Metagenomic shotgun data from poultry houses and mock communties

Here we tested the application of shotgun metagenomics on airfilter samples from poultry houses or from artificial mock communities. Both types of samples were spiked with different quantities of two Campylobacter jejuni isolate to study the usefulness of the specific DNA extraction protocol as well as sequence depth needed to detect these species in a complex background. These analyses were performed as part of the European Joint Project - AIRSAMPLE (https://onehealthejp.eu/jrp-air-sample/). AIR-SAMPLE aims to develop and validate air sampling as a low-cost and multi-purpose alternative to fecal droppings or boot swab for surveillance, monitoring and eradication of Campylobacter in confined and biosecured broiler production. The 16 samples deposited here are 8 mock community samples (ZymoBIOMICS Microbial Community Standard II (Log Distribution)) and 8 airfilter samples from two poultry houses from the same farm. Four of the mock community samples were spiked with the C. jejuni isolate CCUG11284T and four of the poultry farm samples were spiked with C. jejuni 927. Both spikes were applied in different concentrations. For the exact genome assemblies go to project accession number: PRJEB43619