A. L. Borges

Infant gut bacteriophage strain persistence during the first three years of life

The paper investigates phage succession in infants over three years, finding that 9% of early phage colonizers persist, with maternal transmission and stop codon reassignment playing key roles.

Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile

This study identifies AcrIB2, an anti-CRISPR protein from a C. difficile phage that inhibits the type I-B CRISPR-Cas system, showing that a partial cas operon is sufficient for interference.

Genomic analysis of cultivated infant microbiomes identifies Bifidobacterium 2'-fucosyllactose utilization can be facilitated by co-existing species

The paper shows that Bifidobacterium breve can utilize 2'-fucosyllactose with help from co-existing species like Ruminococcus gnavus in infant microbiomes.

Phage-encoded ribosomal protein S21 expression is linked to late stage phage replication

The paper investigates the expression of the bS21 gene in phages, finding it is active during late-stage replication and may aid in phage particle assembly.

Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes

The paper surveys stop codon recoding in bacteriophages, finding it widespread and suggesting it regulates gene expression and lysis timing.

Mobile element warfare via CRISPR and anti-CRISPR in Pseudomonas aeruginosa

This study identifies seven new anti-CRISPR proteins and characterizes their mechanisms against Type I-C CRISPR-Cas systems in Pseudomonas aeruginosa, revealing co-evolutionary dynamics between MGEs.

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.

CRISPR-Cas immunity repressed by a biofilm-activating pathway in Pseudomonas aeruginosa

The paper identifies a regulatory pathway that represses CRISPR-Cas immunity in Pseudomonas aeruginosa, showing that biofilm activators inhibit CRISPR-Cas activity.

Cryptic inoviruses are pervasive in bacteria and archaea across Earth's biomes

The paper identifies 10,295 inovirus-like genomes across diverse ecosystems, revealing their widespread presence and complex interactions with bacterial and archaeal hosts.

Bacteriophage cooperation suppresses CRISPR-Cas3 and Cas9 immunity

The paper shows that phages cooperate by sharing anti-CRISPR proteins to suppress bacterial CRISPR-Cas immunity, enabling successful infection when individual phages fail to replicate.