Nicola Segata

The paper describes the development of En-ISPmu1, a modified TnpB nuclease, and demonstrates its ability to achieve targeted genome integration in mouse liver with a single AAV vector.

The paper investigates how probiotic interventions in infants affect bacterial strain dynamics and immune responses, finding that specific strains are displaced regardless of IgA binding.

The paper identifies genome-wide selective sweeps in the human gut microbiome, revealing ecologically distinct populations linked to age and colorectal cancer.

The paper compiles 2,658 Desulfovibrio genomes from 90 diseases and 32 countries to identify species-specific functional traits linked to inflammatory diseases.

The paper identifies distinct microbiome and metabolomic signatures in treatment-naive multiple sclerosis patients compared to healthy controls across multiple biofluids.

The paper investigates how dietary components and Enterobacteriaceae influence competition between Prevotellaceae and Bacteroidaceae in the gut microbiota, finding that Enterobacteriaceae enhance Prevotellaceae dominance under specific conditions.

LAMPP provides a standardized benchmark for evaluating host phenotype prediction from gut metagenomic data, showing that traditional methods remain competitive.

The paper benchmarks differential abundance methods using microbiome datasets with known biological ground truth, finding that compositional methods are less effective than commonly used non-compositional approaches.

The paper evaluates metagenomic analysis methods in simulated and real environmental data, finding that newer marker-based methods perform better at lower taxonomic levels.

The paper presents a method to discover new human gut viruses using enriched virome samples and reports over 162,000 novel viral sequences.

Marker genes for 26,970 species-level genome bins, 4,992 defined only by metagenome-assembled genomes, let MetaPhlAn 4 quantify uncharacterized species and beat MetaPhlAn 3, mOTUs and Bracken on synthetic benchmarks.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

The paper introduces STORMS, a reporting guideline for human microbiome studies, providing a 17-item checklist to standardize and improve the organization and reporting of microbiome research.

The paper analyzes the viral-host interactome of SARS-CoV, MERS-CoV, and HCoV-229E using a network-based approach to predict SARS-CoV-2 pathogenesis.

HMP16SData provides integrated 16S rRNA sequencing data from the Human Microbiome Project, enabling easier analysis for researchers with basic R skills.

The paper introduces curatedMetagenomicData, a resource providing curated metagenomic profiles for analysis in R with minimal bioinformatic expertise.