Biology subjects

Angelov, A.

Publications and source records attributed to Angelov, A..

4 recordsLinked to original sources

bioRxiv2025

COMPARATIVE METAGENOMIC ASSESSMENT OF SHORT- AND LONG-READ SEQUENCING TECHNOLOGIES REVEALS UNKNOWN MICROBIAL INFORMATION IN A COMPLEX ENVIRONMENTAL SAMPLE

Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina short-read library kits at 2x150 bp and 2x250 bp read lengths alongside PacBio HiFi long-read sequencing using a complex environmental sample. Longer short reads (2x250 bp) combined with optimal library preparation approaches notably improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results similar to those of long-read sequencing. Although long reads yield more contiguous and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating the importance of strategic selection of library preparation chemistry and sequencing parameters in revealing unknown microbial information in complex biomes without requiring additional sequencing depth. IMPORTANCEMetagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2x150 bp and 2x250 bp across multiple library preparation kits, alongside PacBio long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. Optimized short-read sequencing at 2x250 bp recovered high-quality MAGs approaching those obtained with long-read technologies while substantially improving protein discovery compared to 2x150 bp at the same sequencing depth. Together, these results provide actionable guidance for experimental design and reveal how sequencing read length can be leveraged to improve the recovery of microbial and functional diversity in complex biomes.

genomics↗

bioRxiv2022

A personal, reference quality, fully annotated genome from a Saudi individual

We have used multiple sequencing approaches to sequence the genome of a volunteer from Saudi Arabia. We use the resulting data to generate a de novo assembly of the genome, and use different computational approaches to refine the assembly. As a consequence, we provide a contiguous assembly of the complete genome of an individual from Saudi Arabia for all chromosomes except chromosome Y, and label this assembly KSA001. We transferred genome annotations from reference genomes and predicted genome features using methods from Artificial Intelligence to fully annotate KSA001, and we make all primary sequencing data, the assembly, and the genome annotations freely available in public databases using the FAIR data principles.

bioinformatics↗

bioRxiv2022

The uncharacterized protein YgfB contributes to β-lactam resistance in Pseudomonas aeruginosa by inhibiting the expression of the amidase AmpDh3

YgfB-mediated {beta}-lactam resistance was recently identified in multi drug resistant Pseudomonas aeruginosa. We show that YgfB upregulates expression of the {beta}-lactamase AmpC by repressing the function of the regulator of the programmed cell death pathway AlpA. In response to DNA damage, the antiterminator AlpA induces expression of the alpBCDE autolysis genes and of the peptidoglycan amidase AmpDh3. YgfB interacts with AlpA and represses the ampDh3 expression. Thus, YgfB indirectly prevents AmpDh3 from reducing the levels of cell wall-derived 1,6-anhydro-N-acetylmuramyl-peptides, required to induce the transcriptional activator AmpR in promoting the ampC expression and {beta}-lactam resistance. Ciprofloxacin-mediated DNA damage induces AlpA-dependent production of AmpDh3 as previously shown, which should reduce {beta}-lactam resistance. YgfB, however, counteracts the {beta}-lactam enhancing activity of ciprofloxacin by repressing ampDh3 expression and lowering the benefits of this drug combination. Altogether, YgfB represents a new player in the complex regulatory network of AmpC regulation.

microbiology↗

bioRxiv2021

Strain diversity of plant-associated Lactiplantibacillus plantarum

The intraspecific phenotypic and genetic diversity of Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) was examined for five strains isolated from fermented olives and eight strains from cactus fruit, fermented tomatoes, teff injera, wheat boza, and wheat sourdough starter sources. Carbohydrate utilization and stress tolerance characteristics showed that the olive isolates grew more robustly in galactose and raffinose, showed higher tolerance to 12% v/v EtOH, and exhibited a greater capacity to inhibit an olive spoilage strain of Saccharomyces cerevisiae than L. plantarum from the other plant sources. Certain traits were variable between fermented olive isolates such as the capacity for biofilm formation and survival at pH 2 or 50 {degrees}C. By comparison, all L. plantarum from fruit sources grew better at a pH of 3.5 than the strains from fermented grains. Multi-locus sequence typing and genome sequencing indicated that strains from the same source type tended to be genetically related. Comparative genomics was unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness of L. plantarum within individual habitats.

microbiology↗