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Gastrointestinal Microbiome

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Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases.

American journal of physiology. Gastrointestinal and liver physiology
Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus, there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in patients wi...

Optimization of probiotic therapeutics using machine learning in an artificial human gastrointestinal tract.

Scientific reports
The gut microbiota's metabolome is composed of bioactive metabolites that confer disease resilience. Probiotics' therapeutic potential hinges on their metabolome altering ability; however, characterizing probiotics' metabolic activity remains a formi...

Host variables confound gut microbiota studies of human disease.

Nature
Low concordance between studies that examine the role of microbiota in human diseases is a pervasive challenge that limits the capacity to identify causal relationships between host-associated microorganisms and pathology. The risk of obtaining false...

Temporal variation and sharing of antibiotic resistance genes between water and wild fish gut in a peri-urban river.

Journal of environmental sciences (China)
Antibiotic resistance genes (ARGs) as emergence contaminations have spread widely in the water environment. Wild fish may be recipients and communicators of ARGs in the water environment, however, the distribution and transmission of ARGs in the wild...

Gut microbiome-mediated epigenetic regulation of brain disorder and application of machine learning for multi-omics data analysis.

Genome
The gut-brain axis (GBA) is a biochemical link that connects the central nervous system (CNS) and enteric nervous system (ENS). Clinical and experimental evidence suggests gut microbiota as a key regulator of the GBA. Microbes living in the gut not o...

Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life.

BMC bioinformatics
BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new ref...

Machine Learning Strategy for Gut Microbiome-Based Diagnostic Screening of Cardiovascular Disease.

Hypertension (Dallas, Tex. : 1979)
Cardiovascular disease (CVD) is the number one leading cause for human mortality. Besides genetics and environmental factors, in recent years, gut microbiota has emerged as a new factor influencing CVD. Although cause-effect relationships are not cle...

Capsule robot for gut microbiota sampling using shape memory alloy spring.

The international journal of medical robotics + computer assisted surgery : MRCAS
BACKGROUND: Human gut microbiota can provide lifelong health information and even influence mood and behaviour. We currently lack the tools to obtain a microbial sample, directly from the small intestine, without contamination.

Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome.

BMC genomics
BACKGROUND: Technological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure th...

Gut microbiome, big data and machine learning to promote precision medicine for cancer.

Nature reviews. Gastroenterology & hepatology
The gut microbiome has been implicated in cancer in several ways, as specific microbial signatures are known to promote cancer development and influence safety, tolerability and efficacy of therapies. The 'omics' technologies used for microbiome anal...