AIMC Topic: Metagenomics
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Gut microbiota alterations are linked to COVID-19 severity in North African and European populations.
NPJ biofilms and microbiomes
Jun 13, 2025
Although COVID-19 primarily affects the respiratory system, many patients experience gastrointestinal symptoms, suggesting a role for the gut microbiota in disease pathogenesis. To explore this, we performed shotgun metagenomic sequencing on stool sa...
TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.
BMC bioinformatics
May 26, 2025
BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S...
The Gut Microbiota in Young Adults with High-Functioning Autism Spectrum Disorder and Its Performance as Diagnostic Biomarkers.
Nutrients
May 22, 2025
Diagnosing ASD in adults presents unique challenges, and there are currently no specific biomarkers for this condition. Most existing studies on the gut microbiota in ASD are conducted in children; however, the composition of the gut microbiota in c...
Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH.
Gut microbes
May 21, 2025
Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and w...
Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity.
mBio
May 20, 2025
Dose-limiting toxicities pose a major barrier to cancer treatment. While preclinical studies show that the gut microbiota influences and is influenced by anticancer drugs, data from patients paired with careful side effect monitoring remains limited....
Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.
Microbiological research
May 19, 2025
Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible micro...
Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.
Microbiology spectrum
Apr 17, 2025
UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generat...
Enhancing fever of unknown origin diagnosis: machine learning approaches to predict metagenomic next-generation sequencing positivity.
Frontiers in cellular and infection microbiology
Apr 15, 2025
OBJECTIVE: Metagenomic next-generation sequencing (mNGS) can potentially detect various pathogenic microorganisms without bias to improve the diagnostic rate of fever of unknown origin (FUO), but there are no effective methods to predict mNGS-positiv...
Modeling microbiome-trait associations with taxonomy-adaptive neural networks.
Microbiome
Mar 29, 2025
The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun met...
Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.
Frontiers in immunology
Mar 18, 2025
INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.
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