Gut microbiota play a central role in the health of animals. The bacteria that individuals acquire as they age may therefore have a profound effect on their future fitness. Since most birds are capable of flight, they can be widely distributed in and adapted to various ecosystems. Moreover, birds are also challenged by the need to digest a wide range of food resources in their guts. However, little is known regarding how the microbial community structure in birds, especially wild birds, changes with host age. Here, we used high-throughput sequencing of the 16S rRNA V3–V4 region to depict the microbial composition and structure in the adults and nestlings of Jankowski’s bunting (Emberiza jankowskii), an endangered species of bird, during the breeding season. The results showed that the phyla Proteobacteria (52.45%), Firmicutes (13.87%), Bacteroidetes (5.76%), Actinobacteria (4.95%), Planctomycetes (4.36%), Euryarchaeota (3.20%), Acidobacteria (2.59%), Fusobacteria (2.24%), and Chloroflexi (1.8%) dominated the gut microbial communities in Jankowski’s bunting. There was no significant difference in the alpha diversity and richness among different age groups. There was also no significant difference in species richness and diversity between the nestlings and adults. However, we observed different bacterial compositions at the genus level. The genera Photobacterium and Brochothrix were detected only in the nestling groups (at days 3, 6, and 9), while Diplorickettsia was detected only in the adult group. In summary, this study can provide additional information regarding the intestinal microorganisms of wild passerine and grassland birds and provide theoretical evidence for methods to protect Jankowski’s bunting.
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Benskin CM, Rhodes G, Pickup RW, Wilson K (2010) Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch. Mol Ecol 19:5531–5544. https://doi.org/10.1111/j.1365-294X.2010.04892.x
Bjerrum L, Engberg RM, Leser TD, Jenson BB (2006) Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques. Poultry Sci 85:1151–1164. https://doi.org/10.1093/ps/85.7.1151
Du HC, Li XX, Lu ZX, Bie XM (2018) Antibacterial activity and mechanism of action of Plantaricin 163 against Brochothrix thermosphacta. Microbiol CHN 45:2439–2448. https://doi.org/10.13344/j.microbiol.china.171049
Edgar RC, Haas BJ, Clemente JC, Quince C (2011) UCHIME improves sensitivity and speed of chimeradetection. Bioinformatics 27:2194–2200. https://doi.org/10.1093/bioinformatics/btr381
Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. https://doi.org/10.1093/bioinformatics/btq461
Wei G (2002) Ecology in Jankowski’s bunting. Jilin Science and Technology Press, Changchun
Godoy-Vitorino F, Goldfarb KC, Brodie EL, Garcia-Amado MA (2010) Developmental microbial ecology of the crop of the folivorous hoatzin. ISME J 4:611. https://doi.org/10.1038/ismej.2009.147
Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S (2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6:531. https://doi.org/10.1038/ismej.2011.131
Gong J, Si W, Forster RJ, Huang R (2006) 16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: from crops to ceca. FEMS Microbiol Eco 59:147–157. https://doi.org/10.1111/j.1574-6941.2006.00193.x
Han Z, Zhang LS, Qin B, Wang L (2018) Updated breeding distribution and population status of Jankowski’s Bunting Emberiza jankowskii in China. Bird Conserv Int. https://doi.org/10.1017/S0959270917000491
Herlemann DPR, Labrenz M, Jürgens K, Bertilsson S (2011) Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J 5:1571. https://doi.org/10.1038/ismej.2011.41
Hoekstra JM, Boucher TM, Ricketts TH, Roberts C (2005) Confronting a biome crisis: global disparities of habitat loss and protection. Ecol Lett 8:23–29. https://doi.org/10.1111/j.1461-0248.2004.00686.x
Horrocks M, Salter J, Braggins J, Nichol S (2008) Plant microfossil analysis of coprolites of the critically endangered kakapo (Strigops habroptilus) parrot from New Zealand. Rev Palaeobot Palyno 149:229–245. https://doi.org/10.1016/j.revpalbo.2007.12.009
Jiang YL, Gao W, Lei FM, Wang HT (2008) Nesting biology and population dynamics of Jankowski's Bunting Emberiza jankowskii in Western Jilin, China. Bird Conserv Int 18:153–163. https://doi.org/10.1017/S0959270908000154
Kenzaka T, Katsuji T (2017) Public health implications of intestinal microbiota in migratory birds. Metagenomics for gut microbes. IntechOpen. https://doi.org/10.5772/intechopen.72456
