Rationale The nasopharyngeal (NP) microbiota of newborns and infants plays a key role in modulating airway inflammation and respiratory symptoms during viral infections. Premature (PM) birth modifies the early NP environment and is a major risk factor for severe viral respiratory infections. However, it is currently unknown if the NP microbiota of PM infants is altered relative to full-term ...
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- The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 2014 Sep 10. PMID: 25211071
- Apr 21, 2020 · Analysis of differential abundance showed increased abundance for several fungi species in the persistent group compared to the intermittent and non-carriers . However, the species Candida orthopsilosis was the only one with significant difference in abundance between the persistent and non-carrier groups ( p<0.05, Kruskal-Wallis test ...
RNA-Seq (named as an abbreviation of "RNA sequencing") is a technology-based sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome.
- To facilitate the analysis of microbiome metabolic network, mmnet provides func-tions for sequence annotation linking R with MG-RAST. MG-RAST [Glass et al., 2010] is a stable, extensible, online analysis platform for annotation and statistic metagenomes based on sequence data. Moreover, MG-RAST is freely available to all researchers. For
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16s rRNA Short read libraries target variable V3 and V4 regions of 16s rRNA genes. Although, 16s rRNA sequencing is an amplicon sequencing technique, usually the environment or clinical samples are as clean and need expert hands to process and amplify 16s rRNA genes.
- Aug 19, 2020 · To visualise the differences in microbial composition between gut contents and tissue, a taxonomic profile was generated by conducting differential abundance analysis using balances in gneiss. v. To identify the features characterising the differences between groups, the LEfSe method of analysis was performed to compare abundances of all bacterial clades [ 53 ].
Mar 15, 2020 · For each feature, the assay produces a value that is a proxy for the relative abundance of that feature. For genes, this is the number of RNA transcripts that are expressed. Thus I will refer to ...
- Differential Abundance. Uses DESeq2 to identify differentially abundant taxa, at any taxonomic level, for a user-selected pairwise comparison. Results are displayed as a bubble chart that incorporates statistics.
In this exploratory analysis, we found similar results to our main analysis in the larger dataset with regard to the differences in genus abundance and richness. The nasal microbiome significantly differed by the Bray-Curtis index at both the genus and OTU levels, and richness remained significantly lower during acute RSV infection ( P < 0.05 for all estimates).
- Differential abundance testing: univariate data. This section covers basic univariate tests for two-group comparison, covering t-test, Wilcoxon test, and multiple testing. The following example compares the abundance of a selected bug between two conditions. Let us assume that the data is already properly normalized. Let us load example data
The three highest values of R RS obtained after each dose were averaged to construct dose–response curves. 2.5 Bronchoalveolar lavage. The lungs were lavaged twice with 1 ml of ice‐cold PBS. These two lavages were pooled and centrifuged at 400g at 4°C for 10 min. The supernatant was stored at −80°C until further analysis.