Abstract
Gut microbiota have a significant impact on host physiology and health, and host genetics and diet are considered as two important factors, but it is difficult to discriminate the influence of each single factor (host or diet) on gut microbiota under natural conditions. Moreover, current studies of avian microbiota mainly focus on domestic or captive birds, and it is still uncertain how host and diet take part in changing avian gut microbiota composition, diversity, and function in the wild. Here, high-throughput sequencing of 16S rRNA was used to identify the gut microbiota communities for sympatric wintering Great Bustards and Common Cranes at different diets. The results showed that 8.87% operational taxonomic units (OTUs) were shared among all sampling birds; in contrast, 39.43% of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were common among all individuals, indicating the existence of gut microbiota conservatism both in microbiota structure and function. Microbiota abundance and diversity differed between Great Bustards and Common Cranes in a specific wintering site, and microbiota variation was detected for the same host species under two different sites, suggesting that the change of gut microbiota was induced by both host and diet. Furthermore, we found that changes of both microbial communities and functional pathways were larger between hosts than those between diets, which revealed that host might be the dominant factor determining microbiota characteristics and function, while diet further drove the divergence of gut microbiota. Gut microbiota functions appeared to be more conserved than bacterial community structure, indicating that different bacteria may function in a similar way, while microbiota OTU diversity might not be necessarily associated with functional diversity. With diet shifting, gut microbiota changed both in terms of microbial communities and functional pathways for the sympatric birds, which implies that avian habitats and their physiological microbiota would be influenced by different farmland management regimes.
Key points
• Gut microbiota can be shaped by both diets and hosts in sympatric species.
• Host was the dominant factor shaping the gut microbiota communities and functional pathways.
• Gut microbiota were conservative both in structure and in function, but more conservative in function.
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Data availability
The original sequencing data of gut microbiota can be found in NCBI, under accession number PRJNA698750.
Code availability
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Acknowledgements
We are particularly grateful to Lijuan Cui, Xiaoming Kang, and Chunyi Li for their help during the study. Great thanks to Mr. Lian Yu, Mr. Keming Song, and Mr. Yinguo Xiao for helping with sample collection in the field.
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This study was funded with Fundamental Research Fund of Chinese Academy of Forestry (Grant No. CAFYBB2018QB010), and the Fundamental Research Funds for the Central Non-profit Research Institution of CAF (Grant No. CAFYBB2018GB001). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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CL analyzed the data, prepared figures and tables, authored or reviewed drafts of the paper, and approved the final draft. YL, MHG, CMZ, and CLZ collected samples and provided basic data about the Great Bustard wintering sites and analyzed the data. HXL, WYW, and YHW authored or reviewed drafts of the paper. GL conceived and designed the experiments, analyzed the data, prepared figures and tables, authored or reviewed drafts of the paper, and approved the final draft.
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Li, C., Liu, Y., Gong, M. et al. Diet-induced microbiome shifts of sympatric overwintering birds. Appl Microbiol Biotechnol 105, 5993–6005 (2021). https://doi.org/10.1007/s00253-021-11448-y
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DOI: https://doi.org/10.1007/s00253-021-11448-y