Biology subjects

Rayko, M.

Publications and source records attributed to Rayko, M..

8 recordsLinked to original sources

bioRxiv2026

Genomic insights into the human gut commensal Megasphaera elsdenii: Relatedness and metabolic potential compared to animal isolates

Megasphaera elsdenii is best known as a prominent lactate consumer within the rumen microbial community in livestock, and its metabolic properties are relatively well studied. In humans, it can be isolated from healthy donors feces and, more often, from patients feces with diverse inflammatory conditions. Genetic diversity of this species is poorly understood, and it is currently unclear whether human and animal gut isolates are genetically related and perform the same metabolic function. In this study, we compared 86 M. elsdenii genomes from human feces (as a proxy for the human gut) to those of animal gut isolates. Phylogenetic analysis revealed that human and animal gut lineages intermingle within a single, genetically homogeneous branch, lacking any host-specific clustering. Human gut lineages shared most of their genes and biochemical pathways with those of swine and cattle gut isolates, despite differences in their digestive tracts. Neither unsupervised nor supervised approaches identified any notable differences in encoded pathways between different host-specific gut lineages. Genome-scale metabolic modeling suggests that human and animal gut lineages likely share identical carbon and energy source requirements. Moreover, the requirements for lactate and acetate were conserved across all studied samples, regardless of the host. Finally, we found no virulence genes, and lactate utilization remains a plausible explanation for M. elsdenii accumulation in the host intestine. IMPORTANCEMegasphaera elsdenii is considered a commensal in the human gut and animal rumen. However, M. elsdenii tends to be more abundant in patients feces with diverse inflammatory conditions. As we know little about the strain diversity and biology of human gut lineages, comparisons with better-studied animal isolates can be informative. In this study, we compared human gut M. elsdenii genomes to those from better-studied isolates from ruminant and non-ruminant animal hosts. Human gut samples associated with patients and healthy donors were genetically very similar to gut isolates from animals and may have shared a common origin. We found that human and animal gut lineages have a similar genomic makeup and metabolic potential, and that neither group harbors virulence genes. We hypothesize that M. elsdenii is a benign commensal that grows in response to lactate accumulation in the inflamed gut.

microbiology↗

bioRxiv2025

Machine learning-assisted selection of informative loci for strain-level phylogenetics of Neisseria gonorrhoeae

AO_SCPLOWBSTRACTC_SCPLOWEpidemiological surveillance of Neisseria gonorrhoeae is hindered by the limitations of existing molecular typing methods, such as NG-MAST and MLST, which either suffer from excessive variability or insufficient resolution. In this study, we propose and evaluate a machine learning (ML) algorithm for the automated selection of a minimal set of informative genetic loci for accurate strain classification. Using a collection of 29 reference genomes of N. gonorrhoeae, we developed a pipeline that integrates Random Forest models and DNABERT embeddings to generate optimized gene panels. The results demonstrate that ML-selected panels substantially outperform traditional schemes, yielding markedly improved phylogenetic accuracy and branch support consistently above 90%. The proposed approach significantly reduces computational costs compared to whole-genome analysis and represents a promising resource-efficient tool for routine epidemiological monitoring, tracking transmission pathways, and identifying antibiotic-resistant strains.

bioinformatics↗

bioRxiv2023

Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil

Chernevaya taiga in Western Siberia, Russia, is a special environment with fertile soil, extraordinarily high herbaceous plant sizes, and incredibly quick rates of plant residues breakdown. We postulated that a unique rhizospheric fungal community would be created when growing crops on chernevaya soil, which has never been used for agriculture. These may be the source for the novel effective biostimulator and biocontrol fungal agents for modern agriculture. In this study, we analyzed the fungal communities in the rhizosphere of spring wheat and radish cultivated in greenhouse experiments on chernevaya and control soils using high-throughput ITS sequencing. Additionally reprehensive fungal strains were isolated and examined for the stimulation of wheat seedlings growth. The research shows that Ascomycota and Mortierellomycota were the most abundant phyla in the rhizospheric fungal community, mainly composed of Mortierella species. The control soils were abundant in Mucoromycota, represented mostly by Mucor and Umbelopsis. Potentially plant-pathogenic fungi Fusarium and Oidiodendron were found only in the rhizosphere of crops grown in the control soil. Whereas plants grown on chernevaya soil have a wide variety of possible biocontrol fungi. Novel fungal isolates demonstrated stimulating effect on the growth and biomass accumulation of wheat seedlings. The findings of the study imply that the creation of biorational products for crop growth and protection may depend on the taxonomic composition analysis of the rhizospheric mycobiota of the crops growing on the soil with the unique characteristics.

