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Papers
20 resultsShowing papers similar to The virtual microbiome: A computational framework to evaluate microbiome analyses
ClearMicrobiome differential abundance methods produce different results across 38 datasets
Researchers compared 14 commonly used methods for identifying differentially abundant microbes across 38 microbiome datasets. They found that different methods often produced substantially different results when applied to the same data, with high rates of disagreement between tools. The study highlights that the choice of analytical method can significantly influence microbiome research conclusions and calls for greater standardization in the field.
Evaluating bioinformatics pipelines for population‐level inference using environmental DNA
Researchers evaluated twelve bioinformatics pipelines for their ability to reliably infer intraspecific genetic variability from environmental DNA samples, finding that amplification and sequencing errors can substantially inflate estimates of genetic diversity. The study provides guidance on pipeline selection for population-level eDNA analysis.
Unveiling 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.
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
Researchers developed VEBA, a modular bioinformatics software suite that automates end-to-end metagenomic analysis for recovering and characterizing genomes of bacteria, microeukaryotes, and viruses from environmental samples, enabling new biological discoveries from existing datasets.
The concept of balance in microbiome research
This essay critically examines how the concept of "balance" is used in microbiome research and medical literature. Researchers analyzed multiple interpretations of what a balanced versus imbalanced microbiome means, finding that the term is often used loosely without precise scientific definition. The study argues for more rigorous conceptual frameworks to better understand how microbiome composition relates to health outcomes.
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.
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.
Precision Metagenomics in a Low-End Computation Infrastructure: A Tool to Augment Research on Bioremediation of Plastic and Microplastic Contamination
This study used precision metagenomic analysis of landfill soil to identify microorganisms with plastic-degrading capabilities without needing to culture them in a lab. The approach identified three distinct microbial groups with potential to break down synthetic polymers, pointing toward biological strategies for managing plastic waste at landfill sites.
In vitro modelling of oral microbial invasion in the human colon
Researchers developed an in vitro model combining the M-ARCOL colon simulator with a salivary enrichment protocol and shotgun metagenomics to study oral microbial invasion of intestinal microbiota, finding that the mucosal compartment retained the highest species richness and that oral microorganisms introduced via enriched saliva competed with established commensal communities.
Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems
Researchers examined how ecological niches shape bacterial community structure and assembly in polluted urban water ecosystems. The study found that the specific environmental conditions within different niches play a key role in determining how microbial communities respond to water pollution. These findings have implications for understanding microbial ecology and maintaining aquatic ecosystem health.
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.
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.
Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures
This study developed flow cytometry methods for accurately quantifying the composition of synthetic bacterial communities, evaluating how well different fluorescent labeling and gating strategies distinguish species. Accurate community composition quantification is essential for microbiome research and biotechnology applications.
Improving the assessment of ecosystem and wildlife health: microbiome as an early indicator
Researchers reviewed evidence that the microbiome — the community of microorganisms living in environments and within animals — can serve as an early warning system for ecosystem disturbance, rapidly reflecting the impact of human activities before other signs of harm are visible.
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.
Evidence for strong environmental control on bacterial microbiomes of Antarctic springtails
Researchers studied the bacterial communities living inside four species of Antarctic springtails (tiny soil insects) and found that geography — where the springtails lived — was a stronger influence on their gut microbiome than which species they were. This finding helps explain how extreme environments shape the microbial ecosystems inside animals, including those exposed to microplastic contamination.
Rare Bacteria Can Be Used as Ecological Indicators of Grassland Degradation
Researchers used full-length 16S rRNA sequencing to study bacterial communities across degraded grasslands on the Qinghai-Tibet Plateau, finding that rare bacterial taxa were more sensitive to grassland degradation and soil nutrient changes than abundant taxa, and that rare bacteria may serve as reliable ecological indicators of grassland health.
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.
Influence of DNA extraction methods on microbiome and resistome analysis in activated sludge
This study compared different DNA extraction methods for analyzing the microbial communities and antibiotic resistance genes in wastewater treatment sludge. Standardizing these methods is important for accurately tracking how microplastics and their associated microbiome — including resistant bacteria — move through water treatment systems.
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.