Vaginal 16S foetal alcohol spectrum disorder

Project title
Vaginal 16S full length reconstruction in women who give birth to foetal alcohol spectrum disorder babies

People involved
Principal investigator : Prof Sian Hemmings (smjh@sun.ac.za)
Support request made by: Ms Lauren Martin (MSc student, lcmartin@sun.ac.za)
Bioinformatics support team: Katie Lennard

Short description of project
Does our optimised Illumina iSeq100 full-length 16S rRNA gene sequencing technique and gene reassembly, when evaluated alongside PacBio 16S sequencing and V1-V2 hypervariable sequencing data, improve the species-level taxonomic resolution of the bacterial species present in the maternal vaginal swab samples obtained from women who have given birth to infants with and without Foetal Alcohol Spectrum Disorders (FASD)?

Objectives
Assist and teach development of a pipeline that makes use of EMIRGE and dada2 to assemble the tagmented amplicon and subsequently assess the bacterial composition and perform statistical analysis of the samples. Advise on appropriate statistics and scripts to evaluate whether Illumina iSeq100 sequencing technique and PacBio 16S sequencing improves bacterial taxonomic resolution compared with general V1-V2 16S hypervariable region amplification