Mi Ni

A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation.

The paper identifies a single DNA methylation site that regulates sporulation in C. difficile by enhancing spoIIE transcription and sigmaF activation, revealing its role in pathogen persistence and potential as an antimicrobial target.

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

This study identifies epigenetic phase variation in the gut microbiome, showing it enhances bacterial adaptation through gene regulation and bet-hedging strategies.

Critical assessment of intratumor and low-biomass microbiome using long-read sequencing

The paper assesses low-biomass microbiome detection in tissues using long-read sequencing, finding that genuine microbiome signals are limited to tissues with natural microbial exposure.

Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation

This study introduces LongTrack, a long-read metagenomics framework for precise strain tracking in FMT, revealing genomic changes in engrafted bacteria over time.

Incorporating FDR into the assessment of nanopore sequencing for the reliable detection of DNA modifications in real applications

This paper introduces modFDR, a framework to assess nanopore sequencing for DNA modification detection, showing it reliably detects abundant modifications but has high false positives for rare ones.

Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer

The paper analyzes fecal metagenomic data from NSCLC patients to identify Akkermansia phylogroups associated with response to PD-1 blockade, finding AmIa linked to better outcomes.

mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome

mEnrich-seq selectively sequences specific bacterial taxa from microbiome samples by using methylation-sensitive restriction enzymes to enrich target DNA while depleting background microbiota.