Optimization of 16S rRNA gut microbiota profiling of extremely low birth weight infants

Infants born prematurely, particularly extremely low birth weight infants (ELBW), have altered gut microbial communities. There is a requirement to optimally characterize microbial profiles in this at-risk cohort, via standardization of methods, particularly for studying the influence of microbiota therapies (e.g. probiotic supplementation) on community profiles and health outcomes. Profiling of faecal samples using the 16S rRNA gene is a cost-efficient method for large-scale clinical studies to gain insights into the gut microbiota and additionally allows characterization of cohorts where sample quantities are compromised. To this end, the bacterial DNA extraction protocol from ELBW infant faeces was optimized by testing three different DNA extraction methods.