Allergy and Microbiota:Linköping trial

SNIC 2017/7-243


SNAC Small

Principal Investigator:

Thomas Abrahamsson


Linköpings universitet

Start Date:


End Date:


Primary Classification:

30109: Microbiology in the medical area




Originally a randomized controlled trial trial evaluating allergy prevention with probiotics in 188 children that have been followed until 7 years of age. Stool samples were collected from the mother at gestational week (during pregnancy) and from the child at 1 week, 1, 3 and 24 months and at 7 years of age. The half of the included children in these two cohorts have got placebo. The stool samples have been stored in -70 C. We have previously shown a lower microbial diversity in infants developing asthma with 454 pyrosequencing at Lars Engstrands lab in Stockholm. The aim of the present study is to do shotgun metagenomics in a selected population in this cohort in order to assess functional genes in their gut microbiome. 12 children/mothers have been selected: 6 children with and 6 without asthma, and 6 children with a low BMI and 6 with a high BMI at 7 years of age. There are 6 samples from each mother/child pair. DNA preparation has been made at Prof Stefan Bertilsson´s lab in Uppsala with the Fast Prep kit. This study is also a pilot for future whole genome sequencing analysis in a larger trial. Thus, since we want to evaluate the DNA preparation method and hopefully find a method that fits to our Qiagen robot in Linköping, we have also added another 12 samples that are made in in doublet (i.e both prepared with Fast prep kit and the new the preparation method). In total 84 samples are going to be analysed. There is no personal data in the file. Thus, none of the subjects can be identified.