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Our bodies are hosts to a wide range of microbial communities, one of the most important of which is the huge numbers of bacteria that live in our guts: the gut microbiome. These bacteria are not just passively influenced by the immune system but can also shape the intestinal immune response [1]. Recent developments in sequencing technologies allow the exploration of this community using techniques like 16S rRNA sequencing or shotgun metagenomics.
Great Ormond Street Hospital for Children is a centre for treating patients who have an underlying congenital immune defect, such as missing T cells or B cells, in immune diseases like Severe Combined Immunodeficiency (SCID) [2]. These patients usually require a bone marrow transplant or gene therapy to correct the defect and survive. It has become increasingly clear that, during recovery, short-term and long-term outcomes can be influenced by environmental factors.
In particular, there is evidence that gut microbiome composition may be an important determinant of outcome [3] [4]. We aim to investigate the short and longterm impact of host immunity and antibiotics on the composition and complex structure of the gut microbiome by sequencing from longitudinal faecal samples. We are examining these data together with indices of immune function to explore interactions between the immune system and the gut microbiome.
[1] Round and Mazmanian, 2009, doi:10.1038/nri2515
[3] Taur et al., 2014, doi:10.1182/blood-2014-02-554725
[4] Biagi et al. 2015, doi:10.1038/bmt.2015.16