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Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes
BackgroundMetagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology...
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Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data
Viral metagenomics enables the detection, characterization, and quantification of viral sequences present in shotgun-sequenced datasets of purified...
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Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess
Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our...
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Full Shotgun DNA Metagenomics
Full DNA metagenomics is the sequencing of all DNA from a sample followed by assembly and annotation and assignment of sequence information to...
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Flow-based method for biofilm microbiota enrichment and exploration of metagenomes
Most bacteria live in biofilms in their natural habitat rather than the planktonic cell stage that dominates during traditional laboratory...
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Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes
AbstractReconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms...
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Wochenende — modular and flexible alignment-based shotgun metagenome analysis
BackgroundShotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and...
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Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study
BackgroundGastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in...
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Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes
BackgroundOver half of the world’s population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by...
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Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale
The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens...
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Reconstruction of Archaeal Genomes from Short-Read Metagenomes
As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in...
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Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis
BackgroundFor a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity,...
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A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes
AbstractCulture-independent metagenomic approaches offer a promising solution to the discovery of therapeutically relevant compounds such as...
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Metagenomes Binning Using Proximity-Ligation Data
Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical...
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VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
BackgroundWith the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience,...
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Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases
We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91...
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Assessments of the impacts of chemical and hydrocarbon pollution on Ologe Lagoon water and its prokaryotic community structure
Ologe Lagoon, in Lagos State Nigeria, is one of the freshwaters exposed to chemical and hydrocarbon pollution. The impacts of anthropogenic pollution...
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Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities
Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA...
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Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial...
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Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data
Recovering genomes from shotgun metagenomic sequence data allows detailed taxonomic and functional characterization of individual species or strains...
