Publications by authors named "Rodolfo Toscan"

Article Synopsis
  • The study investigates how factors like species abundance, sequencing depth, and taxonomic relationships affect the recovery of metagenome-assembled genomes (MAGs) in microbial communities.
  • Different recovery pipelines were tested, revealing that the DT pipeline offered the most accurate results, whereas the 8K pipeline produced the most MAGs but with lower accuracy.
  • Findings indicate that simply having more MAGs doesn't reflect true community composition, emphasizing the importance of sequencing depth and caution in interpreting MAG recovery data for biological conclusions.
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Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination.

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Motivation: Computational analysis of large-scale metagenomics sequencing datasets have proven to be both incredibly valuable for extracting isolate-level taxonomic, and functional insights from complex microbial communities. However, due to an ever-expanding ecosystem of metagenomics-specific methods and file-formats, designing studies which implement seamless and scalable end-to-end workflows, and exploring the massive amounts of output data have become studies unto themselves. One-click bioinformatics pipelines have helped to organize these tools into targeted workflows, but they suffer from general compatibility and maintainability issues.

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Article Synopsis
  • Most eukaryotic genomes are still unsequenced, limiting our understanding of their roles in ecosystems, while efforts to recover prokaryotic genomes are more common.* -
  • This study utilized the EukRep pipeline to analyze 6000 metagenomes, successfully obtaining 447 eukaryotic bins, predominantly from streptophytes and fungi, with many coming from diverse environments.* -
  • The research highlights gaps in existing genome completeness assessments and suggests improvements through long-read sequencing and better reference databases to enhance eukaryotic genome recovery.*
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  • Every year, antimicrobial resistance genes (ARGs) in bacteria lead to millions of deaths, especially as urbanization increases and compounds the problem in cities.
  • This study analyzed over a thousand urban metagenomes to explore the presence and behavior of ARGs in urban bacteria, focusing on their distribution and whether they were found on plasmids.
  • Findings revealed that while multidrug and glycopeptide ARGs are common in urban bacteria, they are not primarily transferred via plasmids and the strains studied showed limited virulence, indicating a need for further research on the prevalence and spread of these resistance genes.
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Article Synopsis
  • * Researchers combined flow cytometry cell sorting with bioinformatics to classify cells from a wastewater microbial community into different abundance groups and sequenced their genomes.
  • * Results showed a significant increase in species identification (two-fold improvement), revealing that sorting allows the recovery of genomes that are otherwise undetected in unsorted samples.
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Article Synopsis
  • The study investigates the roles of bacterial symbionts in octocorals by analyzing 66 metagenome-assembled genomes from 30 prokaryotic species found in three octocoral species and seawater.
  • The findings identify unique symbiotic bacteria, particularly from the novel genus Ca. Gorgonimonas, which have specific adaptations to thrive in suboxic environments and possess genes that aid in colonizing and persisting within their octocoral hosts.
  • Additionally, the research highlights potential substrate interactions, such as chitin turnover, and suggests that some symbiotic lineages may specialize in chemical defense, indicating a complex interplay between the coral microbiome and its bacterial residents.
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We present the draft genome sequence of Fusarium equiseti strain K3, a fungus isolated from a hexachlorocyclohexane (HCH)-contaminated soil (Kitengela, Kenya). The 37.88-Mb draft genome sequence consists of 206 contigs, 12,311 predicted protein-coding sequences, and 261 tRNA sequences.

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