Family matters: Skin microbiome reflects the social group and spatial proximity in wild zebra finches

Abstract

Background: An animal’s skin is densely populated with a physiological community of bacteria that represents the first barrier to its environment. Investigations on the physiological skin flora have emerged in recent years, but especially in avian taxa our understanding of the ecology and function of these bacteria remains incomplete. The involvement of skin bacteria in intra-specific communication has received attention, and has highlighted the need to understand what information is potentially being encoded in bacterial communities. Using next generation sequencing techniques, we characterized the skin microbiome of wild zebra finches, aiming to understand the impact of sex, age, group composition, spatial distribution among families, and environment on skin bacteria communities. For this purpose, we sampled skin swabs from both sexes and two age classes (adults and nestlings) of 12 different zebra finch families and analysed the bacterial communities. Results: Using 16S rRNA sequencing we found that animals of social groups (families) harbour highly similar bacterial communities on their skin with respect to community composition. Closely related individuals shared significantly more bacterial taxa than non-related animals. While we did not find any effect of sex and age on bacterial diversity, we found that spatial proximity of nest sites, and therefore individuals, correlated with the skin microbiome. Conclusions: Birds harbour very diverse and complex bacterial assemblages on their skin. These bacterial communities are distinguishable and characteristic for intraspecific social groups. Our findings are indicative for a family-specific skin microbiome in wild zebra finches. Genetics and the (social) environment are influential factors shaping the complex bacterial communities. Bacterial communities associated with the skin have a potential to emit volatiles and therefore these communities may play a role in intraspecific social communication, e.g. via signalling social group membership.

Comparing different sample collection and storage methods for field‐based skin microbiome research

“…Although most studies focus on the microbial communities of the gut, researchers are now exploring additional body sites that vary by host environments and lifestyle practices, including the skin (Dimitriu et al, 2019;Grice et al, 2009;Manus et al, 2017Manus et al, , 2020Yu et al, 2018). Because the skin serves as the primary interface between the body and the surrounding environment, its microbial communities are constantly exposed to environmental factors, including plant and soil material (Selway et al, 2020;Vandegrift et al, 2019), household surfaces (Dunn et al, 2013;Flores et al, 2013;Lax et al, 2014), and microbiomes of other individuals (Dominguez-Bello et al, 2010;Engel et al, 2020). Furthermore, skin microbiome samples can be collected from multiple body sites (e.g., armpit, palm, and cheek), where local, nichespecific environmental conditions like pH or humidity dictate which microbes are able to persist on the skin (Ederveen et al, 2020;Grice et al, 2009).…”