Evaluation of commercially available DNA extraction kits for the analysis of the broiler chicken cecal microbiota

et al. 2020

Preprint

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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.

Section: Data Filtering and Statistical Analysesmentioning

confidence: 99%

“…Taxonomic profiling of the skin microbiome of the zebra finch was done according to Pankoke et al [54]. In short, read counts of all OTUs belonging to one specific taxon were summed up and normalized by the total number of read counts, yielding proportions.…”

Section: Data Filtering and Statistical Analysesmentioning

confidence: 99%

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

et al. 2020

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“…After bioinformatic processing, we applied additional ltering steps to the OTU table as described in Pankoke et al [52]. In short, only bacterial OTUs that could be classi ed at phylum level were used for further ltering steps.…”

Section: Data Ltering and Statistical Analysesmentioning

confidence: 99%

“…Taxonomic pro ling of the skin microbiome of the zebra nch was done according to Pankoke et al [52]. In short, read counts of all OTUs belonging to one speci c taxon were summed up and normalized by the total number of read counts, yielding proportions.…”

Section: Data Ltering and Statistical Analysesmentioning

confidence: 99%

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

et al. 2020

Preprint

Self Cite

Background: So far, large numbers of studies investigating the microbiome have focused on gut microbiota and less have addressed the microbiome of the skin. 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 recently received attention, and has highlighted the need to understand what information is potentially being encoded in bacterial communities. Using next generation sequencing techniques, we characterised the skin microbiome of wild zebra finches, aiming to understand the impact of sex, age and group composition 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 no effect of age, sex and family on bacterial diversity (alpha diversity). However, when comparing the composition (beta diversity), we found that animals of social groups (families) harbour highly similar bacterial communities on their skin with respect to community composition. Within families, closely related individuals shared significantly more bacterial taxa than non-related animals. In addition, we found that age (adults vs. nestlings) affected bacterial composition. Finally, we found that spatial proximity of nest sites, and therefore individuals, correlated with the skin microbiome similarity. 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 seem to be the 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.

“…[45] and Primer-e software version 7 [46]. After bioinformatic processing, we applied additional ltering steps to the OTU table as described in Pankoke et al [47]. In short, only bacterial OTUs that could be classi ed at phylum level were used for further ltering steps.…”

Section: Data Ltering and Statistical Analysesmentioning

confidence: 99%

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

et al. 2020

Preprint

Self Cite

Background: So far, large numbers of studies investigating the microbiome have focused on gut microbiota and less have addressed the microbiome of the skin. 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 recently received attention, and has highlighted the need to understand what information is potentially being encoded in bacterial communities. Using next generation sequencing techniques, we characterised the skin microbiome of wild zebra finches, aiming to understand the impact of sex, age and group composition 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 no effect of age, sex and family on bacterial diversity (alpha diversity). However, when comparing the composition (beta diversity), we found that animals of social groups (families) harbour highly similar bacterial communities on their skin with respect to community composition. Within families, closely related individuals shared significantly more bacterial taxa than non-related animals. In addition, we found that age (adults vs. nestlings) affected bacterial composition. Finally, we found that spatial proximity of nest sites, and therefore individuals, correlated with the skin microbiota similarity. 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 seem to be the 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.