Background Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST. Results In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as ‘ocean’. The ‘Quick Search’ and ‘Advanced Search’ tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the MarineMetagenomeDB web app to select estuarine metagenomes for potential large-scale microbial biogeography studies. Conclusion The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/.
Ficus capensis (farin baure) has wide application in traditional medicine especially in the Northan part of Nigeria in the treatment and management of diarrhoea and digestive distress. This is attributed to the presence of many biologically active compounds in their different parts. In this study, stem bark of F. capensis was extracted with four (4) solvents of different polarities ranging from non-polar, moderately polar to polar. Qualitative phytochemical screening of these extracts was conducted using standard laboratory procedures. The results revealed that only alkaloids, glycosides and carbohydrates were detected from the n-hexane (non-polar) extract of F. capensis while the chloroform and ethyl acetate (moderately polar solvents) and methanol (polar solvent) extracts showed the presence of tannins, saponins, alkaloids, carbohydrates, glycosides, flavonoids and proteins. But anthraquinones were not detected in all the extracts. Antimicrobial properties of the extracts were evaluated using clinical isolates of four different bacteria and fungi each. Different concentration of extracts was prepared and activity was measured using zone of inhibition in millimetres (mm). Methanol extracts showed activities against E. coli with the zone of inhibition 10 mm, 11 mm, 12 mm and 14 mm; B. subtilis with the zone of inhibition 10 mm, 11 mm, 13 mm and 15 mm all for 10, 20, 25 and 30% concentration of extracts respectively. Chloroform and ethyl acetate extracts showed antimicrobial activities against S. aureus (12 mm, 14 mm), E. coli (12 mm, 14 mm), P. aeruginosa (14 mm, 12 mm) and B. subtilis (12 mm, 16 mm) respectively for 20% concentration of the extracts. The methanol and ethyl acetate extracts showed considerable antifungal activities against Aspergillus flavus and Aspergillus fungatus. But the n-hexane extract did not show any reasonable antibacterial and no antifungal activities.
BackgroundMetagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading entries of metadata. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.ResultsIn total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature, oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most of the samples were sequenced using Illumina sequencing technology (84.33%). More than 55%of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as ‘ocean’. The ‘Quick Search’ and ‘Advanced Search’ tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allow easy download of raw sequence data of selected samples from their respective repositories. We demonstrated how users may use the MarineMetagenomeDB web app to select estuarine metagenomes for large-scale microbial biogeography studies quickly.ConclusionThe MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.