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Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing


An animals’ body is densely populated with bacteria. Although a large number of investigations on physiological microbial colonisation have emerged in recent years, our understanding of the composition, ecology and function of the microbiota remains incomplete. Here, we investigated whether songbirds have an individual-specific skin microbiome that is similar across different body regions. We collected skin microbe samples from three different bird species (Taeniopygia gutatta, Lonchura striata domestica and Stagonopleura gutatta) at two body locations (neck region, preen gland area). To characterise the skin microbes and compare the bacterial composition, we used high-throughput 16S rRNA amplicon sequencing. This method proved suitable for identifying the skin microbiome of birds, even though the bacterial load on the skin appeared to be relatively low. We found that across all species, the two evaluated skin areas of each individual harboured very similar microbial communities, indicative of an individual-specific skin microbiome. Despite experiencing the same environmental conditions and consuming the same diet, significant differences in the skin microbe composition were identified among the three species. The bird species differed both quantitatively and qualitatively regarding the observed bacterial taxa. Although each species harboured its own unique set of skin microbes, we identified a core skin microbiome among the studied species. As microbes are known to influence the host’s body odour, our findings of an individual-specific skin microbiome might suggest that the skin microbiome in birds is involved in the odour production and could encode information on the host’s genotype.

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We are particularly grateful to Elke Hippauf for support in the laboratory and to Ursula Kodytek, Kristina Ruhe and Brigitta Otte-Eustergerling for taking care of the birds. Furthermore, we thank Sebastian Dörrenberg and Sarah Golüke for helping in skin microbe sampling, Helga Pankoke for statistical advice and Oliver Krüger for logistical support. This study was financially supported by a Freigeist Fellowship from the Volkswagen Foundation to B.A.C. This work was supported in part by grants from the German Federal Ministry of Education and Research (BMBF) for the ‘Bielefeld-Gießen Center for Microbial Bioinformatics - BiGi’ project (grant number 031A533A) within the German Network for Bioinformatics Infrastructure (de.NBI). We also thank the de.NBI for the opportunity to take part in a bioinformatics workshop. We thank Sonja Engel for creating the beautiful zebra finch artwork. Additionally, we thank three anonymous reviewers for their helpful comments and suggestions.

Author information




B.A.C. and A.T. conceived the experiment; K.E., J.S. and B.A.C. designed the experiment; K.E., J.S. and A.W. carried out the experiment; J.S., D.W., S.J. and B.A.C. analysed the data; S.J. contributed analytical tools; K.E., J.S. and B.A.C. wrote the manuscript with input from S.J., D.W., J.K. and A.T.

Corresponding authors

Correspondence to Kathrin Engel or Jan Sauer.

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Conflict of Interest

The authors declare that they have no conflict of interest.

Ethical Approval

All applicable national guidelines for the care and use of animals were followed.

Additional information

K.E. and J.S. are joint first authors of this work.

Data accessibility

The 16S rRNA sequence reads obtained in this study have been deposited in the EMBL-EBI database under the Bioproject ID PRJEB23205.

Electronic supplementary material


Contains the detailed description of the ‘Library preparation and DNA sequencing’ part. (DOCX 19 kb)


Contains all raw and metadata used for statistical analysis, the consensus sequences used for phylogenetic tree reconstruction and the full OTU table with taxonomy. (XLSX 1158 kb)


Contains Figs. S3.1–S3.6, showing the skin microbiome data separately visualised for each species and the skin microbiomes of all three species based on a weighted UniFrac distance matrix (S3.1–S3.4). S3.5 and S3.6 show two Venn diagrams including only those OTUs present in at least 50 and 75% of the samples per bird species (DOCX 176 kb)

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Engel, K., Sauer, J., Jünemann, S. et al. Individual- and Species-Specific Skin Microbiomes in Three Different Estrildid Finch Species Revealed by 16S Amplicon Sequencing. Microb Ecol 76, 518–529 (2018).

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  • Microbial community
  • Estrildid finches
  • Skin microbiome
  • 16S rRNA gene amplicon sequencing
  • Individuality