Stability of fecal microbiota during degradation in ex situ Cheetahs in the US

Objective: Gut health and its relationship to gut microbiota is an important consideration in the care and well-being of managed endangered species, such as the cheetah (Acinonyx jubatus). Non-invasive fecal sampling as a proxy for gut microbiota is preferred and collecting fresh fecals is the current gold standard. Unfortunately, even in managed facilities, collecting fresh samples from difficult to observe or dangerous animals is challenging. Therefore, we conducted a study to determine the terminal collection timepoint for fecal microbial studies in the cheetah.
Methods: We longitudinally sampled eight freshly deposited fecals every 24 h for 5 days and assessed bacterial relative abundance, diversity, and composition changes over time.
Results: Our data indicated that fecal samples up to 24 h post defecation provided accurate representations of the fresh fecal microbiome. After 24 h, major changes in community composition began to occur. By 72 h, individual cheetah fecal microbiota s..., , , # Data from: Stability of fecal microbiota during degradation in ex situ Cheetahs in the US

## Description of the data and file structure

Files and code for preprocessing and analyses of 16S rRNA fecal microbiota data from cheetahs associated with the article \"Comparing Stability of Fecal Microbiota by Time and Weather Conditions in a Carnivore, the Cheetah (Acinonyx jubatus)\".

Fecal samples were collected fresh and analyzed for an additional 5 days to observe microbial changes in fecals exposed to the environment.

## Data files included (needed to run analyses without running all preprocessing code)

1. Feature file - Aju_featuretable.csv (ASV counts for each sample, first column are row names and there is no header for column 1 as is expected format for phyloseq processing)
2. Taxonomy file - Aju_taxonomy.csv (taxonomy file for mapping ASV numbers to taxonomy classifications, first column has no header as expected format for phyloseq processing)
1. NAs: when NAs are present it ...

目标：肠道健康及其与肠道微生物群（gut microbiota）的关系是圈养濒危物种（如猎豹，Acinonyx jubatus）养护与福祉的重要考量因素。非侵入性粪便采样（non-invasive fecal sampling）作为肠道微生物群研究的替代手段备受青睐，而采集新鲜粪便样本是当前的金标准。遗憾的是，即便在圈养设施中，从难以观察或具有危险性的动物身上收集新鲜样本仍具挑战。因此，我们开展了一项研究，旨在确定猎豹粪便微生物研究中的终端采集时间点。

方法：我们对8份新排出的粪便样本进行纵向采样，每24小时采集一次，持续5天，并评估细菌相对丰度、多样性及群落组成随时间的变化。

结果：我们的数据表明，排便后24小时内的粪便样本可准确反映新鲜粪便微生物组（fecal microbiome）的特征。24小时后，群落组成开始发生显著变化。至72小时时，个体猎豹粪便微生物群... , , , # 数据来源：美国圈养猎豹粪便微生物群降解过程中的稳定性研究

## 数据与文件结构描述

本数据集包含与文章《食肉动物猎豹（Acinonyx jubatus）粪便微生物群稳定性随时间及天气条件变化的比较研究》相关的16S核糖体RNA（16S rRNA）粪便微生物群数据预处理及分析所需的文件与代码。

粪便样本采集于新鲜状态，并额外分析5天，以观察暴露于环境中的粪便微生物变化。

## 包含的数据文件（无需运行所有预处理代码即可开展分析）

1. 特征文件 - Aju_featuretable.csv（每份样本的扩增子序列变体（ASV）计数，第一列为行名，无列标题，符合phyloseq处理格式）
2. 分类学文件 - Aju_taxonomy.csv（用于将ASV编号映射至分类学分类的文件，第一列无列标题，符合phyloseq处理格式）
1. 缺失值（NA）：当存在缺失值时...