Kohl KD, Brun A, Caviedes-Vidal E, Karasov WH (2019) Age-related changes in the gut microbiota of wild House Sparrow nestlings. Ibis 161:184–191. https://doi.org/10.1111/ibi.12618
Kreisinger J, Kropáčková L, Petrželková A et al (2017) Temporal stability and the effect of transgenerational transfer on fecal microbiota structure in a long distance migratory bird. Front Microbiol 8:50. https://doi.org/10.3389/fmicb.2017.00050
Lu J, Santo Domingo J (2008) Turkey fecal microbial community structure and functional gene diversity revealed by 16S rRNA gene and metagenomic sequences. J Microbiol 46:469–477. https://doi.org/10.1007/s12275-008-0117-z
Lucas Françoise S, Heeb P (2005) Environmental factors shape cloacal bacterial assemblages in great tit Parus major and blue tit P. caeruleus nestlings. J Avian Bio 36:510–516. https://doi.org/10.1111/j.0908-8857.2005.03479.x
Pinto RM, Tortelly R, Rodrigo CM, Delir CG (2004) Trichurid nematodes in ring-necked pheasants from backyard flocks of the State of Rio de Janeiro, Brazil: frequency and pathology. Mem I Oswaldo Cruz 99:721–726. https://doi.org/10.1590/S0074-02762004000700010
Preest MR, Folk DG, Beuchat CA (2003) Decomposition of nitrogenous compounds by intestinal bacteria in hummingbirds. Auk 120:1091–1101. https://doi.org/10.1093/auk/120.4.1091
Roggenbuck M, Schnell IB, Blom N, Bælum J (2014) The microbiome of New World vultures. Nat Commun 5:5498. https://doi.org/10.1038/ncomms6498
Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27(6):863–864. https://doi.org/10.1093/bioinformatics/btr026
Sekercioglu CH (2006) Increasing awareness of avian ecological function. Trends Ecol Evol 21:464–471. https://doi.org/10.1016/j.tree.2006.05.007
Na-Ri S, Whon TW, Jin-Woo B (2015) Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol 33:496–503. https://doi.org/10.1016/j.tibtech.2015.06.011
Subramanian G, Mediannikov O, Angelakis E, Socolovschi C (2012) Diplorickettsia massiliensis as a human pathogen. Eur J Clin Microbiol 31:365–369. https://doi.org/10.1007/s10096-011-1318-7
Teyssier A, Lens L, Matthysen E, White J (2018) Dynamics of gut microbiota diversity 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
van Dongen WFD, White J, Brandl HB et al (2013) Age-related differences in the cloacal microbiota of a wild bird species. BMC Ecol 13(1):11. https://doi.org/10.1186/1472-6785-13-11
Videvall E, Elin SJ, Bensch HM, Strandh M (2018) The development of gut microbiota in ostriches and its association with juvenile growth. bioRxiv. https://doi.org/10.1101/270017
Waite DW, Eason DK, Taylor MW (2014) Influence of hand rearing and bird age on the fecal microbiota of the critically endangered kakapo. Appl Environ Microb 80:4650–4658. https://doi.org/10.1128/AEM.00975-14
Waite DW, Taylor MW (2014) Characterizing the avian gut microbiota: membership, driving influences, and potential function. Front Microbiol 5:223. https://doi.org/10.3389/fmicb.2014.00223
Waite DW, Taylor M (2015) Exploring the avian gut microbiota: current trends and future directions. Front Microbiol 6:673. https://doi.org/10.3389/fmicb.2015.00673
Wang HQ, Dong YY, Wang LW (2018) Study on the toxicity of three emerging pollutants to Photobacterium phosphoreum. Asia J Ecotoxicol 13:179–184
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73:5261–5267. https://doi.org/10.1128/AEM.00062-07
World Resources Institute (2000) World Resources: People and ecosystems: the fraying web of life. World Resources Institute, Washington
Xie QK (1985) Location observation of breeding and feeding habits of Great tits. Liaoning For Sci Technol. 05.
Zhang C, Pan Y, Gu J, Li M (2018) Archaea diversity and carbon metabolism in mangrove sediments. Acta Microbiol Sin 58:608–617. https://doi.org/10.13343/j.cnki.wsxb.20170519
Zhang J, Kobert K, Flouri T, Stamatakis A (2013) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30:614–620. https://doi.org/10.1093/bioinformatics/btt593
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The authors declare that they have no conflict of interest.
This study conformed to the guidelines for the care and use of experimental animals established by the Ministry of Science and Technology of the People's Republic of China (Approval number: 2006-398). The research protocol was reviewed and approved by the Ethical Committee of Jilin Agriculture University.
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Shang, W., Li, S., Zhang, L. et al. The Composition of Gut Microbiota Community Structure of Jankowski’s Bunting (Emberiza jankowskii). Curr Microbiol (2020). https://doi.org/10.1007/s00284-020-02048-6