Research Articles
Contamination Correction in Microbiome Research: A Comprehensive Guide from Prevention to Validation
This article provides a systematic framework for addressing contamination in microbiome studies, a critical challenge that disproportionately impacts low-biomass samples and can compromise research validity.
Solving the Depth Dilemma: A Strategic Guide to Troubleshooting Low Sequencing Depth in Metagenomic Studies
Low sequencing depth is a critical bottleneck that can compromise the validity of metagenomic findings, particularly for detecting rare taxa, antimicrobial resistance (AMR) genes, and strain-level variations.
Microbiome Sequencing QC: Best Practices for Robust and Reproducible Results from Sample to Analysis
This article provides a comprehensive guide to quality control for microbiome sequencing, tailored for researchers and drug development professionals.
Navigating Batch Effects in Longitudinal Microbiome Studies: A Comprehensive Guide for Robust Biomedical Research
Longitudinal microbiome studies are essential for understanding dynamic host-microbiome interactions but are particularly vulnerable to batch effects—technical variations that can obscure true biological signals and lead to spurious findings.
Strategies for Minimizing PCR Amplification Bias in 16S rRNA Sequencing: A Comprehensive Guide for Biomedical Researchers
PCR amplification is an integral but problematic step in 16S rRNA gene sequencing, introducing significant bias that distorts microbial community profiles and threatens the validity of scientific conclusions.
Optimizing DNA Extraction from Gram-Positive Bacteria: Advanced Strategies for Robust Yield and Purity in Clinical and Research Applications
Efficiently extracting high-quality DNA from Gram-positive bacteria is a critical yet challenging step in molecular diagnostics, pathogen surveillance, and drug development.
Conquering Contamination: A Comprehensive Guide to Addressing Low Microbial Biomass in NGS Samples
Next-generation sequencing (NGS) of low microbial biomass samples presents a significant challenge in biomedical research, where contaminating DNA can critically distort results and lead to spurious conclusions.
Strategies for Reducing Host DNA Contamination in Metagenomic Sequencing: A Comprehensive Guide for Researchers
Metagenomic next-generation sequencing (mNGS) is revolutionizing pathogen detection and microbiome studies, but its accuracy is critically limited by high levels of host nucleic acids in clinical samples.
QIIME vs. Mothur: A Comprehensive Guide to Choosing and Optimizing Your 16S rRNA Bioinformatics Pipeline
This article provides a foundational to advanced overview of the two predominant bioinformatics pipelines, QIIME and mothur, for 16S rRNA amplicon data analysis.
Unlocking Microbial Function: A Comprehensive Guide to RNA Sequencing for Microbiome Transcriptome Analysis
This article provides a comprehensive overview of RNA sequencing for characterizing the microbiome transcriptome, tailored for researchers and drug development professionals.