AIMC Topic: Bacteria

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New chemicals fuel the evolution of microbial biodegradation.

Microbiology and molecular biology reviews : MMBR
Most known chemicals originate from humans, thousands enter industrial usage annually, and new chemicals pose a continuous challenge to microbial evolution. The evolution of microbes to biodegrade new chemicals is crucial in protecting human and ecos...

TXSelect: A multi-task learning model to identify secretory effectors.

PLoS computational biology
Secretory effectors from pathogenic microorganisms significantly influence pathogen survival and pathogenicity by manipulating host signalling, immune responses, and metabolic processes. However, because of sequence and structural heterogeneity among...

Algal-bacterial granular sludge process for sustainable wastewater treatment: Technological advances and challenges.

Water research
The algal-bacterial granular sludge (ABGS) process is a promising solution for sustainable wastewater treatment, owing to its synergistic contaminant removal, carbon sequestration potential, and reduced energy demand. This review critically synthesiz...

Principal component analysis-assisted fluorescent phenylboronic acid probes for discrimination and detection of living pathogenic bacteria.

Analytical methods : advancing methods and applications
A simple analytical platform was constructed based on a phenylboronic acid-functionalized fluorescent probe with machine learning methods. Under the optimized experimental conditions, both fluorescein isothiocyanate-aminophenylboronic acid (FITC-APBA...

Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.

Applied and environmental microbiology
The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of specimens through state-of-the-art long-rea...

Machine Learning, Generalization, and Transfer Learning for Predicting the Exceedance of Fecal Indicator Bacteria Thresholds at Beaches.

Environmental science & technology
Beach water testing for fecal indicator bacteria (FIB) is a key element of public health protection for beachgoers. Because the process can be expensive and time-consuming, many beaches are infrequently monitored, putting the health of the public at ...

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 ...

Predicting microbial community structure and temporal dynamics by using graph neural network models.

Nature communications
Understanding species-level abundance dynamics in complex microbial communities is key to managing microbial ecosystems, yet it remains a major challenge. In wastewater treatment plants (WWTPs), the presence and abundance of process-critical bacteria...

iPro-MP: a BERT-based model to predict multiple prokaryotic promoters.

Genome biology
BACKGROUND: Promoters, as essential cis-regulatory elements in prokaryotes, govern gene expression by mediating RNA polymerase binding through core motifs and long-range regulatory interactions, playing a pivotal role in cell metabolism and environme...

Machine Learning-Assisted Terahertz Metagrating Biosensor for Label-Free Bacterial Identification Based on Spectral Fingerprinting.

Analytical chemistry
Rapid and accurate identification of pathogenic bacteria is pivotal for enabling early clinical diagnosis and precision antimicrobial therapy. In this study, we developed a label-free bacterial detection platform that integrates terahertz (THz) metag...