This volume aims to capture the entire microbiome analysis pipeline, sample collection, quality assurance, and computational analysis of the resulting data. Chapters detail several example applications of micro
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...
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 ...
Combined analysis of subsets of studies that shared specific experimental protocols or indoor habitats revealed community patterns indicative of consistent source environments and environmental filtering. Additionally, we were able to identify several consistent sources for indoor microorganisms, particularly out...
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...
LC–MS metabolomic analysis showed a total of 154 metabolites in all the fecal samples. Cultivation yielded 184 bacterial isolates with Escherichia coli, Enterococcus faecium, Enterococcus hirae, and Paeniclostridium sordellii as most common isolates. Moreover, 7 potential beneficial gut bacteria ...
, 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 ...
MetaDAVis: An R shiny application for metagenomic data analysis and visualization –Sankarasubramanian Jagadesan and Chittibabu Guda – PlosOne Anita & I chatted abt #opensource tools, dbs and **community** around the microbiome science in #OpenSourceDiaries!I mentioned @bioconductor.bsky.social ...
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...
Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am. J. Gastroenterol. 108, 500–508 (2013). Article PubMed Google Scholar van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368...