Exploring the faecal microbiome of the Eurasian nuthatch (Sitta europaea)

Abstract

Gastrointestinal microbiota fulfill pivotal roles in providing a host with nutrition and protection from pathogenic microorganisms. Up to date, most microbiota research has focused on humans and other mammals, whereas birds and especially wild birds lag behind. Within the field of the avian gut microbiome, research is heavily biased towards poultry. In this study, we analyzed the gut microbiome of the Eurasian nuthatch (Sitta europaea), using faecal samples of eight nestlings originating from three nuthatch nests in the south of Ghent (Belgium), using Illumina sequencing of the 16S rRNA gene. Relative frequency analysis showed a dominance of Firmicutes and Actinobacteria and to a lesser extent Proteobacteria. Bacteroidetes and other phyla were relatively rare. At higher taxonomic levels, a high degree of inter-individual variation in terms of overall microbiota community structure as well as dominance of certain bacteria was observed, but with a higher similarity for the nestlings sharing the same nest. When comparing the nuthatch faecal microbiome to that of great tit nestlings that were sampled during the same breeding season and in the same forest fragment, differences in the microbial community structure were observed, revealing distinct dissimilarities in the relative abundancy of taxa between the two bird species. This study is the first report on the nuthatch microbiome and serves as a reference study for nuthatch bacterial diversity and can be used for targeted screening of the composition and general functions of the avian gut microbiome.

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Data availability

The raw sequencing data are available on NCBI under the BioProject ID PRJNA615317.

References

  1. Alabrudzińska J, Kaliński A, Słomczyński R, Wawrzyniak J, Zieliński P, Bańbura J (2003) Effects of nest characteristics on breeding success of Great Tits Parus major. Acta Ornithol 38:151–154. https://doi.org/10.3161/068.038.0202

    Article  Google Scholar 

  2. Benskin CMH, Wilson K, Jones K et al (2009) Bacterial pathogens in wild birds: a review of the frequency and effects of infection. Biol Rev 84:349–373. https://doi.org/10.1111/j.1469-185X.2008.00076.x

    Article  PubMed  Google Scholar 

  3. Bokulich NA, Subramanian S, Faith JJ et al (2013) Quality-filtering vastly improves diversity estimates from illumine amplicon sequencing. Nat Methods 10:57–59. https://doi.org/10.1038/nmeth.2276

    CAS  Article  PubMed  Google Scholar 

  4. Bolger AM, Lohse M, Usadel B (2014) Trimmomtic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Boonyarittichaikij R, Pomian B, Dekeukeleire D et al (2019) Season as a discriminating factor for faecal metabolomic composition of great tits (Parus Major). Belg J Zool 150:169–184. https://doi.org/10.26496/bjz.2020.79

    Article  Google Scholar 

  6. Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. Cenit MC, Sanz Y, Codoñer-Franch P (2017) Influence of gut microbiota on neuropsychiatric disorders. World J Gastroenterol 23:5486–5498. https://doi.org/10.3748/wjg.v23.i30.5486

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. Danzeisen JL, Calvert AJ, Noll SL et al (2013) Succession of the turkey gastrointestinal bacterial microbiome related to weight gain. PeerJ 1:e237. https://doi.org/10.7717/peerj.237

    Article  PubMed  PubMed Central  Google Scholar 

  9. Danzeisen JL, Clayton JB, Huang H et al (2015) Temporal relationships exist between cecum, ileum, and litter bacterial microbiomes in a commercial Turkey flock, and subtherapeutic penicillin treatment impacts ileum bacterial community establishment. Front Vet Sci 2:56. https://doi.org/10.3389/fvets.2015.00056

    Article  PubMed  PubMed Central  Google Scholar 

  10. Deeming DC, Mainwaring MC (2015) Functional properties of nests. In: Deeming DC, Reynolds SJ (eds) Nests, eggs, and incubation: new ideas about avian reproduction. Oxford University Press, Oxford, pp 29–49

    Google Scholar 

  11. Dekeukeleire D, Hertzog LR, Vantieghem P et al (2019) Forest fragmentation and tree species composition jointly shape breeding performance of two avian insectivores. For Ecol Manag 443:95–105. https://doi.org/10.1016/j.foreco.2019.04.023

