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To ensure efficacy and trust, probiotic strains in commercial products should be accurately identified. However, studies have consistently reported discrepancies between labeling and actual microbial composition. Therefore, we developed a full-length 16S rRNA amplicon sequencing …
Read PDFWe isolated a strain of the genus <i>Alkalibacterium</i> from Daihai Lake in Inner Mongolia. The complete genome size is 2,614,554 bp, with a genomic DNA G + C content of 39.3%. Metabolic pathway analysis indicates …
Read PDFThe bacterium <i>Phascolarctobacterium faecium</i> frequently colonizes the human gut and has been reported to have reduced abundance in people with Crohn's disease. Here, we report the complete genome sequences of two <i>P. faecium</i> strains isolated …
Read PDFThe bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses …
Read PDFDiscovery of disease-related bacterial biomarkers could be a useful approach for early prevention or diagnosis of various afflictions, such as colorectal cancer. This typically involves analyzing small regions of the 16S rRNA gene (e.g. V3V4) …
Read PDF<i>Rothia</i> are understudied commensal bacteria within the human oral cavity and respiratory tract and can cause opportunistic infections. We report the complete genome sequences of seven <i>Rothia</i> spp. strains isolated from pooled human saliva, including …
Read PDFA whole-genome assembly and annotation of <i>Wolbachia</i> sp. infecting <i>Anastrepha fraterculus</i> sp. 1 were generated by a metagenomic analysis of sequencing reads from a host genome project. This study contributes to the characterization of this …
Read PDFAtmospheric pollution poses a major threat to human health, causing millions of deaths worldwide each year. Green infrastructures may help mitigate the toxicity of airborne contaminants through the combined action of plants and their associated …
Read PDFRecent studies have revealed that the long-recognized link between the historically defined <i>Fusobacterium nucleatum</i> group and colorectal cancer is largely driven by <i>Fusobacterium animalis</i>. This species, along with two others (<i>Fusobacterium polymorphum</i> and <i>Fusobacterium vincentii</i>), …
Read PDF<h4>Background</h4>Long-read sequencing has revolutionised metagenomics through improved metagenome assembly, taxonomic classification and functional characterisation. Automation can enhance the throughput, reproducibility, and accuracy of library preparation. However, the validation of automated library preparation protocols remains undetermined …
Read PDFSequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occasional wastewater contamination. Restricted water exchange also allows for occasional …
Read PDFThe oral microbiome is a diverse ecosystem that plays a critical role in health and disease and contains numerous bacterial species capable of metabolizing host-derived glycans, particularly sialic acids. Sialidase enzymes can be produced by …
Read PDFFungal DNA is systematically under-detected in shotgun metagenomics, likely due in part to physical barriers like melanized cell walls and complex DNA conformations. Additionally, Oxford Nanopore Technologies sequencing with native fungal DNA often results in …
Read PDF<h4>Premise</h4>The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable …
Read PDFWe present a genome assembly from an individual <i>Rhopaloeides odorabile</i> (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. …
Read PDFThe human gut microbiome comprises a diverse community of bacteria whose interactions with the host range from beneficial mutualism to opportunistic pathogenicity. These interactions are shaped by genomic plasticity and ecological pressures that influence whether …
Read PDFIn host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most …
Read PDFClinical metagenomic next-generation sequencing (mNGS) is a diagnostic tool allowing near-universal pathogen detection directly from clinical specimens. Despite promising clinical data, broad adoption of mNGS has been hindered by high cost and reduced sensitivity relative …
Read PDFMarine sediments harbor diverse <i>Vibrio</i> populations that play critical roles in benthic microbial ecology; however, the genomic determinants underlying the dominance of sediment-associated <i>Vibrio</i> taxa remain insufficiently characterized at the genome level. In this study, …
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