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Ida Romano

Publications and source records attributed to Ida Romano.

3 recordsLinked to original sources
PubMed2026

A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.

BACKGROUND: Accurate species-level identification of bacteria in complex environmental samples is essential for applications in biotechnology, ecological monitoring, and clinical diagnostics. Short-read platforms such as Illumina frequently truncate the 16S rRNA gene, limiting taxonomic resolution. In this work, we applied Oxford Nanopore Technology (ONT) long-read sequencing to full-length 16S rRNA amplicon in samples from natural soil amended with lignocellulosic biomass and a simplified microbial community derived from cultures grown on selective and differential carboxymethyl cellulose (CMC)-based substrates, with the aim to evaluate the difference in performance between a real, complex community and a less complex system. To reduce consumable costs, we substituted the standard ONT Barcoding kits with an in-house hybrid barcoding workflow. Specifically, PacBio PCR-based barcoding protocol was used for sample indexing, followed by library preparation using the ONT Ligation Sequencing Kit. This simplified approach retained compatibility with MinION and Flongle flow cells and supported accurate downstream demultiplexing while lowering barcode costs substantially. Additionally, a new bioinformatic workflow tailored to ONT data was implemented. RESULTS: Overall, the hybrid protocol significantly reduced per-sample barcoding costs while preserving high sequencing quality and throughput. The sequencing run yielded over 5 Gb of quality-filtered data (Q-score ≥ 10). Furthermore, the new bioinformatic workflow allowed taxonomic assignment at the species level for 49.38% of annotated taxa, compared to just 4.59% using Illumina NovaSeq sequencing of the V3-V4 region. ONT also recovered 2.3 times more genera and 1.3 times more families. Although 16S rRNA gene sequencing often cannot distinguish between closely related species, particularly within taxonomically complex groups, in this work, full-length reads substantially improved both taxonomic resolution and database matching. CONCLUSIONS: These results show that full-length 16S rRNA sequencing with ONT, paired with a low-cost barcoding strategy, enhanced taxonomic resolution compared to short-read workflows. This approach also offers a scalable and cost-effective option for high-resolution microbiome profiling in research and applied settings.

RNA, Ribosomal, 16S↗
PubMed2026

Genomic and bioreactor evaluation of newly isolated cellulase-producing bacteria.

Cellulose is a renewable resource with broad biotechnological potential, and its hydrolysis by cellulases underpins applications such as biofuel production and biowaste valorization. This study combined isolation, screening, molecular identification, enzyme assays, genome sequencing, and bioreactor evaluation to characterize novel cellulase-producing bacteria. Preliminary screening identified and selected bacterial isolates by hydrolysis halo formation, with strains showing halos ≥ 20 mm selected for further quantitative assays. Streptomyces olivaceus C1_7A, Bacillus thuringiensis FBB7BB, and Bacillus licheniformis strains AT081C and AT082C showed the highest endoglucanase activities (from 0.11 to 0.26 U mL-1). Further testing on Arundo donax and Avicel led to the selection of B. thuringiensis FBB7BB and S. olivaceus C1_7A as the most promising strains for biotechnological application. Whole genome sequencing confirmed the presence of genes involved in polysaccharide degradation. Finally, lab-scale fermentation trials using 1-2% CMC showed that B. thuringiensis FBB7BB reached a maximum endo-1,4-β-glucanase activity of 0.30 ± 0.04 U mL-1 after 8 h at 37 °C, whereas S. olivaceus C1_7A achieved 0.36 ± 0.03 U mL-1 after 216 h at 30 °C.

Cellulase↗
PubMed2026

Rhodoglobus galactosidasius sp. nov., a psychrophilic Actinomycetota producing a cold-active β-galactosidase isolated from Cape Hallett, Antarctica.

A novel psychrophilic member of the phylum Actinomycetota, designated strain CPHL_1T, was isolated from the shoreline of Cape Hallett, Antarctica. Cells were Gram-positive, aerobic, non-motile, non-spore-forming rods (0.7-1.0 µm in length) with orange to yellow pigmentation. Optimal growth occurred at 15 °C, pH 8.0, with NaCl tolerance up to 3% (w/v). Strain CPHL_1T exhibited cytosolic cold-active β-galactosidase activity, with an optimum at 15 °C and pH 7.0 and formed non-adherent biofilms. Phylogenetic analysis based on 16S rRNA gene sequence placed the strain within the genus Rhodoglobus, showing high similarity to Rhodoglobus vestalii LV3T (99.4%) and Rhodoglobus aureus CMS 81yT (97.6%). Chemotaxonomic characteristics, including the predominance of anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 fatty acids, the presence of MK-11, MK-10 and MK-12 as the major respiratory quinones, and genomic G+C content of 60%, further supported its assignment to the genus Rhodoglobus. Whole-genome comparisons revealed clear taxonomic distinction, with strain CPHL_1T sharing 88.9% average nucleotide identity (ANI) and 38.3% digital DNA-DNA hybridization (dDDH) values with R. aureus, and 81.7% ANI and 25.1% dDDH with R. vestalii, confirming its status as a novel species. Phylogenetic analysis revealed that the β-galactosidases from these Rhodoglobus strains form a well-supported clade with high sequence similarity. Based on these data, a novel species is proposed: Rhodoglobus galactosidasius sp. nov. (type strain CPHL_1T =ITEM 19986T =KCTC 59592T). Genomic analyses also highlighted its biosynthetic potential for specialized metabolites, consistent with the recognized metabolic diversity of the genus.

Phylogeny↗