    Article  Google Scholar 

  12. Dixon F (2003) VEGAN, a package of R functions for community ecology. J Veg Sci 14:927–993. https://doi.org/10.1111/j.1654-1103.2003.tb02228.x

    Article  Google Scholar 

  13. Drovetski SV, O’Mahoney MJV, Matterson KO et al (2019) Distinct microbiotas of anatomical gut regions display idiosyncratic seasonal variation in an avian folivore. Anim Microbiome 1:2. https://doi.org/10.1186/s42523-019-0002-6

    Article  PubMed  PubMed Central  Google Scholar 

  14. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. https://doi.org/10.1093/bioinformatics/btq461

    CAS  Article  PubMed  Google Scholar 

  15. Edgar RC, Haas BJ, Clemente JC et al (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. https://doi.org/10.1093/bioinformatics/btr381

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. Griffiths RI, Whiteley AS, O’Donnell AG et al (2000) Rapid method for coextraction of 593 DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based 594 microbial community composition. Appl Environ Microbiol 66:5488–5491. https://doi.org/10.1128/aem.66.12.5488-5491.2000

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Grizotte-Lake M, Zhong G, Duncan K et al (2018) Commensals suppress intestinal epithelial cell retinoic acid synthesis to regulate interleukin-22 activity and prevent microbial dysbiosis. Immunity 49:1103–1115. https://doi.org/10.1016/j.immuni.2018.11.018

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. Grond K, Sandercock BK, Jummpponen A et al (2018) The avian gut microbiota: community, physiology and function in wild birds. J Avian Biol 49:e01788. https://doi.org/10.1111/jav.01788

    Article  Google Scholar 

  19. Hird SM, Carstens BC, Cardiff SW et al (2014) Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird (Molothrus ater). PeerJ 2:e321. https://doi.org/10.7717/peerj.321

    Article  PubMed  PubMed Central  Google Scholar 

  20. Hird SM, Sanchez C, Carstens BC et al (2015) Comparative gut microbiota of 59 Neotropical bird species. Front Microbiol 6:1403. https://doi.org/10.3389/fmicb.2015.01403

    Article  PubMed  PubMed Central  Google Scholar 

  21. Kamada N, Chen GY, Inohara N et al (2013) Control of pathogens and pathobionts by the gut microbiota. Nat Immmunol 14:685–690. https://doi.org/10.1038/ni.2608

    CAS  Article  Google Scholar 

  22. Klindworth A, Pruesse E, Schweer T et al (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1. https://doi.org/10.1093/nar/gks808

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Kohl KD (2012) Diversity and function of the avian gut microbiota. J Comp Physio B Biochem Syst Environ Physiol 183:591–602. https://doi.org/10.1007/s00360-012-0645-z

    Article  Google Scholar 

  24. Kohl KD, Brun A, Bordenstein SR et al (2018) Gut microbes limit growth in house sparrow nestling (Passer domesticus) but not through limitations in digestive capacity. Integr Zool 13:139–151. https://doi.org/10.1111/1749-4877

    Article  PubMed  PubMed Central  Google Scholar 

  25. Kowalchuk GA, Naoumenko ZS, Derikx PJL et al (1999) Molecular analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in compost and composted materials. Appl Environ Microbiol 65:396–403

    CAS  Article  Google Scholar 

  26. Kreisinger J, Čížková D, Kropáčková L et al (2015) Cloacal microbiome structure in a long-distance migratory bird assessed using deep 16sRNA pyrosequencing. PLoS ONE 10:e0137401. https://doi.org/10.1371/journal.pone.0137401

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. Kropáčková K, Pechmanová H, Vinkler M et al (2017) Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major). PLoS ONE 12:e0179945. https://doi.org/10.1371/journal.pone.0179945

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  28. Lewis WB, Moore FR, Wang S (2016) Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the gulf of Mexico. J Avian Biol 47:659–668. https://doi.org/10.1111/jav.00954

    Article  Google Scholar 

  29. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. Macke E, Tasiemski A, Massol F et al (2017) Life history and eco-evolutionary dynamics in light of the gut microbiota. Oikos 126:508–531. https://doi.org/10.1111/oik.03900

    Article  Google Scholar 

  31. Macpherson AJ, Harris NL (2004) Interactions between commensal intestinal bacteria and the immune system. Nat Rev immunol 4:478–485. https://doi.org/10.1038/nri1373

