AIMC Topic: Metagenomics

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Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.

Journal of clinical periodontology
AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.

TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.

BMC bioinformatics
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
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...

Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity.

mBio
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....

Exploring deep learning in phage discovery and characterization.

Virology
Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The d...

A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.

Molecular ecology resources
Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community compositi...

Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.

Microbiology spectrum
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...

Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.

Gut microbes
Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencin...

Enhancing fever of unknown origin diagnosis: machine learning approaches to predict metagenomic next-generation sequencing positivity.

Frontiers in cellular and infection microbiology
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...