Effect of ethanol exposure in utero on infant mice gut microbiotas assessed by nanopore and illumina sequencing

The gut microbiome plays a vital role in host homeostasis and understanding of its biology is essential for a better comprehension of the etiology of disorders such as Foetal Alcohol Spectrum Disorder. Foetal Alcohol Spectrum Disorder represents a cluster of abnormalities including growth deficiencies and neurological impairments, which are not easily diagnosed nor treated. Here the effect of ethanol exposure in utero on the gut microbial profiles of 16 infant mice (nine exposed in utero and seven non-exposed) was assessed by targeted nanopore sequencing and Illumina sequencing approaches. The nanopore sequencing was implemented using MinION system targeting PCR-amplified amplicons made from the full-length 16S rRNA gene. The Illumina sequencing was performed using Miseq system targeting the V3-V4 region of the 16S rRNA gene. Ethanol exposure did not affect the microbial profiles. Several low prevalent taxa, like Akkermansia muciniphila, were detected but further studies must be performed to detail the effect of ethanol exposure to these taxa since no clear pattern was detected throughout this study. Importance Detailed knowledge about the interactions between gut microbes and the developing nervous system is still scarce. Foetal Alcohol Spectrum Disorder represents a clinically relevant set of conditions with cumbersome diagnostic and treatment. In this work the microbial profiles of infant mice gut exposed to ethanol in utero were analysed through third-generation Illumina and optimized next-generation nanopore sequencing technologies. The fungal (albeit not detected) and bacterial microbial profiles here obtained through nanopore and Illumina sequencing represent a technological and biological advancement towards a better comprehension of the microbial landscape in Foetal Alcohol Spectrum Disorder at early post-natal periods.