B. E. Dutilh

Phylogeny and disease links of a widespread and ancient gut phage lineage

The paper identifies a widespread gut phage lineage, Ca. Heliusvirales, present in ancient and modern humans, and links its diversity to lifestyle and disease.

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

The paper studies bacteriophage outbreaks in compost communities, finding that viral migration accelerates evolution through recombination and mutation spread.

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

The paper identifies an ultraconserved bacteriophage genome in 1300-year-old human faeces, showing 97.7% identity to its modern counterpart and reconstructs 297 other ancient phage genomes.

Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

The paper develops a bioinformatic pipeline to detect horizontal gene transfer in compost communities, revealing new mobile genetic elements and their ecological roles.

Copiotrophs dominate rhizosphere microbiomes and growth rate potential is a major factor explaining the rhizosphere effect

This study identifies growth rate potential as a key factor explaining the rhizosphere effect by analyzing microbial communities and genome data from multiple plant-soil systems.

A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists

The paper identifies microbial generalists and specialists across host, soil, and aquatic environments, showing their ecological roles and genomic features.

iPHoP: an integrated machine-learning framework to maximize host prediction for metagenome-assembled virus genomes

iPHoP integrates multiple methods to predict viral hosts from metagenome-derived genomes with low false discovery rate.

High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

The paper examines the relationship between viral abundance and diversity and CRISPR-Cas prevalence across microbial ecosystems using metagenomic data.

Optimized DNA isolation method for microbiome analysis of human tissues

The paper presents a DNA isolation method that reduces host DNA interference in human tissue microbiome analysis, enabling accurate microbial profiling.

Members of a highly widespread bacteriophage family are hallmarks of metabolic syndrome gut microbiomes

The paper identifies phage families associated with metabolic syndrome by analyzing gut phageome changes and their relationship to bacterial communities.

Nutrition or nature: disentangling the complex forces shaping prokaryote pan-genomes

The paper disentangles the forces shaping prokaryote pan-genomes by simulating metabolic reaction loss in different environments and identifying reactions constrained by nutrition or nature.

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria

This study screens over 150 gut bacteria to determine their effects on colorectal cancer cell growth, identifying strain-level differences and specific genes associated with growth modulation.

A symbiont phage protein aids in eukaryote immune evasion

The paper identifies a phage-encoded ankyrin domain protein that modulates eukaryotic immune responses, enabling immune evasion in host-microbe interactions.

Bacterial Zombies And Ghosts: Production Of Inactivated Gram-Positive And Gram-Negative Species With Preserved Cellular Morphology And Cytoplasmic Content

This study compares bacterial inactivation methods to generate intact Gram-positive and Gram-negative 'zombies' and identifies beta-propiolactone and ethanol as the most effective.

The gill-associated symbiont microbiome is a main source of woody-plant polysaccharide hydrolase genes and secondary metabolite gene clusters in Neoteredo reynei, a unique shipworm from south Atlantic mangroves.

This study uses metagenomics to show that the gill-associated symbionts of Neoteredo reynei harbor genes for wood-degrading enzymes and secondary metabolites, highlighting their biotechnological potential.

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Bacteriophages

The paper evaluates taxonomy methods for bacteriophages using Spounavirinae as a case study, finding they should be divided into at least five subfamilies.

Induction of differentiation and metabolic reprogramming in human hepatoma cells by adult human serum

This study shows that culturing human hepatoma cells in adult human serum restores liver-like morphology, metabolism, and organ-specific functions, suggesting that FBS may suppress these features.