Fecal microbiota transplants (FMT) of three distinct human communities to germ-free mice exacerbated inflammation and decreased lung function in their offspring

Despite explosive rise in allergies, little is known about early life gut microbiota effects on postnatal respiratory function. We hypothesized that Enterobacteriaceae-dominant gut microbiota from eczemic infants increases Type 2 inflammation and decreases lung function in transplanted mice, while Bacteroidaceae-dominant gut microbiota from non-eczemic infants is protective. FMT from eczemic infants “Infant A” and non-eczemic infants “Infant B” were successfully transplanted into germ-free C57BL/6 mice passing to offspring unchanged. Infant A and B, Adult C-human-derived (positive control), and mouse (negative control) microbiotas all in C57BL/6 mice were tested for effects on airway function in non-allergic (PBS) and allergic (HDM) conditions. Baseline lung mechanics in mice with human microbiotas (HUmicrobiota) were significantly impaired compared to mouse microbiota controls (MOmicrobiota) with or without HDM; Respiratory system resistance (Rrs) was increased (p< 0.05-p<0.01) and Respiratory system compliance (Crs) was decreased (p<0.05-p<0.01). HUmicrobiota mice showed statistically significant impairment compared to MOmicrobiota mice in lung parameters Rrs, Ers, Rn, and G at baseline, and at multiple Mch doses with baseline removed. Impairment manifested as increased small airway resistance and tissue resistance. HDM significantly elevated IL-4, eosinophils, lung inflammation and mucus cell metaplasia and decreased macrophages and lung function (p<0.05) in mice of all microbiotas, yet each HUmicrobiota produced distinct features. Infant B and Adult C mice had elevated basal levels of total IgE compared to MOmicrobiota and Infant A mice (p<0.05). In HUmicrobiota mice given HDM, only Adult C had elevated IL-5 and IL-13 (p<0.05), only Adult C and Infant B mice had elevated neutrophils (p<0.05) and only Infant A had elevated lymphocytes (p<0.01).

Methods
Fecal pellets of C57BL/6 germ-free mice receiving transplant of fecal materials collected from 3-month-old infants of the Isle of Wight third generation birth cohort were collected at the endpoint of the experiment. Bacterial DNA was isolated using the FastDNA SPIN Kit then sequeced for the 16S rRNA V4 region using Illumina MiSeq using MiSeq v2 flow cell and 500 cycle MiSeq v2 reagen kit with paired-end 250 base reads. Base calling was performed by Illumina Real Time Analysis (RTA) v1.18.54 and output of RTA was de-multiplexed and converted to FastQ format files with Illumina Bcl2fastq v1.8.4. 109,085 high-quality reads from Illumina sequencing remained - average read number per group: 3896 (min 3245, max 5053).