To further their understanding of the factors affecting wildlife microbiomes, Bartlow and his team compared the diversity and make-up of the bacterial communities of two owl species: the western screech owl (Megiscops kenicottii) and the whiskered screech owl (Megiscops trichopsis). The study area was in the Peloncillo Mountains in south-east Arizona, where the ranges of the two species overlap. The team set up nesting boxes in one canyon. These species have much the same habitat and niche – feeding, nesting, and surviving using very similar resources.

The researchers took faecal samples and cloacal swabs (from the rear end of the birds). They then identified the different species in the microbial communities using next generation DNA sequencing of the 16S rRNA gene; the region of DNA that is sufficiently unique to most microbial species that it enables researchers to tell different kinds of bacteria apart.

Because the microbes can be very similar genetically, Bartlow wanted to use a different analysis than that typically used to tell them apart. So, the team targeted two separate locations within the DNA, improving their ability to identify each species or subspecies – known as taxonomic resolution – and enabling them to study microbiome diversity in greater detail.