AIMC Topic: Bacteriophages

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A machine learning approach to predict strain-specific phage-host interactions.

Scientific reports
The use of bacteriophages for biological control of bacterial infections is a promising approach to combat antimicrobial resistant bacteria. Prediction of phage-bacteria interactions is key to identify sensitive bacterial strains to phage therapy. Si...

Design of Specific Peptide Inhibitors of Toxin-Antitoxin-Mediated Antiphage Defense.

ACS synthetic biology
Toxin-antitoxin (TA) systems are widespread antiphage defense elements in bacteria that may impede successful phage therapy. Phage-encoded inhibitors of these systems have been discovered that enhance phage infection capacity. We used fragment-based ...

Empathi: embedding-based phage protein annotation tool by hierarchical assignment.

Nature communications
Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of ...

Deep Learning-Assisted Lens-Free Holography Integrated Pd Nanozyme-Armed Phages for the Rapid and Extraction-Free Detection of Viable Bacteria.

Analytical chemistry
Bacterial infections represent a serious global threat to public health, often leading to severe infectious diseases and even fatalities. The most effective approach to prevent outbreaks is through the implementation of rapid, accurate, and simple po...

Evolutionary selection of trimethoprim-resistant genes in lytic phages affects phage and host fitness during infection.

Science advances
Temperate phages and prophages are well-known carriers of antibiotic resistance genes (ARGs) facilitating their transmission. In contrast, lytic phages rarely harbor functional ARGs. However, by a lenient threshold search strategy combined with a mac...

Computational Pipeline for Targeted Integration and Variable Payload Expression in Bacteriophage Engineering.

ACS synthetic biology
Bacteriophages offer a promising alternative to conventional antimicrobials, especially when such treatments fail. While natural phages are viable for therapy, advances in synthetic biology allow precise genome modifications to enhance their therapeu...

Computational function prediction of bacteria and phage proteins.

Microbiology and molecular biology reviews : MMBR
SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial...

Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.

NPJ biofilms and microbiomes
Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder frequently accompanied by psychological symptoms. Bacterial microbiota plays a critical role in mediating local and systemic immunity, and alterations in these microbial communities...

Underestimated roles of phages in biological wastewater treatment systems: Recent advances and challenges.

Journal of hazardous materials
Bacteriophages (phages) are vital components in biological wastewater ecosystems, whose concentrations are far exceeding those bacteria. Despite their importance, they are often overlooked and regarded as the "dark matter" in biological treatment pro...

Discovery and affinity maturation of antibody fragments from an unfavorably enriched phage display selection by deep sequencing and machine learning.

Journal of bioscience and bioengineering
Phage display selection has been used for directed evolution of antibody fragments. However, variants with binding affinity cannot be always identified due to undesirable enrichment of target-unrelated variants in the biopanning process. Here, our go...