Computational protocol: Impact of maternal antibodies and infant gut microbiota on the immunogenicity of rotavirus vaccines in African, Indian and European infants: protocol for a prospective cohort study

Similar protocols

Protocol publication

[…] V3/V4 sequences will undergo a validated error correction protocol. Quality filtering, including the trimming of low-quality bases at the start and end of each read with Sickle (https://github.com/najoshi/sickle) and error correction using Bayes Hammer, will be performed prior to the assembly of paired reads with PEAR (V.0.9.1) or equivalent. A size selection filter set to the expected amplicon size and BLAST searches ensure that PhiX spike in control is detected and removed.These corrected and assembled reads will then be analysed with QIIME (Quantitative Insights Into Microbial Ecology). USEARCH will be run using de novo and open reference operational taxonomic units (OTU) clustering methods, and de novo chimera detection conducted with UCHIME V.5.1. Taxonomy will be assigned to OTUs using the naïve Bayesian RDP (Ribosomal Database Project) Classifier using the SILVA and GREENGENES taxonomic databases.Estimates of within-sample species richness (number of OTUs) and diversity (Shannon index) at multiple rarefaction depths will be compared between infants who seroconvert and those who fail to seroconvert using Student's t-test. Weighted and unweighted UniFrac distances will be used to assess potential clustering of microbiota composition according to seroconversion status, as well as the degree of overlap in composition according to the age and geographical location. These results will be visualised using principal coordinates analyses and statistically significant clusters will be identified using Adonis. Random forests will be used to identify OTUs that distinguish individuals according to RV vaccine response, age and geographical location. […]

Pipeline specifications

Software tools PEAR, QIIME, USEARCH, UCHIME
Application 16S rRNA-seq analysis
Organisms Homo sapiens
Diseases Gastroenteritis