Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples

Welcome! Here you will find the codes used in the analysis we ran for our manuscript titled "Reviving diversity: cryoprotectants and culturing methods enhance recovery of mammalian gut microbes from field samples". We would be happy to help in way we can, so please do not hesitate to reach out if you have questions or suggestions. In summary, we developed this study in response to challenges encountered in our own field research. Recent advancements in culturomics and microbiology are enabling us to further explore the realm of microbiome science. We aspire for this study to serve as a foundational step toward identifying preservation methods that can help protect the microbial communities of wild animals. Our study aims are: The primary objective of this study was to evaluate the effectiveness of various preservation solutions in maintaining microbial integrity of gut samples during collection and for a short duration, simulating transportation conditions, prior to long-term storage at -80°C. We cultivated the samples in three distinct culture media to maximize the recovery of microbial diversity. The second objective was to compare the inventory of the preserved and cultured microbial community to that of the original uncultured samples, aiming to determine whether the preservation solutions retained unique taxa absent in the frozen original samples. Notes to keep in mind: We chose preservation solutions that have already been described for microbial culturing. We chose culture media that have already been described for microbial culturing, especially gut microbiome samples. As you go through the Rmd document included here, please make sure all documents have been properly downloaded. Additionally, please make sure to change the names of the alpha diversity metric files in the Rmd to that of the files here as they were modified for proper uploading methods here.欢迎访问本数据集资源。 本页面提供我们为发表于题为《复苏多样性：低温保护剂与培养方法提升野外样本中哺乳动物肠道微生物的复苏率》的研究论文所开展的分析所用的代码。我们将尽力为您提供协助，若您有任何疑问或建议，欢迎随时联系。 简言之，本研究旨在解决我们自身野外调研中遇到的难题。当前培养组学（culturomics）与微生物学领域的最新进展，为我们进一步探索微生物组科学的前沿疆域提供了可能。我们期望本研究能够为筛选可有效保护野生动物肠道微生物群落的保存方法奠定基础。 本研究的目标如下： 本研究的首要目标为：评估多种保存液在样本采集阶段及模拟运输的短期保存过程中，维持肠道样本微生物完整性的效果，为后续-80℃长期储存做好准备。我们采用三种不同的培养基对样本进行培养，以最大化微生物多样性的复苏效果。 本研究的第二目标为：将经保存处理与培养后的微生物群落组成，与原始未培养样本的群落组成进行比对，旨在明确保存液是否能够保留冷冻原始样本中缺失的独特分类单元。 注意事项： 本次研究所选用的保存液均为已被报道可用于微生物培养的试剂。 本次研究所选用的培养基均为已被报道可用于微生物培养、尤其是肠道微生物组样本培养的试剂。 请您在查阅本页面附带的R Markdown（Rmd）文档时，确保已正确下载所有关联文件。此外，请将文档内的α多样性指数（alpha diversity metric）文件名称修改为本次上传所用的对应文件名称，因本次上传已对文件名进行了适配调整。