosa is a prevalent opportunistic pathogen and is a leading cause of nosocomial infections around the world. Its ability to form biofilms increases its tolerance to antibiotics and with the number of multidrug resistant isolates on the rise, treatment becomes a complex puzzle as the choice of antibiotics available is diminished. T...

Proteus mirabilis is a Gram-negative, rod-shaped, opportunistically pathogenic bacterium, often found in the urinary tract. P. mirabilis strains are characterised by their ability to produce urease, which catalyses the hydrolysis of the urine’s urea into ammonia and carbon dioxide. The released ammonia increases the pH of the urine, promoting the f...

Proteus mirabilis is a Gram-negative, rod-shaped, opportunistically pathogenic bacterium, often found in the urinary tract. P. mirabilis strains are characterised by their ability to produce urease, which catalyses the hydrolysis of the urine’s urea into ammonia and carbon dioxide. The released ammonia increases the pH of the urine, promoting the f...

Transaminase enzymes (TAms) are becoming increasingly valuable in the chemist’s toolbox as a biocatalytic route to chiral amines. Despite high profile successes, the lack of (R)-selective TAms and robustness under harsh industrial conditions continue to prove problematic. Herein, we report the isolation of the first haloarchaeal TAm (BC61-TAm) to b...

Bacteriophages or phages are a unique type of virus that recognize a specific type of bacteria and then infect, replicate and kill the host via cell lysis. The application of phages and their enzymes for treating bacterial biofilms has recently gained significant interest due to a number of significant advantages compared to traditional antibiotics...

A new lytic phage Andromeda, specific to the economically important plant pathogen Pseudomonas syringae was isolated. It belongs to the Podoviridae family, Autographivirinae subfamily and possesses a linear dsDNA genome of 40,008 bp with four localized nicks. We reveal that Andromeda represents an atypical member of the phiKMVlviruses and establish...

Understanding autotrophic bacterial community structure and function along a naturally occurring iron deposit gradient. Naturally occurring iron deposits in upland streams have been studied in the context of their chemical composition, epilithic biomass, and impacts upon invertebrate community structure over an iron gradient in the Sperrin Mountain...

100 years have passed since the independent discovery of the humble bacteriophage (phage) by Frederick Twort and Felix d’Herelle in 1915 and 1917 respectively, and since then, it has become commonly accepted that phages represent the most abundant biological entities on Earth. Despite this fact, viral taxonomy lies in extremely treacherous waters,...

Exploring and understanding the phylogeny of the Butyrivibrio group is imperative if we are ever to fully understand the consortium of ruminal microbial enzymes that are responsible for the catalysis of multifaceted reactions, such as biohydrogenation. At present, taxonomic classification of the Butyrivibrio group is based primarily on butyrate pro...

There is remarkable potential for research at the interface between the earth sciences and environmental microbiology that may lead to advances in our understanding of the role of bacterial communities in the surface or subsurface environment of our planet. One mainstay of sedimentary classification is the concept of differential soil and/or paleos...

Chiral amines are valuable building blocks for the pharmaceutical industry, and are increasingly synthesized by transaminase-mediated (TAm) synthesis. Currently available TAms, primarily isolated from the genomes of cultured mesophilic bacteria, often suffer from a number of drawbacks, including poor substrate range and an inability to tolerate the...

We report here the draft genome sequence of Rhodococcus sp. strain NCIMB 12038, an industrially important bacterium, possessing a large and diverse repertoire of genes involved in the biotransformation of various organic compounds, including naphthalene.

A draft genome sequence of Halobacteriovorax sp. strain JY17 was assembled from a metagenomic data set. The 3.47-Mbp genome of this unusual predatory bacterium contains 3,263 protein-coding sequences, 33 tRNAs, and 2 copies each of the 16S, 23S, and 5S rRNA genes. This is only the third sequenced representative of this genus.

Here, we present draft genome sequences of Pseudomonas putida strains UV4 and UV4/95, which demonstrate an ability to conduct a wide range of industrially important biotransformations of arenes, alkenes, and phenols.

Phenylacetone monooxygenase is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenases family, and therefore it is an ideal candidate for the synthesis of industrially relevant ester or lactone compounds. However, its limited substrate scope has largely limited its industrial applications. Linear substrates are interesting...

Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bact...

Phenylacetone monooxygenase (PAMO) is the most stable and thermo-tolerant member of the Baeyer-Villiger monooxygenases family, and therefore it is an ideal candidate for the synthesis of industrially relevant compounds. However, its limited substrate scope has largely limited its industrial applications. In the present work, we provide, for the fir...

Amine transaminases offer an environmentally sustainable synthesis route for the production of pure chiral amines. However, their catalytic efficiency towards bulky ketone substrates is greatly limited by steric hindrance and therefore presents a great challenge for industrial synthetic applications. Hereby we report an example of rational transami...

Rarefaction analysis of Lough Neagh virome. (A) A rarefaction curve of the total viral metagenome was obtained after high-throughput sequencing of the Lough Neagh sample. The rarefaction curve was constructed within MetaVir with clustering set at 90% identity; 2,295,055 reads were analysed. (B) Comparison of the rarefaction curves of the three fres...

