N. Segata

Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples

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

Fusobacterium sphaericum sp. nov., isolated from a human colon tumor, adheres to colonic epithelial cells and induces IL-8 secretion

The paper isolates and characterizes a novel Fusobacterium species from a human colon tumor, showing its adherence to epithelial cells and IL-8 induction.

Outer Membrane Vesicles from the gut microbiome contribute to tumor immunity by eliciting cross-reactive T cells

The paper shows engineered outer membrane vesicles from E. coli can elicit T cell responses against tumors through molecular mimicry.

Evolutionary epidemiology of a zoonosis

This study analyzes whole genome sequences of Cryptosporidium parvum isolates to show genetic exchanges between human and ruminant hosts, leading to increased nucleotide diversity and potential virulence gene enrichment.

Wide distribution of alternatively coded Lak megaphages in animal microbiomes

The paper identifies a wide distribution of alternatively coded Lak phages in animal microbiomes, including new genomes and associations with specific animal types.

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

The paper introduces bioBakery 3, a set of tools for microbial community analysis, improving taxonomic, functional, and strain-level profiling with applications to CRC and IBD datasets.

A step-by-step sequence-based analysis of virome enrichment protocol for freshwater and sediment samples

The paper evaluates virome enrichment protocols by analyzing microbial community changes during filtration steps in water and sediment samples, finding significant non-viral taxa in the final virome.

Taxonomic variability over functional stability in the microbiome of Cystic Fibrosis patients chronically infected by Pseudomonas aeruginosa

This study examines taxonomic and functional dynamics in the microbiome of CF patients with chronic P. aeruginosa infection, finding high taxonomic variability but functional stability despite antibiotic treatment.

The signal and the noise - characteristics of antisense RNA in complex microbial communities

This paper examines antisense RNA in microbial communities, finding high variability and mixed evidence for its origin in transcriptional noise.

A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

The paper presents a comprehensive genomic resource of over 280,000 human gut microbiome genomes and their protein sequences, highlighting gaps in functional annotations and genomic diversity.

Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates

This study examines polysaccharide growth profiles of 83 P. copri isolates from 11 donors, revealing genomic and functional differences in polysaccharide utilization.

The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations

The study identifies four distinct clades within the Prevotella copri complex, showing reduced prevalence in Westernised populations compared to non-Westernised ones.

Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling

This study identifies vertically transmitted microbial strains from mothers to infants using strain-level metagenomic profiling and metatranscriptomics.