Biology subjects

Kryukov, K.

Publications and source records attributed to Kryukov, K..

9 recordsLinked to original sources

bioRxiv2023

TEM Experiment and Complete Genome Sequencing with Comparative Genomic Analysis to Uncover Potential Probiotic Features of Isolated Lactobacillus delbrueckii subsp. indicus TY-11

BackgroundProbiotics refer to living microorganisms that exerts a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed Transmission Electron Microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. These experiments on subspecies indicus were not studied previously. ResultsThe strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1916674bp) contained genes to adapt to diverse and stressful environments of the human gut, and no gene was identified for either antibiotic resistance or toxic metabolites. It embraced genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance in the gut, and acidic pH tolerance in the stomach. Genes were annotated for inhibiting pathogenic bacteria in the gut by inhibitory substances, (bacteriocin: Helveticin-J (331bp) and Enterolysin-A (275bp), hydrogen peroxide, and acid); blockage of adhesion sites; and competition for nutrients. Its metabolic pathway helped the human gut to recover the digestive disorders and digest indigestible nutrients. The TY-11 genome possessed additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subspecies bularicus. ConclusionsThis is the first study to explore the molecular insights into intestinal residence and probiotic roles including antimicrobial activities of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.

genomics↗

bioRxiv2021

MinION™, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting

It has been suggested that the local microbiota in the reproductive organs is relevant to womens health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for the rapid analysis of small samples in a clinical context. We demonstrated a simple workflow using the nanopore sequencer MinION that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION. The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The vaginal microbiota results could be reported within 2 days of specimen receipt. Although bacterial vaginosis (BV) was not diagnosed by the Nugent score in any cases, groups with both healthy and BV-like vaginal microbiota were clearly characterized by MinION sequencing. We conclude that full-length 16S rRNA gene sequencing analysis with MinION provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage.

microbiology↗

bioRxiv2020

Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer

Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.

microbiology↗

bioRxiv2020

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

BackgroundSpecies-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples. ResultsWe modified our existing protocol for full-length 16S amplicon sequencing by MinION. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition. ConclusionsOur present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene, which provided the requisite species-level resolution and accuracy in clinical settings.

microbiology↗

bioRxiv2019

Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases

BackgroundNearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available. FindingsWe systematically benchmarked 410 settings of 44 compressors (including 26 specialized sequence compressors and 18 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 25 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/) that allows building custom visualizations for selected subsets of benchmark results. ConclusionWe found that modern compressors offer large improvement in compactness and speed compared to gzip. Our benchmark allows comparing compressors and their settings using a variety of performance measures, offering the opportunity to select the optimal compressor based on the data type and usage scenario specific to particular application.

bioinformatics↗

bioRxiv2019

Comprehensive genomic analysis reveals dynamic evolution of mammalian transposable elements that code for viral-like protein domains

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes. Hence, we investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small ([~]0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences suggested that a large proportion of ERV-ORFs either recently or anciently inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify ERV-ORFs transcribed as proteins, we compared ERV-ORFs with various multi-omics data including transcriptome data, trimethylation at histone H3 lysine 36, and transcription initiation sites from 2,834 cell types, and found 408 and 752 ERV-ORFs, accounting for 2-3% of all ERV-ORFs, with high transcriptional potential in humans and mice, respectively. Moreover, many of these ERV-ORFs with transcriptional potential were lineage-specific sequences exhibiting tissue-specific expression. These results suggest a possibility for the expression of uncharacterized functional genes containing ERV-ORFs hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

genomics↗

bioRxiv2018

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences

SummaryDNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF) - a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. NAF compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli, and zstd. AvailabilityNAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use. Contactkkryukov@gmail.com

bioinformatics↗

bioRxiv2018

Direct PCR amplification of 16S rRNA genes offers accelerated bacterial identification using the MinION™ nanopore sequencer

Rapid identification of bacterial pathogens is crucial for appropriate and adequate antibiotic treatment, which significantly improves patient outcomes. 16S ribosomal RNA (rRNA) gene amplicon sequencing has proven to be a powerful strategy for diagnosing bacterial infections. We have recently established a sequencing method and bioinformatics pipeline for 16S rRNA gene analysis utilizing the Oxford Nanopore Technologies MinION sequencer. In combination with our taxonomy annotation analysis pipeline, the system enabled the molecular detection of bacterial DNA in a reasonable timeframe for diagnostic purposes. However, purification of bacterial DNA from specimens remains a rate-limiting step in the workflow. To further accelerate the process of sample preparation, we adopted a direct PCR strategy that amplifies 16S rRNA genes from bacterial cell suspensions without DNA purification. Our results indicate that differences in cell wall morphology significantly affect direct PCR efficiency and sequencing data. Notably, mechanical cell disruption preceding direct PCR was indispensable for obtaining an accurate representation of the specimen bacterial composition. Furthermore, 16S rRNA gene analysis of mock polymicrobial samples indicated that primer sequence optimization is required to avoid preferential detection of particular taxa and to cover a broad range of bacterial species. This study establishes a relatively simple workflow for rapid bacterial identification via MinIONTM sequencing, which reduces the turnaround time from sample to result, and provides a reliable method that may be applicable to clinical settings.

microbiology↗

bioRxiv2017

A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions

We developed a portable system for metagenomic analyses consisting of nanopore technology-based sequencer, MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all of 20 bacteria present in the mock bacterial community. Time course analysis indicated that sequence data obtained during the first 5-minute sequencing were enough to detect all 20 bacteria species in the mock sample and determine their compositions with sufficient accuracy. Additionally, using a clinical sample extracted from the pleural effusion of a patient with empyema, we could identify major bacteria in a pleural effusion by rapid sequencing and analysis. All of these results are comparable to or even better than the conventional 16S rDNA sequencing results using IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination is possible within 2 hours.Our integrative system is applicable to rapid diagnostic tests for infectious diseases in near future.

genomics↗