microbiology↗

bioRxiv2023

cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data

MotivationRecent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining high coverage using long reads can be difficult, making barcoded RNA-seq data a valuable alternative for this task. However, most annotation pipelines are not able to work with a set of short reads instead of a single transcript, also not able to work with coverage gaps within a molecule if any. In order to overcome this challenge, we present an RNA-seq assembler allowing the determination of the expressed isoform per barcode. ResultsIn this paper, we present cloudrnaSPAdes, a tool for assembling full-length isoforms from barcoded RNA-seq linked-read data in a reference-free fashion. Evaluating it on simulated and real human data, we found that cloudrnaSPAdes accurately assembles isoforms, even for genes with high isoform diversity. AvailabilitycloudrnaSPAdes is a feature release of a SPAdes assembler and available at https://cab.spbu.ru/software/cloudrnaspades/. Contactdmm2017@med.cornell.edu

bioinformatics↗

bioRxiv2022

Varidnaviruses in the human gut: a major expansion of the order Vinavirales

BackgroundBacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail. ResultsHere we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages of the families Corticoviridae and Autolykiviridae that jointly comprise the order Vinavirales and are mostly integrated as prophages in genomes of Alphaproteobacteria and Verrucomicrobia. Phylogenetic analysis of the major capsid proteins (MCP) and packaging ATPases suggests that at least three new families within Vinavirales should be established to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and ATPase genes were reported to be conserved in all members of Vinavirales. Here we identify a core set of 12 proteins that are shared by most of these viruses including previously undetected lysis enzymes. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses. ConclusionsThe results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by proviruses, suggesting that there are few if any active varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that was virtually overlooked in previous work.

microbiology↗

bioRxiv2020

Unique genomic features of crAss-like phages, the dominant component of the human gut virome

CrAssphage is the most abundant virus identified in the human gut virome and the founding member of a large group of bacteriophages that infect bacteria of the phylum Bacteroidetes and have been discovered by metagenomics of both animal-associated and environmental habitats. By analysis of circular contigs from human gut microbiomes, we identified nearly 600 genomes of crAss-like phages. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, which can be expected to become a new order of viruses, and of 5 distinct branches, likely, families within that order. Two of these putative families have not been identified previously. The phages in one of these groups have large genomes (145-192 kilobases) and contain an unprecedented high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable readthrough of UGA or UAG stop-codons, mostly, in late phage genes, which could represent a distinct anti-defense strategy. Another putative anti-defense mechanism that might target an unknown defense system in Bacteroidetes inhibiting phage DNA replication involves multiple switches of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals several unusual features of genome architecture and expression as well as phage biology that were not apparent from the previous crAssphage analyses.

microbiology↗

bioRxiv2020

Quality control of low-frequency variants in SARS-CoV-2 genomes

During the current outbreak of COVID-19, research labs around the globe submit sequences of the local SARS-CoV-2 genomes to the GISAID database to provide a comprehensive analysis of the variability and spread of the virus during the outbreak. We explored the variations in the submitted genomes and found a significant number of variants that can be seen only in one submission (singletons). While it is not completely clear whether these variants are erroneous or not, these variants show lower transition/transversion ratio. These singleton variants may influence the estimations of the viral mutation rate and tree topology. We suggest that genomes with multiple singletons even marked as high-covered should be considered with caution. We also provide a simple script for checking variant frequency against the database before submission.

genomics↗

bioRxiv2019

metaFlye: scalable long-read metagenome assembly using repeat graphs

Long-read sequencing technologies substantially improved assemblies of many isolate bacterial genomes as compared to fragmented assemblies produced with short-read technologies. However, assembling complex metagenomic datasets remains a challenge even for the state-of-the-art long-read assemblers. To address this gap, we present the metaFlye assembler and demonstrate that it generates highly contiguous and accurate metagenome assemblies. In contrast to short-read metagenomics assemblers that typically fail to reconstruct full-length 16S RNA genes, metaFlye captures many 16S RNA genes within long contigs, thus providing new opportunities for analyzing the microbial \"dark matter of life\". We also demonstrate that long-read metagenome assemblers significantly improve full-length plasmid and virus reconstruction as compared to short-read assemblers and reveal many novel plasmids and viruses.

bioinformatics↗