AIMC Topic: Metagenomics

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Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.

Computational biology and chemistry
The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populatio...

Modeling microbiome-trait associations with taxonomy-adaptive neural networks.

Microbiome
The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun met...

The dawn of the revolution that will allow us to precisely describe how microbiomes function.

Journal of proteomics
The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit w...

DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.

Microbiome
BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefi...

Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.

Genome research
Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations...

Effects of data transformation and model selection on feature importance in microbiome classification data.

Microbiome
BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, composi...

Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation.

Journal of hazardous materials
Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to ide...

Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.

NPJ biofilms and microbiomes
Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, ...

Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.

Critical reviews in microbiology
Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes ob...