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All taxa found in the Saiga data were included in the differential abundance testing, regardless of whether they are unique to one population or not. Asymptotic alpha diversity (ASV richness and Shannon diversity) was estimated using package iNEXT53,54. Differences in alpha diversity and Jaccard ...
(MIC) testing via broth microdilution as defined by EUCAST recommendations55,56, with the alteration of LB Miller broth for growth media and the use ofP. aeruginosaPAO1 as a reference strain. Resistance to meropenem was assayed along a 2-fold dilution series between 0.25–64 μg/mL. We...
Quality control was performed on the resulting FastQ files using FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc), and bioinformatics analyses were conducted by using the Quantitative Insights into Microbial Ecology (QIIME 1.9.1) software package [33] with the subsampled ...
squared test. For datasets in which the condition of normality was violated, the non-parametric Kruskal–Wallis test was used and post-hoc analysis was done using the Wilcoxon test. Ap-value of <0.05 was deemed significant. To correct for multiple testing in tests correlating volatility and ...
DNA was extracted from blood samples using the DNeasy Blood and Tissue kit (Qiagen, Crawley, UK) according to the manufacturer’s protocol. Molecular sexing was carried out using an established PCR-based method [59,61]. Individuals were genotyped at 30 polymorphic microsatellite loci [57,59],...
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Series B Stat Methodol. 1995;57:289–300. Google Scholar Download references Acknowledgements The authors thank the staff at the Danish National High-Throughput DNA Sequencing Centre for ...
In the murine model data analysis part, the Tukey post hoc test was chosen due to its high testing efficiency in comparing equal or similar sample size data. Results Alterations of the intestinal microbiota in the unmedicated- and sertraline-treated-depressive adolescents Healthy female controls (...
(Leiden, The Netherlands) using the NEXTflex 16S V4 Amplicon-Seq Kit (BiooScientific, Austin, TX) and the Illumina 2500 system (rapid mode, paired-end, 250 bp; Illumina, San Diego, CA, USA). Raw sequencing data are available in the European Nucleotide Archive (http://www.ebi.ac.uk/...
Additionally, the Mann-Whitney-Wilcoxon (MWW) test was done as a post-hoc test corrected for multiple testing with a Benjamini-Hochberg correction of 0.01 FDR to determine specific differences in each of the presented pairwise comparisons for relative abundance differences for the various taxonomic ...