Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes

Primates acquire gut microbiota from conspecifics through direct social contact and shared environmental exposures. Host behavior is a prominent force in structuring gut microbial communities, yet the extent to which group or individual-level forces shape the long-term dynamics of gut microbiota is poorly understood. We investigated the effects of three aspects of host sociality (social groupings, dyadic interactions, and individual dispersal between groups) on gut microbiome composition and plasticity in 58 wild Verreaux’s sifaka (Propithecus verreauxi) from six social groups. Over the course of three dry seasons in a five-year period, the six social groups maintained distinct gut microbial signatures, with the taxonomic composition of individual communities changing in tandem among co-residing group members. Samples collected from group members during each season were more similar than samples collected from single individuals across different years. In addition, new immigrants and in..., In this study, we utilize behavioral, genetic, and demographic data obtained as part of The Sifaka Research Project, a continuous long-term field study of wild lemurs (Verreaux’s sifaka, Propithecus verreauxi) in western Madagascar, to consider the impact of dynamic contact patterns on the gut microbiome at multiple scales, including between social groups (i.e., at the population-level), among individuals within groups, and within individual hosts. To measure short- and long-term gut microbial plasticity, we assayed sifaka gut microbial communities during three dry seasons over a five-year period. We collected fecal samples from six social groups on a weekly basis during one-to-two-month periods in 2012, 2015, and 2016, with a total of 65 unique individuals (58 of known identity) sampled across the entire study period. 

Fecal sample processing and 16S rRNA gene sequencing

We preserved fecal samples in RNAlater® (ThermoFisher, Waltham, MA, USA) and stored them at ambient temperatu..., The README.md file contains information on R scripts and inputs to reproduce the main results and figures in the associated manuscript referenced above. The data dictionary file (perofsky_2021_mol_ecol_data_dictionary.xlsx) defines variables in each dataset (\"Column\"), allowable values for variables (\"Value\"), whether variables contain sample or host information (\"Category\"), and variable definitions (\"Explanation\").

灵长类动物通过直接社会接触与共同环境暴露，从同种个体处获得肠道微生物群（gut microbiota）。宿主行为是塑造肠道微生物群落的关键驱动力，但群体或个体层面的因素在多大程度上影响肠道微生物群的长期动态，目前仍知之甚少。我们针对来自6个社会群体的58只野生维氏冕狐猴（Verreaux's sifaka，*Propithecus verreauxi*），探究了宿主社交性的三个维度——社会群体结构、二元互动以及群体间个体扩散——对肠道微生物组（gut microbiome）组成与可塑性的影响。在五年周期内的三个旱季观测期间，这6个社会群体始终保有独特的肠道微生物特征，且同居群体成员的个体肠道微生物群落分类组成会同步发生变化。各季节从群体成员中采集的样本，其相似度高于不同年份从单个个体采集的样本。此外，新迁入的个体以及……

本研究依托「冕狐猴研究项目」（The Sifaka Research Project）所获取的行为学、遗传学与人口统计学数据展开——该项目是对马达加斯加西部野生狐猴（维氏冕狐猴，*Propithecus verreauxi*）的长期持续野外研究——旨在从多个尺度探究动态接触模式对肠道微生物组的影响，包括社会群体间（即种群层面）、群体内个体间以及宿主体内的尺度。为评估肠道微生物组的短期与长期可塑性，我们在五年周期内的三个旱季对冕狐猴的肠道微生物群落进行了检测。我们于2012、2015及2016年的1至2个月周期内，每周采集6个社会群体的粪便样本，整个研究期间共采样了65只独个个体（其中58只身份明确）。

粪便样本处理与16S rRNA基因测序

我们将粪便样本保存于RNAlater®试剂（ThermoFisher，美国马萨诸塞州沃尔瑟姆市赛默飞世尔科技）中，并于室温下储存……

README.md文件包含了复现上述关联论文中主要结果与图表所需的R脚本及输入文件信息。数据字典文件（perofsky_2021_mol_ecol_data_dictionary.xlsx）对各数据集的变量（"Column"，即列）、变量允许取值（"Value"，即取值范围）、变量是否包含样本或宿主信息（"Category"，即类别）以及变量定义（"Explanation"，即解释说明）进行了说明。