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Papers
61,005 resultsShowing papers similar to VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
ClearUnveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing
Researchers introduced VEBA 2.0, an open-source bioinformatics software suite for analyzing complex microbial communities including bacteria, archaea, eukaryotes, and viruses from sequencing data. The tool enables comprehensive microbiome research, which is relevant to understanding how microbial communities interact with environmental contaminants like microplastics.
GiantHunter: Accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search
Researchers developed GiantHunter, a tool using reinforcement learning and Monte Carlo tree search to accurately detect nucleocytoplasmic large DNA viruses (NCLDVs) in metagenomic data, addressing challenges posed by high genomic diversity and limited reference genomes in environmental samples.
The virtual microbiome: A computational framework to evaluate microbiome analyses
Researchers created virtual bacterial populations mimicking real microbiome ecology to test the accuracy of standard microbiome analysis pipelines, finding that gaps in genomic databases significantly compromise microbiome characterization reliability — an issue typically overlooked in microbiome studies.
The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data
Researchers developed the electronic Tree of Life (eToL), a tool that uses long RNA probes to identify and characterize the full range of microbes living in a sample from standard RNA-sequencing data. This method broadens the ability to study the microbiome — the community of microorganisms in a given environment — with potential uses in diagnostics and environmental monitoring.
Novel bacterial lineages assembled from wastewater-impacted river metagenomes unveil ecosystem functions and risk of antibiotic resistance spread in the community
Researchers assembled novel bacterial lineages from metagenomes of wastewater-impacted river sediments, identifying previously undescribed microbial taxa with metabolic capabilities for plastic degradation and emerging contaminant breakdown.
The electronic tree of life (eTOL): a net of long probes to characterize the human microbiome from RNA-seq data
This paper describes a bioinformatics method called the electronic Tree of Life (eTOL) for detecting and classifying microbiome organisms from human tissue RNA sequencing data without requiring PCR or dedicated metagenomic sequencing. Better tools for characterizing the human microbiome from standard genomic data could help researchers understand how environmental exposures — including microplastics — alter microbial communities in the body.
Integrating Metagenomics and Immunoinformatics to Prioritize Antigens and Immune-Modulating Molecules from Environmental Microbiomes
Researchers explored how combining metagenomic sequencing of environmental microbiomes with computational immunology tools can identify microbial proteins and metabolites that modulate immunity. The study describes workflows that screen metagenome-assembled genomes from soil, water, and microplastic-associated biofilms to predict potential antigens and immune-stimulating molecules. The findings suggest this integrated approach could accelerate discovery of novel immune-modulating compounds from environmental microorganisms.
Review of microplastic degradation: Understanding metagenomic approaches for microplastic degrading organisms
This review explores how metagenomics, the study of genetic material from environmental samples, is helping scientists identify microorganisms that can break down plastics. The paper covers the methods used to find and characterize plastic-degrading bacteria, as well as the environmental consequences of plastic degradation including health risks from inhaling and ingesting microplastics. While biological solutions to plastic pollution show promise, the review notes that more research is needed to develop effective, scalable approaches.
Microbial Community in a Wastewater System
Researchers characterized microbial community composition in a wastewater treatment system, examining how treatment stage and operational conditions shape bacterial diversity and functional potential relevant to pollutant degradation.
Diversity and potential functional characteristics of phage communities colonizing microplastic biofilms
Researchers used metagenomics to characterize phage communities colonizing microplastic biofilms, discovering 240 distinct virus types across polypropylene, polyethylene, and PET plastics that differed from those on stone surfaces, suggesting microplastics host unique viral communities with potential ecological implications.
Functional Potential of Microbial Communities and Their Roles in Degrading Microplastics and Other Compounds in The Winam Gulf of Lake Victoria, Kenya
Researchers used shotgun metagenomics to characterize microbial communities in Kenya's Winam Gulf of Lake Victoria, identifying diverse functional categories and potential plastic-degrading microbes, with carbohydrate metabolism and clustering subsystems showing the highest abundance.
Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing
Whole-genome sequencing of microbial biofilms on four types of marine microplastics revealed that plastic surfaces harbor distinct microbial communities with unique functional potential, including enrichment of Vibrio species with pathogenic and plastic-degrading capabilities.
