Immune stimulation induced changes to the native gut microbiota of bumble bees

Understanding factors influencing the maintenance and membership of beneficial host-associated microbial communities is central to understanding ecological, evolutionary, and health consequences of these communities for their hosts. Host immunity is often implicated as a potential regulator of these microbiota. However, conversely, immunity may play a disruptive role, with immune responses to infection causing collateral damage. Such effects may be more prominent from innate immune responses, with more rapid-acting and relatively non-specific components. We investigated how upregulation of antibacterial immunity in the bumble bee Bombus impatiens affects the core gut microbiota, testing the hypothesis of immunity-induced perturbation of the beneficial microbiota structure. Freshly emerged adult bees received a native microbiota inoculation before being subjected to non-pathogenic immune stimulation treatments. We quantified the microbial community using 16S rRNA amplicon sequencing and ..., , See the uploaded readme (ReadME.md). In addition to this, the latest version of R statistical software and the latest versions of the following packages: MASS, car, plyr, dplyr, lme4, msme, emmeans, phyloseq, ggplot2, cowplot, vegan, dplyr, metagMisc, glmmTMB, DHARMa, NetCoMi, AICcmodavg and a Linux system with the latest version of Ubuntu, Conda, and QIIME2 will be required to recreate the analysis. , Explanation of files for Sauers et al. \"Membership robustness but structural change of the native gut microbiota of bumble bees upon systemic immune induction\" File: Immune_PerturbationData_06042023.csv Data sheet containing sample meta data, qPCR determined values for total bacterial 16S rRNA, downstream relative abundances calculated from 16S amplicon sequencing analysis with QIIME2 and phyloseq, the adjusted amplicon read values for core bacteria (Relative abundance * total bacteira 16S rRNA for the sample), and species-specific qPCR values. Analytical script: Immune_perturbation_R_Code_06042023 sampleID: The unique sample id for each sample collected in the experiment. Colony: The colony of origin for each sample Bee_ID: The initial ID, nested within colony, before assignment of the unique ID Block: Sampling block for each sample ImmuneChallenge: The immune challenge treatment for each sample, N = naive, C = wounding, E = gram negative, and S = gram positive TreatmentDay: The da...解析影响宿主相关有益微生物群落维持与成员组成的核心因素，是理解这些群落对宿主产生的生态、进化与健康效应的关键所在。宿主免疫常被认为是这类微生物群的潜在调控因子。然而，反之，免疫也可能发挥干扰作用：针对感染的免疫应答会引发附带损伤。这类效应在天然免疫应答中可能更为显著，因其组成成分起效更快且相对非特异性。 本研究针对熊蜂（Bombus impatiens）的抗菌免疫上调如何影响其核心肠道微生物群展开探究，验证了免疫诱导会扰动有益微生物群结构这一假说。研究中，刚羽化的成年熊蜂先接受天然微生物群落接种，随后接受非致病性免疫刺激处理。我们通过16S rRNA扩增子测序（16S rRNA amplicon sequencing）对微生物群落进行定量分析，并……详见上传的ReadME.md文件。 若要复现本研究的分析流程，需使用最新版R统计软件及以下工具包的最新版本：MASS、car、plyr、dplyr、lme4、msme、emmeans、phyloseq、ggplot2、cowplot、vegan、dplyr、metagMisc、glmmTMB、DHARMa、NetCoMi、AICcmodavg，同时需搭载最新版Ubuntu的Linux系统、Conda及QIIME2。 以下为Sauers等人发表的《系统性免疫诱导后熊蜂天然肠道微生物群的成员稳健性与结构变化》一文中相关文件的说明： 文件Immune_PerturbationData_06042023.csv：该数据表包含样本元数据、通过qPCR测定的总细菌16S rRNA定量值、经QIIME2与phyloseq分析得到的16S扩增子测序相对丰度、核心细菌的校正扩增子读值（即样本相对丰度乘以总细菌16S rRNA定量值），以及物种特异性qPCR测定值。 分析脚本：Immune_perturbation_R_Code_06042023 各字段说明如下： sampleID：实验中采集的每个样本的唯一标识符 Colony：样本所属的蜂群来源 Bee_ID：在分配唯一标识符前，嵌套于蜂群下的初始编号 Block：样本的采样批次 ImmuneChallenge：样本的免疫刺激处理分组，其中N代表空白对照，C代表创伤处理，E代表革兰氏阴性菌刺激，S代表革兰氏阳性菌刺激 TreatmentDay：处理天数：……