Approximately 13 million US residents reported owning backyard poultry (BYP) in 2014, and interest in BYP ownership is nearly four times that amount. However, BYP ownership and disease treatment is largely under-regulated unlike commercial poultry production. Lack of regulation poses public health concerns of transmission of antimicrobial resistant (AMR) bacteria commonly associated with BYP. Therefore further research is needed on the bacterial communities of BYP and the associated biological factors that modulate community dynamics, such as AMR and bacteriophage. It has been hypothesized that a combination of bacteriophage and antibiotics decreases bacterial survival compared to antibiotics or bacteriophage alone. These previous findings suggest that it is imperative to understand how bacteriophage and AMR coevolve in order to better utilize bacteriophage in combination with existing antibiotics to combat AMR.However, the evolutionary relationship between AMR and bacteriophage community composition has yet to be investigated in the context of the intersection of poultry husbandry and built environment microbiomes of BYP owners. For this study 18 environmental swabs were taken from interior and exterior surfaces of residential door frames of 9 homes as part of a 2018 citizen science study where BYP owners reported current and historical poultry antibiotic usage. Total DNA was extracted from the swabs and was sequenced using Illumina for shotgun metagenomic analysis of the microbiome.
Results/Conclusions
Metagenomic reads were bidirectionally trimmed and filtered for quality using BBDuk to retain reads 80bp or longer, and with quality of a Q10 Phred score, and adapters removed. An average of 89.58% of reads were retained, with a range of 2608934 - 42605342 reads. Retained reads were assembled individually using MEGAHIT, with an average of 123510 contigs, averaging 694 bp per contig, and an average N50 of 772.59. Average bacterial genome size was estimated using MicrobeCensus. Average bacterial genome size was 10347349 bp with a range of 5070348 - 26162138 bp. Bacterial taxonomic diversity was determined using Centrifuge and bacteriophage taxonomic diversity was determined using VIBRANT and HMMER. AMR presence was determined using the CARD database, from both bacteriophage and bacterial reads. Preliminary analysis suggests an evolutionary relationship between AMR type and bacteriophage presence. Continued analysis of this data set is underway and will further elucidate additional potential evolutionary trends. This study highlights the importance of understanding evolutionary relationships from the perspective of microbial ecology; and how to use information about these ecological interactions to tentatively inform industrial applications, such as combating AMR.