Infant microbiome colonisation- a systematic review and secondary bioinformatic re-analysis of 16s sequencing data

Objectives and Study<br/>The gut microbiota is increasingly appreciated as having an important impact on health. Its development in<br/>infancy remains an important topic but understanding of this is hampered by many small studies with<br/>heterogeneous methodology.<br/>We employed a systematic review methodology to identify studies that have reported on gut microbiome in<br/>infancy. We performed a unified bioinformatic reanalysis of sequence outputs to characterise changes in gut<br/>microbiome in infants aged 8 weeks to 1 year of life.<br/>Methods<br/>MEDLINE and Embase searches to February 2024 identified studies of interest. Where available, 16S rRNA<br/>sequence datasets were downloaded and missing datasets requested. Integrated datasets were run through a<br/>unified QIIME2 pipeline supplemented by phyloseq.<br/>Results<br/>3664 studies were screened, of which 11 manuscripts, comprising 1508 stool samples from 902 infants, were<br/>suitable for bioinformatic re-analysis. Age at time of sampling was grouped by 2 month bands for the purposes<br/>of analysis (2-4m, 4-6m, 6-8m, 8-10m and 10-12m with 458, 394, 109, 340, 207 samples respectively).<br/>Shannon diversity was shown to increase over the first year of life, with an acceleration after 8 months of age<br/>(Figure 1A). Principal components analysis of Bray-Curtis beta diversity (PCoA) Figure 1B) demonstrated<br/>contraction of the range of microbial community structures and migration away from the starting point with<br/>time, particularly after 8 months. Compositional data demonstrated the arrival and expansion of<br/>Faecalibacterium and Blautia spp. after 6 months, in keeping with a change in available dietary substrate.<br/>Conclusions<br/>This singular re-analysis of sequence data from over 900 infants reiterates the growth in microbial diversity<br/>throughout infancy and demonstrates a rapid acceleration post 8-months months, coinciding with the pivot<br/>towards a solid food diet. Further study is required to understand the specific drivers of this change and to<br/>explore the therapeutic potential of directly influencing this phase of colonisation.