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Bacteria

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Precision classification and quantitative analysis of bacteria biomarkers via surface-enhanced Raman spectroscopy and machine learning.

Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy
The SERS spectra of six bacterial biomarkers, 2,3-DHBA, 2,5-DHBA, Pyocyanin, lipoteichoic acid (LTA), Enterobactin, and β-carotene, of various concentrations, were obtained from silver nanorod array substrates, and the spectral peaks and the correspo...

Tracing the origin and authenticity of Spanish PDO honey using metagenomics and machine learning.

International journal of food microbiology
The Protected Designation of Origin (PDO) indication for foods intends to guarantee the conditions of production and the geographical origin of regional products within the European Union. Honey products are widely consumed due to their health-promot...

A Clinical Bacterial Dataset for Deep Learning in Microbiological Rapid On-Site Evaluation.

Scientific data
Microbiological Rapid On-Site Evaluation (M-ROSE) is based on smear staining and microscopic observation, providing critical references for the diagnosis and treatment of pulmonary infectious disease. Automatic identification of pathogens is the key ...

Discovery of antimicrobial peptides in the global microbiome with machine learning.

Cell
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and...

Data-driven learning of structure augments quantitative prediction of biological responses.

PLoS computational biology
Multi-factor screenings are commonly used in diverse applications in medicine and bioengineering, including optimizing combination drug treatments and microbiome engineering. Despite the advances in high-throughput technologies, large-scale experimen...

Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.

Microbiome
BACKGROUND: Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising...

Machine learning-based characterization of the gut microbiome associated with the progression of primary biliary cholangitis to cirrhosis.

Microbes and infection
BACKGROUND: Primary biliary cholangitis (PBC) is associated closely with the gut microbiota. This study aimed to explore the characteristics of the gut microbiota after the progress of PBC to cirrhosis.

Deciphering the microbial landscape of lower respiratory tract infections: insights from metagenomics and machine learning.

Frontiers in cellular and infection microbiology
BACKGROUND: Lower respiratory tract infections represent prevalent ailments. Nonetheless, current comprehension of the microbial ecosystems within the lower respiratory tract remains incomplete and necessitates further comprehensive assessment. Lever...

A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.

BMC microbiology
BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic acti...

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences.

Microbiome
BACKGROUND: Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identific...