Improving viral annotation with artificial intelligence

ZN Flamholz, C Li, L Kelly - Mbio, 2024 - journals.asm.org
ABSTRACT Viruses of bacteria,“phages,” are fundamental, poorly understood components
of microbial community structure and function. Additionally, their dependence on hosts for …

What lies beneath? Taking the plunge into the murky waters of phage biology

M Zünd, SJB Dunham, JA Rothman, KL Whiteson - Msystems, 2023 - Am Soc Microbiol
The sequence revolution revealed that bacteria-infecting viruses, known as phages, are
Earth's most abundant biological entities. Phages have far-reaching impacts on the form and …

Bidirectional Interactions between Arboviruses and the Bacterial and Viral Microbiota in Aedes aegypti and Culex quinquefasciatus

C Shi, L Beller, L Wang, A Rosales Rosas… - MBio, 2022 - Am Soc Microbiol
Mosquitoes are important vectors for many arboviruses. It is becoming increasingly clear that
various symbiotic microorganisms (including bacteria and insect-specific viruses; ISVs) in …

Phage-antibiotic combinations against multidrug-resistant Pseudomonas aeruginosa in in vitro static and dynamic biofilm models

DJ Holger, A El Ghali, N Bhutani, KL Lev… - Antimicrobial Agents …, 2023 - Am Soc Microbiol
Biofilm-producing Pseudomonas aeruginosa infections pose a severe threat to public health
and are responsible for high morbidity and mortality. Phage-antibiotic combinations (PACs) …

A previously undescribed highly prevalent phage identified in a Danish Enteric Virome Catalog

L Van Espen, EG Bak, L Beller, L Close, W Deboutte… - Msystems, 2021 - Am Soc Microbiol
Gut viruses are important, yet often neglected, players in the complex human gut microbial
ecosystem. Recently, the number of human gut virome studies has been increasing; …

Alphaflexivirus genomes in stony coral tissue loss disease-affected, disease-exposed, and disease-unexposed coral colonies in the US Virgin Islands

AJ Veglia, K Beavers, EW Van Buren… - Microbiology …, 2022 - Am Soc Microbiol
Stony coral tissue loss disease (SCTLD) is decimating Caribbean corals. Here, through the
metatranscriptomic assembly and annotation of two alphaflexivirus-like strains, we provide …

Ciprofloxacin in combination with bacteriophage cocktails against multi-drug resistant Pseudomonas aeruginosa in ex vivo simulated endocardial vegetation models

A El Ghali, K Stamper, AJ Kunz Coyne… - Antimicrobial Agents …, 2023 - Am Soc Microbiol
Pseudomonas aeruginosa-associated infective endocarditis represents difficult-to-treat,
deep-seated infections. Phage-antibiotic combinations have shown to eradicate multi-drug …

Spatial and temporal dynamics of prokaryotic and viral community assemblages in a lotic system (Manatee Springs, Florida)

K Malki, NA Sawaya, MJ Tisza… - Applied and …, 2021 - Am Soc Microbiol
Flow from high-magnitude springs fed by the Floridan aquifer system contributes hundreds
of liters of water per second to rivers, creating unique lotic systems. Despite their importance …

Comparative genomics reveals the correlations of stress response genes and bacteriophages in develo** antibiotic resistance of Staphylococcus saprophyticus

K Zhang, RF Potter, J Marino, CE Muenks… - Msystems, 2023 - Am Soc Microbiol
Staphylococcus saprophyticus is the leading Gram-positive cause of uncomplicated urinary
tract infections. Recent reports of increasing antimicrobial resistance (AMR) in S …

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

B Hegarty, J Riddell V, E Bastien, K Langenfeld… - Msystems, 2024 - Am Soc Microbiol
Understanding the ecological impacts of viruses on natural and engineered ecosystems
relies on the accurate identification of viral sequences from community sequencing data. To …