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Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
BackgroundSesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the...
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Metagenomic insights into the differences in gastrointestinal microbe-mediated metabolism and immunity between wild and captive spotted seals (Phoca largha)
Understanding metabolic and immune functional genes in the gut microbiota of sentinel species, such as spotted seals ( Phoca largha ), is essential for...
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16S rRNA metagenomic profiling of red amaranth grown organically with different composts and soils
AbstractIn recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but...
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Use of pus metagenomic next-generation sequencing for efficient identification of pathogens in patients with sepsis
The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site...
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Ultrahigh-Throughput Screening of Metagenomic Libraries Using Droplet Microfluidics
Droplet microfluidics enables the ultrahigh-throughput screening of the natural or man-made genetic diversity for industrial enzymes, with reduced...
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Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism
The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive...
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Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
BackgroundLong-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher...
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Metagenomic highlight contrasting elevational pattern of bacteria- and fungi-derived compound decompositions in forest soils
PurposeCarbohydrate-active enzymes (CAZymes) mediate carbohydrate turnover and play vital roles in plant- and microbial-derived carbon decomposition....
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HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis
BackgroundNext-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature,...
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Analysis of endophytic bacterial flora of mulberry cultivars susceptible and resistant to bacterial wilt using metagenomic sequencing and culture-dependent approach
Endophytes have a wide range of potential in maintaining plant health and sustainable agricultural environmental conditions. In this study, we...
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Metagenomic Assembly: Reconstructing Genomes from Metagenomes
Assembly of metagenomic sequence data into microbial genomes is of critical importance for disentangling community complexity and unraveling the...
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A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment
Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant...
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Analyzing the Capabilities of Actinobacteria for Remediation Through Metagenomic Analysis of Contaminated Habitats
Industrialization has increased the number of pollutants in air, water, and land to toxic levels. Effectively removing these pollutants from the...
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Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors
BackgroundThe phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play...
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MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets
Bacteria can exceptionally evolve and develop pathogenic features making it crucial to determine novel pathogenic proteins for specific therapeutic...
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Cont-ID: detection of sample cross-contamination in viral metagenomic data
BackgroundHigh-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important...
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Effects of rhizosphere microbiome on the fruit of Cinnamomum migao H. W. Li: culture, amplicon sequencing, and metagenomic sequencing
Cinnamomum migao H. W. Li is an evergreen tree belonging to the Lauraceae family and is endemic to China. Previous studies have found that the...
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Comparative analysis of metagenomic classifiers for long-read sequencing datasets
BackgroundLong reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification...
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Metagenomic analysis of wastewater phageome from a University Hospital in Turkey
Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed...
