Anan Ibrahim
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View article: A chemical radar allows bacteria to detect and kill predators
A chemical radar allows bacteria to detect and kill predators Open
Amoebal predation exerts a strong evolutionary selection pressure on bacteria, thus driving the development of effective predator-defense strategies. However, little is known about the molecular interplay between bacteria and predators, pa…
View article: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT Open
Background Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://…
View article: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT Open
Background : Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https…
View article: A mixed-model approach for estimating drivers of microbiota community composition and differential taxonomic abundance
A mixed-model approach for estimating drivers of microbiota community composition and differential taxonomic abundance Open
Next-generation sequencing (NGS) and metabarcoding approaches are increasingly applied to wild animal populations, but there is a disconnect between the widely applied generalized linear mixed model (GLMM) approaches commonly used to study…
View article: Nonribosomal peptides protect <i>Pseudomonas nunensis</i> 4A2e from amoebal and nematodal predation
Nonribosomal peptides protect <i>Pseudomonas nunensis</i> 4A2e from amoebal and nematodal predation Open
Genome mining of the environmental bacterial isolate Pseudomonas nunensis 4A2e led to the discovery of three novel lipopeptides. Ecology-inspired bioassays highlight their importance in protecting the producing organism against various pre…
View article: Investigating the effects of anthropogenic stressors on lake biota using sedimentary <scp>DNA</scp>
Investigating the effects of anthropogenic stressors on lake biota using sedimentary <span>DNA</span> Open
Analyses of sedimentary DNA ( sed DNA) have increased exponentially over the last decade and hold great potential to study the effects of anthropogenic stressors on lake biota over time. Herein, we synthesise the literature that has applie…
View article: Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic
Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic Open
De novo assembly of ancient metagenomes to reconstruct biosynthetic machinery and access Pleistocene bacterial metabolites. This Zenodo archive belongs to the following publication (DOI: 10.1126/science.adf5300): Klapper, M., Hübner, A., I…
View article: Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic
Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic Open
De novo assembly of ancient metagenomes to reconstruct biosynthetic machinery and access Pleistocene bacterial metabolites. This Zenodo archive belongs to the following publication (DOI: 10.1126/science.adf5300): Klapper, M., Hübner, A., I…
View article: SPAAM-community/AncientMetagenomeDir: v22.09.2
SPAAM-community/AncientMetagenomeDir: v22.09.2 Open
Patch release: upload correct release ZIP update Sixth (and long-awaited) major release of AncientMetagenomeDir. This release includes a significant update to the repository, with an extension to DNA sequencing library level metadata! You …
View article: Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment‐core environmental DNA
Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment‐core environmental DNA Open
Many European lake ecosystems, including their respective catchment areas, underwent anthropogenic environmental changes over the last centuries. This has resulted in changes in the aquatic and terrestrial vegetation, but historical record…
View article: Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment-core environmental DNA
Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment-core environmental DNA Open
Many European lake ecosystems, including their respective catchment areas, underwent anthropogenic environmental changes over the last centuries. This has resulted in changes in the aquatic and terrestrial vegetation, but historical record…
View article: Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment-core environmental DNA
Vegetation changes over the last centuries in the Lower Lake Constance region reconstructed from sediment-core environmental DNA Open
Many European lake ecosystems, including their respective catchment areas, underwent anthropogenic environmental changes over the last centuries. This has resulted in changes in the aquatic and terrestrial vegetation, but historical record…
View article: Heterogeneity across Neotropical aquatic environments affects prokaryotic and eukaryotic biodiversity based on environmental DNA
Heterogeneity across Neotropical aquatic environments affects prokaryotic and eukaryotic biodiversity based on environmental DNA Open
Characterizing biological communities and knowledge on the distribution of biodiversity allows the assessment of ecological quality. This provides valuable information for conservation biology and monitoring purposes. While obtaining such …
View article: Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations Open
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there…
View article: A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance
A mixed model approach for estimating drivers of microbiota community composition and differential taxonomic abundance Open
Next-generation sequencing (NGS) and meta-barcoding approaches have revolutionized understanding of within-host communities, such as the gut microbiome, in humans and laboratory animals. The application of such approaches in wild animal po…
View article: Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment‐core environmental DNA
Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment‐core environmental DNA Open
During the 20th century, many lakes in the Northern Hemisphere were affected by increasing human population and urbanization along their shorelines and catchment, resulting in aquatic eutrophication. Ecosystem monitoring commenced only aft…
View article: The making of sedimentary DNA: Insights from distribution patterns of DNA in sediments
The making of sedimentary DNA: Insights from distribution patterns of DNA in sediments Open
<p>Sedimentary ancient DNA has by now become a recognized source of information on past biodiversity change, but our understanding of its dynamics and taphonomy is still limited. While for environmental DNA in water, dedicated invest…
View article: Characterizing diatoms and their correlation with the distribution of macrophytes and parasitic Fungi using sedimentary genetic records from lake Constance, Germany
Characterizing diatoms and their correlation with the distribution of macrophytes and parasitic Fungi using sedimentary genetic records from lake Constance, Germany Open
<p>Algae and macrophytes are two of the main primary producers that interact with higher trophic levels by providing food and habitat.&#160; Their distribution thereby affect the physical and chemical characteristics of the ecosy…
View article: DIA-FastQ-R1andR2
DIA-FastQ-R1andR2 Open
The dataset is from a metabarcoding project on sediment samples from Lake Constance, Germany. The file corresponds to forward and reverse sequences representing Diatoms.
View article: DT-FastQ-R1andR2
DT-FastQ-R1andR2 Open
The dataset is from a metabarcoding project on sediment samples from Lake Constance, Germany. The file corresponds to forward and reverse sequences representing Diatoms.