Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk

Cells, Год журнала: 2024, Номер 13(23), С. 1987 - 1987

Опубликована: Дек. 1, 2024

The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It crucial preserve a healthy microbiome since pathogenic bacteria, such as

Язык: Английский

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Influence of the gut microbiota on immune cell interactions and cancer treatment

Journal of Translational Medicine, Год журнала: 2024, Номер 22(1)

Опубликована: Окт. 15, 2024

The tumour microenvironment represents a novel frontier in oncological research. Over the past decade, accumulating evidence has underscored importance of (TME), including cells, stromal immune and various secreted factors, which collectively influence growth, invasion, responses to therapeutic agents. Immune cells within TME are now widely acknowledged play pivotal roles development treatment. While some perspectives have posited that facilitate progression confer resistance interventions, contrasting conclusions also exist. Affirmative negative appear be context dependent, unified consensus yet reached. burgeoning body research on relationship between gut microbiota tumours recent years led growing understanding. Most studies indicated specific components microbiota, such as unique bacterial communities or secretory diverse regulating TME, thereby influencing prognosis outcomes cancer treatments. A detailed understanding these factors could provide insights into therapy. In this study, we aimed synthesise information interactions providing an in-depth exploration potential guiding implications for future therapies.

Язык: Английский

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Analytical Capabilities and Future Perspectives of Chemometrics in Omics for Food Microbial Investigation

Critical Reviews in Analytical Chemistry, Год журнала: 2025, Номер unknown, С. 1 - 14

Опубликована: Фев. 13, 2025

Microbiomes significantly impact food flavor, quality and human health. The development of omics technologies has revolutionized our understanding the microbiome, generated complex datasets, as well their processing interpretation need to be taken seriously. Currently, chemometrics shown huge potential in data analysis, which is crucial reveal functional attributes mechanisms microbiomes nutrition safety. However, various chemometric tools have own characteristics, selecting appropriate performing multiomics fusion analysis improve precision reliability microbial investigations still a challenge. In this review, we summarized used microbiome studies, overviewed principle applicability omics, discussed challenges prospects chemometrics. urgent for integrate deep learning (DL) artificial intelligence algorithms enhance its analytical capabilities prediction accuracy. We hope review will provide valuable insights integration bioinformatics combined with techniques investigation. future, modern further deepen microbiology

Язык: Английский

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Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota

Microbiology and Molecular Biology Reviews, Год журнала: 2025, Номер unknown

Опубликована: Апрель 2, 2025

SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought play a crucial role in host development, physiology, metabolic functions. Although such studies were initially focused on description compositional shifts microbiota that occur between different health conditions, more recently, they provided key insights into functional contributions gut overall physiology. In this context, an important activity is believed be represented by synthesis various vitamins may elicit considerable benefits health. A growing body scientific literature now available relating (predicted) bacterial vitamin biosynthetic abilities, ever-growing information concerning prevalence these abilities among members microbiota. This review aimed at disentangling if how cooperative trophic contribute production, such, microbiota-mediated production varies according life stages. Moreover, it offers brief exploration diets influence shaping while also providing preliminary potential correlations microbiota-associated occurrence diseases and/or disorders.

Язык: Английский

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Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2

aBIOTECH, Год журнала: 2024, Номер 5(4), С. 465 - 475

Опубликована: Июль 31, 2024

Abstract Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing. However, this task complicated by the vast variety of genomes computational limitations bioinformatics tools. The aim study was evaluate impact reference database selection confidence score (CS) settings on performance Kraken2, a widely used k-mer-based classifier. In study, we generated simulated datasets systematically how choice databases, from compact Minikraken v1 expansive nt- GTDB r202, different CS (from 0 1.0) affect key metrics Kraken2. These include rate, precision, recall, F1 score, accuracy true versus calculated bacterial abundance estimation. Our results show that higher CS, which increases rigor requiring greater k-mer agreement, generally decreases rate. This effect particularly pronounced for smaller databases such as Standard-16, where no reads could be classified when above 0.4. contrast, larger Standard, nt precision scores improved significantly with increasing highlighting their robustness stringent conditions. Recovery rates were mostly stable, indicating consistent detection species under settings. Crucially, comprehensive combined moderate (0.2 or 0.4) improves sensitivity. finding underscores need careful parameters tailored specific scientific questions available resources optimize analyses.

Язык: Английский

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Navigating beyond associations: Opportunities to establish causal relationships between the gut microbiome and colorectal carcinogenesis

Cell Host & Microbe, Год журнала: 2024, Номер 32(8), С. 1235 - 1247

Опубликована: Авг. 1, 2024

Язык: Английский

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