Compositional Analysis of the Human Microbiome in Cancer Research: Methods and ProtocolsCancer researchGut microbiotaMetagenomic sequencingTaxonomic classificationGut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and ...
UPLC-QTOF-MS/MS analysis The culture broth was extracted by ethyl acetate (Supplementary Information) and then analyzed by a SCIEX X500B Q-TOF spectrometer coupled to an ExionLC AC system under the following LC conditions: column temperature of 40 ℃, flow rate of 0.3 mL/min, elution gradien...
the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus...
MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies. It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome data pr...
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Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome ...
The effect of different methods on microbial structures of artificial communities. A: Bray-Curtis PCoA analysis; B: Bray-Curtis distances between each group and the standard; variations of community structures between different groups calculated with PERMANOVA (9999 permutations); One-way ANOVA test wa...
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Analysis of covariates that potentially confound microbiome-disease associations and classification models. The UC dataset from Nielsen et al. [27] contains fecal metagenomes from subjects enrolled in two different countries and generated using different experimental protocols (data shown is fromcuratedMetag...
The effect of different methods on microbial structures of artificial communities. A: Bray-Curtis PCoA analysis; B: Bray-Curtis distances between each group and the standard; variations of community structures between different groups calculated with PERMANOVA (9999 permutations); One-way ANOVA test wa...