16S rRNA gene amplicons from the Lough Neagh water samples. (ZIP)

Score matrices-based global comparisons of Lough Neagh virome to freshwater viromes at MetaVir website. Results of oligonucleotide signatures comparison of full viromes and BLAST-based comparison of 50,000 sequences are shown. Hierarchical clustering and tree generation were done by R package pvclust. (A) Dinucleotide composition bias comparison. (...

Comparison of bacterial communities of Lough Neagh and selected freshwater lakes. (PDF)

Chemical and environmental parameters of the Lough Neagh water sample used for metagenomic analysis. (XLSX)

Identification of mechanisms that contribute to bacterial pathogens survival in the infected organism is a powerful approach to influence the pathogenic bacteria. Recently it was established that bacteria use small RNAs to regulate their metabolism. We studied the expression level of the three most highly expressed M. tuberculosis small RNAs MTS099...

The determination of the mechanisms contributing to the survival of pathogenic bacteria in the infected organism and the possible ways of their blocking is a promising approach to the development of new methods of affecting these bacteria. Among these mechanisms, the regulation of bacterial metabolism by small RNAs attracts particular interest sinc...

The aim of this work was to get deeper insight into genetic factors involved in the adaptive divergence of closely related species, specifically two representatives of Baikal coregonids-Baikal whitefish (Coregonus baicalensis Dybowski) and Baikal omul (Coregonus migratorius Georgi)-that diverged from a common ancestor as recently as 10-20 thousand...

Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5'...

Whole transcriptome profiling is now almost routinely used in various fields of biology, including microbiology. In vivo transcriptome studies usually provide relevant information about the biological processes in the organism and thus are indispensable for the formulation of hypotheses, testing, and correcting. In this study, we describe the resul...

Posttranscriptional regulation of gene expression by small RNAs was shown for multiple pathogenic microorganisms and plays an important role in virulence. 4 putative sRNA genes located in intergenic loci were identified: MAV_0380-0381 (4.5S RNA), MAV_1034-1035 (trans-encoded sRNA), MAV_1415-1416 (antisense or trans-encoded sRNA) and MAV_1531-1532 (...

Mycobacterium tuberculosis causes an infection in humans with clinical manifestations varying from asymptomatic carriage of bacteria to rapidly progressing tuberculosis. Infection outcomes depend on complex and still not fully understood interactions between the pathogenic bacteria and their host organism. Gene expression changes in response to hos...

Posttranscriptional regulation of gene expression mediated by small RNAs plays an important role in the virulence of pathogenic microorganisms. We have detected the expression of the following Mycobacterium avium genes situated in intergenic loci and coding for small RNAs: MAV_0380-0381 (4.5S RNA), MAV_1034-1035 (trans-encoded small RNA), MAV_1415-...

Mycobacterium tuberculosis causes an infection in humans with clinical manifestations varying from asymptomatic carrying of bacteria to rapidly progressing tuberculosis. The range of clinical manifestations depends on complicated and still poorly understood interactions between pathogenic bacteria and the host. Changes in gene expression that resul...

Introduction: Stromal cells associated with cancer cells are considered an important component of tumor microenvironment of pancreatic cancer. The intratumoral desmoplasia characteristic of pancreatic cancer is a result of growing carcinoma paracrine action on surrounding normal tissue cells. Selective targeting of tumor stroma cells can markedly i...

We used methylation-sensitive high resolution melting analysis to assess methylation of CpG islands within the promoters of the TIMP4, GATA4, SOX18, and EGFL7 genes in samples of non-small cell lung cancer and surrounding apparently normal tissue and noncancerous lung tissues. We found that the promoter methylation was heterogeneous in both tumor a...

This review considers modern strategy of whole-transcriptome investigation of intracellular pathogens in vivo. The methods of preliminary enrichment for bacterial RNA are discussed in details, including hybridization-based approaches and the peculiarities of cDNA synthesis in bacteria; methods of synthesizing cDNA from the view of features of proka...

We performed a comparative analysis ofMycobacterium aviumtranscriptomes (strain 724R) in infected mice of two different strains- resistant and susceptible to infection. Sets of mycobacterial genes transcribed in lung tissue were defined, and differentially transcribed genes were revealed. Our results indicate thatM. aviumgenes coding for enzymes of...

We propose a novel experimental approach based on coincidence cloning for analyzing sequences of bacterial intracellular pathogens specifically transcribed in affected tissues. Co-denaturation and co-renaturation of excess bacterial genomic DNA with the cDNA prepared on total RNA of the infected tissue allows one to select the bacterial fraction of...

Two members of the Baikal sig family, a lake sig (Coregonus lavaretus baicalensis Dybovsky) and omul (C. autumnalis migratorius Georgi), are close relatives that diverged from the same ancestor 10-20 thousand years ago. In this work, we studied genomic polymorphism of these two fish species. The method of subtraction hybridization (SH) did not reve...