A5047318557- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Mycobacterium research and diagnosis
- Infant Nutrition and Health
- Gastrointestinal motility and disorders
- FinTech, Crowdfunding, Digital Finance
- Bacteriophages and microbial interactions
- Helicobacter pylori-related gastroenterology studies
- Probiotics and Fermented Foods
- Academic Publishing and Open Access
- Metabolomics and Mass Spectrometry Studies
- Preterm Birth and Chorioamnionitis
- Diverse Scientific and Economic Studies
- Environmental DNA in Biodiversity Studies
- Digestive system and related health
- Infant Development and Preterm Care
Vall d'Hebron Institut de Recerca
2023-2025
Saarland University
2024
Taxonomic assignments of microorganisms have long been hindered by inconsistent nomenclature and annotation issues in existing databases like SILVA, Greengenes, Greengenes2, Genome Taxonomy Database, or Ribosomal Database Project. To overcome these issues, we created Greengenes-SILVA-RDP database (GSR-DB), accurate comprehensive taxonomic annotations 16S amplicon data. Unlike previous approaches, our innovative pipeline includes a unique taxonomy unification step, ensuring consistent...
Abstract The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ diseases do not occur in isolation, comprehensive analysis strategy highlighting the full potential of should include diverse specimen types diseases. To ensure robust data quality comparability across diseases, we employ standardized protocols to generate sequencing from 1931 prospectively collected specimens, including...
Abstract Plasmids are extrachromosomal DNA molecules in bacteria and archaea, playing critical roles horizontal gene transfer, antibiotic resistance, pathogenicity. Since its first release 2018, our database on plasmids, PLSDB, has significantly grown enhanced content scope. From 34 513 records contained the 2021 version, PLSDB now hosts 72 360 entries. Designed to provide life scientists with convenient access extensive plasmid data support computer by offering curated datasets for...
Introduction: Preterm birth is the leading cause of perinatal mortality worldwide, with prevalence rates showing little reduction. Although have decreased, morbidity remain concerningly high. In recent years, there has been a surge in studies examining etiology, risk factors, and management preterm birth. The use vaginal probiotics pregnant women at garnered attention as potential approach for improving outcomes modulating microbiota. However, efficacy this intervention remains unclear....
Abstract Understanding human, animal, and environmental microbiota is essential for advancing global health combating antimicrobial resistance (AMR). We investigate the oral gut of 48 animal species in captivity, comparing them to those wildlife animals. Specifically, we characterize composition, metabolic pathways, AMR genes, biosynthetic gene clusters (BGCs) encoding production specialized metabolites. Our results reveal a high diversity microbiota, with 585 novel species-level genome bins...
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature computational complexity. In Bioinformatics, k-mer-based approaches were long established expedite the analysis of large sequencing data are now widely used annotate data. We make use k-mer counting techniques for efficient accurate compositional microbiota whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual...
ABSTRACT Amplicon-based 16S ribosomal RNA sequencing remains the most widely used method to profile microbial communities, as a low-cost and low-complexity approach. Reference databases are mainstay for taxonomic assignments, which typically rely on popular such SILVA, Greengenes, GTDB, or RDP. However, inconsistency of nomenclature across databases, presence shortcomings in annotation these limiting resolution analysis. To overcome limitations, we created GSR database (Greengenes, RDP...