Northern Cardinal microbiome pilot study 2020-2021

Animal populations can exhibit dramatic variation in individual fitness, and microbiota are emerging as a potentially understudied factor influencing host health. Bacterial diversity and community structure of the gut microbiome are associated with many aspects of fitness in animals, but relatively little is known about the generality of these relationships in wild populations and non-mammalian taxa. We studied the Northern Cardinal (Cardinalis cardinalis), a member of a taxon that is ecologically important but underrepresented in microbiome research: songbirds. To test for relationships between the microbiota and host fitness, we sampled the cloacal microbiomes of wild cardinals and measured body condition index, assessed the coloration of sexual ornaments (beak and plumage), and collected blood to estimate the glucocorticoid response to stress. Both alpha and beta bacterial diversity were related to individual variation in body condition and several sexual ornaments, but not glucocort..., These data come from a wild population of Northern Cardinals (Cardinalis cardinalis) captured in South Florida from 2020-2021. Birds were captured in Tree Tops Park, Davie, FL. Data herein from each bird include 1) fitness-related parameters: coloration values of several sexual ornaments, body condition and morphometrics, and corticosterone concentrations from three sample time points during capture and 2) microbiome diversity, calculated from samples of the birds' cloacal microbiomes. Coloration was processed and calculated by photography analysis or spectroscopy (depending on which ornament is being inspected), corticosterone concentrations were estimated from blood samples using commercial enzyme immunoassay kits, and microbiome samples were processed via DNA extraction, PCR, and subsequent DNA sequencing of the V4 region of the 16S rRNA gene., , # Northern Cardinal microbiome pilot study 2020-2021 The following is a dataset (DOI: [https://doi.org/10.5061/dryad.41ns1rnnq](https://doi.org/10.5061/dryad.41ns1rnnq)) for a paper published in 2024 in the journal Oikos. This dataset includes: * Raw microbiome files. Files included are: * \"NOCA 2020 16S.zip\" - expandable .zip file containing fastq.gz files, each of which is a compressed file containing forward and reverse reads of a DNA sequence that was extracted, amplified, and sequenced. Data in this .zip file are from microbiome samples collected from February 2020 through January 2021. Sequences match sample IDs in \"mapping file allyears.txt\". * \"NOCA sequences Feb2022.zip\" - expandable .zip file containing fastq.gz files, each of which is a compressed file containing forward and reverse reads of a DNA sequence that was extracted, amplified, and sequenced. Data in this .zip file are from microbiome samples collected from February 2021 through October 2021. Sequences match ...动物种群的个体适合度可呈现显著变异，而微生物群正逐渐成为影响宿主健康的一类潜在被低估的因素。肠道微生物群（gut microbiome）的细菌多样性与群落结构与动物适合度的诸多方面密切相关，但目前对于野生种群以及非哺乳类类群中这些关联的普遍性仍知之甚少。 我们以主红雀（Northern Cardinal, *Cardinalis cardinalis*）为研究对象，该类群在生态上具有重要意义，但在微生物组研究中代表性不足：鸣禽类群。 为检验微生物群与宿主适合度之间的关联，我们对野生主红雀的泄殖腔微生物群（cloacal microbiomes）进行了采样，并测量了个体身体状况指数，评估了其性装饰物（sexual ornaments）的着色情况，同时采集血液样本以估算应激状态下的糖皮质激素（glucocorticoid）反应。 细菌的α多样性与β多样性均与个体在身体状况及多种性装饰物上的变异存在关联，但与糖皮质激素…… 本数据集的样本采自2020至2021年在南佛罗里达州捕获的野生主红雀种群，捕获地点为佛罗里达州戴维市树顶公园（Tree Tops Park, Davie, FL）。 本数据集收录的每只鸟类数据包含两部分：1）适合度相关参数：多种性装饰物的着色值、身体状况与形态测量数据，以及捕获期间三个采样时间点的皮质酮（corticosterone）浓度；2）微生物组多样性数据，源自鸟类泄殖腔微生物群样本的测序结果。 着色情况通过摄影分析或光谱法进行处理与计算（根据所检测的装饰物类型而定）；皮质酮浓度通过商用酶联免疫吸附试剂盒（enzyme immunoassay kits）对血液样本进行定量估算；微生物组样本则通过DNA提取、PCR扩增以及16S rRNA基因V4区的后续DNA测序完成实验处理。 # 2020-2021年主红雀微生物组预实验 本数据集（DOI：https://doi.org/10.5061/dryad.41ns1rnnq）对应2024年发表于《Oikos》期刊的一篇学术论文，包含以下内容： * 原始微生物组文件。所包含的文件如下： * "NOCA 2020 16S.zip": 可解压的.zip压缩文件，内含fastq.gz格式文件，每个文件均为压缩后的DNA序列正向与反向读段文件，这些序列源自2020年2月至2021年1月采集的微生物组样本。该压缩包内的数据与"mapping file allyears.txt"中的样本ID一一匹配。 * "NOCA sequences Feb2022.zip": 可解压的.zip压缩文件，内含fastq.gz格式文件，每个文件均为压缩后的DNA序列正向与反向读段文件，这些序列源自2021年2月至2021年10月采集的微生物组样本。序列匹配……