Gut microbiota in colorectal cancer development and therapy

Nature Reviews Clinical Oncology, Journal Year: 2023, Volume and Issue: 20(7), P. 429 - 452

Published: May 11, 2023

Language: Английский

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MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(W1), P. W310 - W318

Published: May 11, 2023

Abstract Microbiome studies have become routine in biomedical, agricultural and environmental sciences with diverse aims, including diversity profiling, functional characterization, translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, potential activities. Here we introduce MicrobiomeAnalyst 2.0 support comprehensive statistics, visualization, interpretation, integrative analysis of data outputs commonly generated from microbiome studies. Compared the previous version, features three new modules: (i) a Raw Data Processing module for amplicon processing taxonomy annotation that connects directly Marker Profiling downstream statistical analysis; (ii) Metabolomics help dissect associations between community compositions metabolic activities through joint paired metabolomics datasets; (iii) Statistical Meta-Analysis identify consistent signatures by integrating across multiple Other improvements include added multi-factor differential interactive visualizations popular graphical outputs, updated methods prediction correlation analysis, expanded taxon set libraries based on latest literature. These are demonstrated using dataset recent type 1 diabetes study. is freely available at microbiomeanalyst.ca.

Language: Английский

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The gut microbiota and its biogeography

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(2), P. 105 - 118

Published: Sept. 22, 2023

Language: Английский

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Advancing CAR T cell therapy through the use of multidimensional omics data

Nature Reviews Clinical Oncology, Journal Year: 2023, Volume and Issue: 20(4), P. 211 - 228

Published: Jan. 31, 2023

Language: Английский

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Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective

Nature Medicine, Journal Year: 2023, Volume and Issue: 29(3), P. 551 - 561

Published: March 1, 2023

Language: Английский

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Critical role of the gut microbiota in immune responses and cancer immunotherapy

Journal of Hematology & Oncology, Journal Year: 2024, Volume and Issue: 17(1)

Published: May 14, 2024

The gut microbiota plays a critical role in the progression of human diseases, especially cancer. In recent decades, there has been accumulating evidence connections between and cancer immunotherapy. Therefore, understanding functional regulating immune responses to immunotherapy is crucial for developing precision medicine. this review, we extract insights from state-of-the-art research decipher complicated crosstalk among microbiota, systemic system, context Additionally, as can account immune-related adverse events, discuss potential interventions minimize these effects clinical application five microbiota-targeted strategies that precisely increase efficacy Finally, holds promising target immunotherapeutics, summarize current challenges provide general outlook on future directions field.

Language: Английский

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Sequencing-based analysis of microbiomes

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(12), P. 829 - 845

Published: June 25, 2024

Language: Английский

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Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(7), P. 1884 - 1898

Published: June 12, 2024

Language: Английский

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From Genotype to Phenotype: Raman Spectroscopy and Machine Learning for Label-Free Single-Cell Analysis

ACS Nano, Journal Year: 2024, Volume and Issue: 18(28), P. 18101 - 18117

Published: July 1, 2024

Raman spectroscopy has made significant progress in biosensing and clinical research. Here, we describe how surface-enhanced (SERS) assisted with machine learning (ML) can expand its capabilities to enable interpretable insights into the transcriptome, proteome, metabolome at single-cell level. We first review advances nanophotonics-including plasmonics, metamaterials, metasurfaces-enhance scattering for rapid, strong label-free spectroscopy. then discuss ML approaches precise spectral analysis, including neural networks, perturbation gradient algorithms, transfer learning. provide illustrative examples of phenotyping using nanophotonics ML, bacterial antibiotic susceptibility predictions, stem cell expression profiles, cancer diagnostics, immunotherapy efficacy toxicity predictions. Lastly, exciting prospects future spectroscopy, instrumentation, self-driving laboratories, data banks, uncovering biological insights.

Language: Английский

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Ushering in a new era of single-cell transcriptomics in bacteria

microLife, Journal Year: 2022, Volume and Issue: 3

Published: Jan. 1, 2022

Abstract Transcriptome analysis of individual cells by single-cell RNA-seq (scRNA-seq) has become routine for eukaryotic tissues, even being applied to whole multicellular organisms. In contrast, developing methods read the transcriptome single bacterial proven more challenging, despite a general perception bacteria as much simpler than eukaryotes. Bacterial are harder lyse, their RNA content is about two orders magnitude lower that cells, and mRNAs less stable counterparts. Most importantly, transcripts lack functional poly(A) tails, precluding simple adaptation popular standard scRNA-seq protocols come with double advantage specific mRNA amplification concomitant depletion rRNA. However, thanks very recent breakthroughs in methodology, now feasible. This short review will discuss recently published approaches (MATQ-seq, microSPLiT, PETRI-seq) spatial transcriptomics approach based on multiplexed situ hybridization (par-seqFISH). Together, these novel not only enable new understanding cell-to-cell variation gene expression, they also promise microbiology enabling high-resolution profiling activity complex microbial consortia such microbiome or pathogens invade, replicate, persist host tissue.

Language: Английский

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