Computational protocol: Correlations between gut microbiota community structures of Tibetans and geography

Similar protocols

Protocol publication

[…] Raw data were first screened, and sequences were removed from considerations when they spanned less than 200 bp. These data presented low-quality score ≤ 20 and contained ambiguous bases or did not exactly match primer sequences and barcode tags. Qualified reads were separated into different samples using sample-specific barcode sequences and trimmed with Illumina Analysis Pipeline Version 2.6. Next, dataset was analyzed using QIIME. Sequences were clustered into OTUs at a similarity level of 97% to generate rarefaction curves and to calculate richness and diversity indices. RDP classifier tool was used to classify all sequences into different taxonomic groups.Core OTUs presented in all samples were detected using QIIME. Clustering analyses and PCA were used based on OTU information from each sample using R package to examine similarity between different samples. VENN analyses were also conducted using R package. Statistical analyses between different groups were analyzed using ANOVA. Mann–Whitney U test was used for diversity and taxonomic comparisons between groups at different levels (phylum, class, order, family, and genus). CCA was used to evaluate linkages between gut microbial structure and environmental attributes using R package. LEfSe was used to detect unique bacterial tax among different groups. To determine the different CSTs across all the locations, hierarchical clustering into CSTs based on genus composition and abundance was conducted according to the methods described by DiGiulio et al.. […]

Pipeline specifications

Software tools QIIME, RDP Classifier, LEfSe
Applications Metagenomic sequencing analysis, 16S rRNA-seq analysis
Organisms Homo sapiens, Bacteroidetes, Firmicutes, Bacteria
Diseases Pulmonary Fibrosis