Known gut virus diversity is currently skewed by challenges in fecal virus-like particles (VLPs) enrichment and towards active viruses detectable in shotgun metagenomic sequencing. Here, we apply a virus detection procedure, including vigorous enrichment to harvest large quantity of VLPs, and combined Illumina and PacBio sequencing, to fecal samples of 180 Chinese volunteers. Integrated assembly of the short- and long-reads generate more and longer viral genomes compared to existing methods. The resulting viral genome dataset, referred as to the Human Gut Virome collection (HGV), covers the full spectrum of the gut virome, i.e., an HGV-trained machine-learning algorithm recognizes most (81~97%) public gut viruses; meanwhile, it contains 71.50% novel genomes, including 20% that cannot be recognized by machine-learning models trained on public viruses. Further analysis of the HGV reveals a substantially higher diversity of the human gut virome. For example, we identify thousands of viral genomes that are more prevalent than crAssphages and Gubaphages, the two most diverse phages in the human gut, and several viral clades that are more diverse than the two. Tother, our results indicate a vastly enlarged gut viral diversity that significantly broadens our knowledge on the viral dark matter of the human gut microbial ecology.

Along with the excessive use of antibiotics, the emergence and spread of multidrug-resistant bacteria has become a public health problem and a great challenge vis-à-vis the control and treatment of bacterial infections. As the natural predators of bacteria, phages have reattracted researchers’ attentions. Phage therapy is regarded as one of the most promising alternative strategies to fight pathogens in the post-antibiotic era. Recently, genetic and chemical engineering methods have been applied in phage modification. Among them, genetic engineering includes the expression of toxin proteins, modification of host recognition receptors, and interference of bacterial phage-resistant pathways. Chemical engineering, meanwhile, involves crosslinking phage coats with antibiotics, antimicrobial peptides, heavy metal ions, and photothermic matters. Those advances greatly expand the host range of phages and increase their bactericidal efficiency, which sheds light on the application of phage therapy in the control of multidrug-resistant pathogens. This review reports on engineered phages through genetic and chemical approaches. Further, we present the obstacles that this novel antimicrobial has incurred.

Pathogenic strains of Escherichia coli are responsible for 0.8 million deaths per year and together ranked the first among all pathogenic species. Here, we obtained, for the first time, an engineered phage, Eλ, that could specifically and efficiently eliminate EHEC, one of the most common and often lethal pathogens that can spread from person to person.

DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. In this study, DNA methylation patterns are analyzed in 8848 metagenome‐assembled high‐quality phages from 104 fecal samples using single‐molecule real‐time sequencing. The results demonstrate that 97.60% of gut phages exhibit methylation, with certain factors correlating with methylation densities. Phages with higher methylation densities appear to have potential viability advantages. Strikingly, more than one‐third of the phages possess their own DNA methyltransferases (MTases). Increased MTase copies are associated with higher genome methylation densities, specific methylation motifs, and elevated prevalence of certain phage groups. Notably, the majority of these MTases share close homology with those encoded by gut bacteria, suggesting their exchange during phage–bacterium interactions. Furthermore, these MTases can be employed to accurately predict phage–host relationships. Overall, the findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems, with a substantial contribution from phage‐encoded MTases.