    CAS  Article  PubMed  Google Scholar 

  32. Masella AP, Bartram AK, Truszkoski JM et al (2012) PANDAseq: pAired-eND assembler for illumine sequences. BMC Bioinf 13:31. https://doi.org/10.1186/1471-2105-13-31

    CAS  Article  Google Scholar 

  33. Matson KD, Versteegh MA, van der Velde M et al (2015) Effects of immune supplementation and immune challenge on bacterial assemblages in the avian cloaca. J Ornithol 156:805–810. https://doi.org/10.1007/s10336-015-1180-y

    Article  Google Scholar 

  34. Matthysen E (1998) The nuthatches. Academic Press, London

    Google Scholar 

  35. McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8:e61217. https://doi.org/10.1371/journal.pone.0061217

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Mirón L, Mira A, Rocha-Ramírez V et al (2014) Gut bacterial diversity of the house sparrow (Passer domesticus) inferred by 16S rRNA sequence analysis. Metagenomics 3:1–11. https://doi.org/10.4303/mg/235853

    Article  Google Scholar 

  37. O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693. https://doi.org/10.1038/sj.embor.7400731

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  38. Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590-596. https://doi.org/10.1093/nar/gks1219

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. Rytkönen S, Vesterinen EJ, Westerduin C et al (2018) From feces to data: a metabarcoding method for analyzing consumed and available prey in a bird-insect food web. Ecol Evol 9:631–639. https://doi.org/10.1002/ece3.4787

    Article  PubMed  PubMed Central  Google Scholar 

  40. Stanley D, Geier MS, Hughes RJ et al (2013) Highly variable microbiota development in the chicken gastrointestinal tract. PLoS ONE 8:e84290. https://doi.org/10.1371/journal.pone.0084290

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  41. Stanley D, Hughes RJ, Moore RJ (2014) Microbiota of the chicken gastrointestinal tract: influence on health, productivity and disease. Appl Microbiol Biotechnol 98:4301–4310. https://doi.org/10.1007/s00253-014-5646-2

    CAS  Article  PubMed  Google Scholar 

  42. Teyssier A, Lens L, Matthysen E et al (2018a) Dynamics of gut microbiota during the early development of an avian host: evidence from a cross-foster experiment. Front Microbiol 9:1524. https://doi.org/10.3389/fmicb.2018.01524

    Article  PubMed  PubMed Central  Google Scholar 

  43. Teyssier A, Rouffaer LO, Hudin NS et al (2018b) Inside the guts of the city: urban-induced alterations of the gut microbiota in a wild passerine. Sci Total Environ 612:1276–1286. https://doi.org/10.1016/j.scitotenv.2017.09.035

    CAS  Article  Google Scholar 

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Acknowledgements

We would like to thank the private owners and the Flemish Forest and Nature Agency (ANB) for granting access to their property, and Robbe De Beelde, Bram Sercu, Irene Van Schrojenstein Lantman and Pieter Vantieghem for help with the fieldwork.

Funding

This work was supported by the UGent GOA project Scaling up Functional Biodiversity Research: from Individuals to Landscapes and Back (TREEWEB). E. V. and E.G. are supported by the Research Foundation Flanders [FWO Grants 12E6616N/1507119N and 12W8919N, respectively].

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Authors

Contributions

AM, LL, KV, DB and EV conceived the study, participated in its design and coordination. Material preparation and sample collection were performed by RB and DD. Sample analysis was performed by SVP, EG and EV. The first draft of the manuscript was written by EV and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Elin Verbrugghe.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval

Bird ringing and handling were carried out under license and guidelines of the Belgian Ringing Scheme and the Flemish authorities (Agentschap voor Natuur en Bos; ANB/BL-FF/V15-00034). All trapping and sampling protocols were approved and permitted by the Ethical Committee VIB (the Flanders Institute for Biotechnology) Ghent site (EC2015-023).

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Communicated by Erko Stackebrandt.

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Goossens, E., Boonyarittichaikij, R., Dekeukeleire, D. et al. Exploring the faecal microbiome of the Eurasian nuthatch (Sitta europaea). Arch Microbiol (2021). https://doi.org/10.1007/s00203-021-02195-9

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Keywords

  • Nuthatch
  • Wild bird
  • Great tit
  • Faeces
  • Microbiota