Individual variation in the avian gut microbiota: The influence of host state and environmental heterogeneity

The gut microbiota have important consequences for host biological processes and there is some evidence that they also affect fitness. However, the complex, interactive nature of ecological factors that influence the gut microbiota has scarcely been investigated in natural populations. We sampled the gut microbiota of wild great tits (Parus major) at different life stages allowing us to evaluate how microbiota varied with respect to a diverse range of key ecological factors of two broad types: (1) host state, namely age and sex, and the life history variables, timing of breeding, fecundity and reproductive success; and (2) the environment, including habitat type, the distance of the nest to the woodland edge, and the general nest and woodland site environments. The gut microbiota varied with life history and the environment in many ways that were largely dependent on age. Nestlings were far more sensitive to environmental variation than adults, pointing to a high degree of flexibilit..., Field monitoring and microbiota sampling
Birds were sampled from nine small woodland fragments across Co. Cork, Ireland, five of which were mixed/deciduous and four coniferous woodlands (see O’Shea et al. (2018)). We collected 262 faecal samples from 204 great tits from 63 nests (see table S1 for final sample sizes post bioinformatic processing) for 16S rRNA gene sequencing. Nest boxes were monitored during April–June 2016 to determine lay dates, hatching dates and nestling survival. Typically, all individuals in a nest were sampled except for cases where nestlings did not produce a sample within 10–15 minutes of being placed in the sampling apparatus and risked becoming chilled or weak. Individual nestlings were sampled when they were 8 days old (+/- 1 day), and again, if they survived, when they were 15 days old (D8 and D15 birds respectively), at which point parents were also sampled. Birds were placed individually into sterile holding bags inside a heated holding case and naturally-...,

肠道微生物群（gut microbiota）对宿主的生物学过程具有关键调控作用，且已有研究证实其可影响宿主适合度。然而，目前针对影响肠道微生物群的各类生态因子的复杂交互作用，在自然种群中的相关研究仍较为匮乏。本研究对不同生命阶段的野生大山雀（Parus major）的肠道微生物群进行采样，以此评估微生物群如何随两类关键生态因子的多样化组合发生变化：其一为宿主状态，包括年龄、性别，以及繁殖时间、繁殖力与繁殖成功率等生活史变量；其二为环境因素，涵盖栖息地类型、巢穴距林缘的距离，以及巢穴与林地生境的整体环境条件。肠道微生物群的变化模式在诸多维度上依赖于宿主年龄，且与生活史及环境因素显著相关。雏鸟相较成鸟对环境波动的敏感性更强，这提示其具备高度的适应性……

野外监测与微生物群采样
研究样本采集自爱尔兰科克郡（Co. Cork）的9处小型林地片段，其中5处为混交/落叶林，4处为针叶林（详见O’Shea等（2018）的研究）。本研究共从63个巢穴的204只大山雀个体中收集了262份粪便样本，用于16S rRNA基因测序（16S rRNA gene sequencing）（生物信息学处理后的最终样本量详见补充表S1）。研究人员于2016年4月至6月期间对巢箱进行监测，以记录产卵日期、孵化日期以及雏鸟的存活情况。通常情况下，同一巢穴内的所有个体均会被采样，但如果雏鸟在被放入采样装置后的10至15分钟内未能排出样本，且存在受冷或身体虚弱的风险，则不予采样。研究人员在雏鸟8日龄（±1日）时对其进行首次采样，若雏鸟存活至15日龄时则进行第二次采样（分别记为D8组与D15组个体），同时在该时间点对亲鸟进行采样。将鸟类个体单独放置于加热收纳箱内的无菌收纳袋中，待其自然……