Toward an intensive understanding of sewer sediment prokaryotic community assembly and function
Researchers characterized prokaryotic communities in sewer sediments across multifunctional, commercial, and residential urban areas using 16S rRNA amplicon sequencing, finding significant compositional differences linked to land use and nutrient levels. Network analysis revealed the residential area harbored the most complex and stable microbial network, while stochastic processes dominated community assembly across all zones.
Technological Advancements in Field Investigations of Marine Microorganisms: From Sampling Strategies to Molecular Analyses
This is not a microplastics study; it reviews advances in field sampling and molecular analysis methods for studying marine microorganisms, covering omics technologies and in-situ sampling strategies for understanding ocean biogeochemical processes.
Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution
Researchers used shotgun metagenomics to characterize microbial communities in Lake Victoria's Winam Gulf, revealing widespread pollution including microplastics, pharmaceuticals, and heavy metals that alter microbial diversity and promote antibiotic resistance genes.
Plastic-degrading clusters of orthologous groups reveal near-universal biodegradation potential in prokaryotes
Bioinformatic analysis of prokaryotic genomes identified a set of Plastic-Degrading Clusters of Orthologous Groups, revealing that plastic-degrading protein families are distributed across diverse bacterial and archaeal lineages, suggesting near-universal biodegradation potential in microbial communities.
Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean
Researchers used advanced sequencing techniques to study the fine-scale diversity and geographic distribution of bacteria in the Southern Ocean. Understanding ocean microbial communities is relevant to microplastic research because plastics in the ocean host distinct microbial communities that can alter local ecology.
Archaeal contribution to carbon-functional composition and abundance in China’s coastal wetlands: Not to be underestimated
Researchers investigated microbial diversity and carbon-functional gene composition across twenty coastal wetlands along China's coast, finding that archaeal rather than bacterial communities dominate carbon-functional gene composition and that Nanoarchaeaeota is the key archaeal phylum driving carbon cycling in anoxic sediments.
A combined metagenomics and metatranscriptomics approach to assess the occurrence and reduction of pathogenic bacteria in municipal wastewater treatment plants
This paper is not relevant to microplastics research — it uses metagenomics and metatranscriptomics to assess pathogenic bacteria, antibiotic-resistant genes, and mobile genetic elements in wastewater treatment plants in South Africa.
Viral diversity and potential environmental risk in microplastic at watershed scale: Evidence from metagenomic analysis of plastisphere
Metagenomic analysis of plastisphere communities on microplastics collected from five freshwater sites revealed diverse viral communities including phages and potential animal pathogens, with plastic-associated viromes differing from those in surrounding water. The study identifies microplastics as previously overlooked carriers of viral diversity and potential environmental health risks in aquatic ecosystems.
Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.
Researchers developed a comprehensive metaproteomics approach to study the microbial communities living on the surface of marine plastic debris, known as the plastisphere. The study reveals how microbes on plastic interact with each other and their environment, with implications for understanding how plastic-colonizing bacteria spread through the ocean.
Unveiling the Potential of Metagenomics for Eradicating Microplastics from Drinking Water
This review discussed metagenomics as a tool for identifying and characterizing microbial communities capable of degrading microplastics in drinking water systems. The paper addressed challenges in detecting microplastics in drinking water and proposed metagenomics-guided approaches for developing sustainable biological remediation strategies.
Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics
Researchers used advanced multi-omics techniques — simultaneously analyzing the DNA, proteins, and metabolic activity of microbes — to study the complex communities of bacteria and other microorganisms that colonize marine plastic debris (the "plastisphere"). The work reveals new ecological functions of these microbial films beyond plastic breakdown, including potential biotechnology applications and risks from pathogen hitchhiking on ocean plastic.
Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward
This review explores how metagenomic approaches are uncovering microbial communities capable of degrading microplastics in various environments. Researchers found that diverse bacteria and fungi in soil, water, and waste systems produce enzymes that can break down plastic polymers, though degradation rates remain slow. The study highlights metagenomics as a powerful tool for discovering new biological solutions to microplastic pollution.