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The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird, the Himalayan bluetail (Tarsiger rufilatus)

Cite this dataset

Zhang, Shangmingyu et al. (2024). The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird, the Himalayan bluetail (Tarsiger rufilatus) [Dataset]. Dryad. https://doi.org/10.5061/dryad.1jwstqk1n

Abstract

Migratory birds experience changes in their environment and diet during seasonal migrations, thus requiring interactions between diet and gut microbes. Understanding the co-evolution of the host and gut microbiota is critical for elucidating the rapid adaptations of avian gut microbiota. However, dynamics of gut microbial adaptations concerning elevational migratory behavior, which is prevalent but understudied in montane birds remain poorly understood. We focused on the Himalayan bluetail (Tarsiger rufilatus) in the montane forests of Mt. Gongga to understand the diet-gut microbial adaptations of elevational migratory birds. Our findings indicate that elevational migratory movements can rapidly alter gut microbial composition and function within a month. There was a significant interaction between an animal-based diet and gut microbiota across migration stages, underscoring the importance of diet in shaping microbial communities. Furthermore, the gut microbial composition of T. rufilatus may be potentially altered by high-altitude acclimatization. An increase in fatty acid and amino acid metabolism was observed in response to low temperatures and limited resources, resulting in enhanced energy extraction and nutrient utilization. Moreover, microbial communities in distinct gut segments varied in relative abundance and responses to environmental changes. While the bird jejunum exhibited greater susceptibility to food and environmental fluctuations, there was no significant difference in metabolic capacity among gut segments. This study provides initial evidence of rapid diet-gut microbial changes in distinct gut segments of elevational migratory birds and highlights the importance of seasonal sample collection. Our findings provide a deeper understanding of the unique high-altitude adaptation patterns of the gut microbiota for montane elevational migratory birds.

README: The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird

https://doi.org/10.5061/dryad.1jwstqk1n

This dataset is a supplemental file based on Article The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird. It contains sample numbers, sample information, primer information, and analysis tables used in that article. This dataset may provide some data reference for vertebrate gut microbiology researchers interested in this study.

Description of the data and file structure

[Zhang, Shangmingyu et al. (Forthcoming 2024). The diet–intestinal microbiota dynamics and adaptation in an elevational migration bird, the Himalayan bluetail (Tarsiger rufilatus) [Dataset]. Dryad. https://doi.org/10.5061/dryad.1jwstqk1n]
We have submitted our raw data (COI_otu_table_class.csv; Gut_microbiotaCleanData_stat; ITS_otu_table_class) and R script (Rcode.R).

COI_otu_table_class

This table contain data related to the Operational Taxonomic Units (OTUs) identified from the COI gene sequencing. It shows the relative abundances of different taxonomic units across different samples. The column headers represent different sample identifiers, categorizing samples based on different altitudes and seasons, “S”, Spring; “A”, Autumn; “L”, 1800 m; “H”, 3000 m. The samples information described in Supplemental Tables S1.

Gut_microbiotaCleanData_stat

This table is a result of the 16S rRNA gene sequencing and subsequent quality control processes.
Sample Name: The identifier for each sample. The samples information described in Supplemental Tables S1.
Raw PE: The raw paired-end reads obtained.
Combined: The number of combined reads after merging paired-end reads.
Qualified: The number of reads that passed the quality filtering criteria.
Nochime: The number of reads after removing chimeras.
Q20 and Q30: The percentage of bases with a quality score above 20 and 30, respectively.
GC: The GC content percentage.
Effective: The effective rate of the reads, which is the percentage of reads that were high-quality and usable.

ITS_otu_table_class

This table contains data related to the Operational Taxonomic Units (OTUs) identified from the ITS2 gene sequencing, which is used for analyzing plant-based food content.
Taxon: The taxonomic classification of each OTU, down to various levels.
Sample Columns: The relative abundances of each taxonomic unit in different samples. The samples information described in Supplemental Tables S1.

Code/Software

R is required to run Rcode; the script was created using version 4.1.3. The script includes the following analyses:
ANOSIM Analysis: Utilizes ANOSIM to test for significant differences between groups based on dissimilarity. Correlation of Diet and Gut Microbes in Different Intestinal Segments: Analyzes and visualizes the correlation between diet and gut microbiota across different intestinal segments using scatter plots and linear regression. Correlation of Diet at Different Migratory Stages with Gut Microbiota Function: Investigates how diet during different migratory stages correlates with the functional aspects of the gut microbiota.

Funding

National Natural Science Foundation of China, Award: 32270454

The Second Tibetan Plateau Scientific Expedition and Research Program, Award: 2019QZKK0501

Fundamental Research Funds for the Central Universities