Bacterial and archaeal diversity on mammalian skin

Characterization of the microorganisms on skin is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, and exploring the origins and etiology of disease. Although many studies have characterized the human microbiome, far less is known about the skin microbiome of non-human mammals. The objective of this research was to create a baseline skin microbiome dataset for the Mammalia class, testing the effects of species, location, hygiene, body region, and biological sex. The back, torso, and inner thigh regions of 187 non-human mammals and 20 human participants were collected to include representatives from 38 species and 10 mammalian orders. Animals were collected from local farms, zoos, households, and the wild. All samples were amplified using the V3-V4 16S rRNA gene region and sequenced using a MiSeq (Illumina). Human skin was significantly less diverse than all other mammalian orders according to Shannon indices (6.54 versus 3.96, p < 0.001). The factor most strongly associated with community variation for all samples was whether the host was a human (PERMANOVA, F = 37.8, p < 0.001; Figure 2). By analyzing all samples together, random forest modelling identified that human and animal samples could be distinguished correctly 98.51.2% of the time. This study represents the largest mammalian skin microbiome project to date and is the first study to elucidate the skin microbiota for 32 distinct species. Additionally, these findings are the first to demonstrate that human skin is distinct, not only distinct from other Primates, but from all 10 mammalian orders sampled. Baseline data on the mammalian skin microbiome is crucial to make informed decisions for veterinarian research and conservation strategies, as well as providing implications for mammalian evolutionary history.皮肤微生物组的表征，对于解析宿主与其微生物共生体的协同演化机制、模拟免疫系统发育进程、辅助疾病诊断，以及探究疾病的起源与病因学均具有重要意义。尽管已有诸多研究对人类微生物组进行了系统表征，但针对非人类哺乳动物皮肤微生物组的认知仍相对匮乏。本研究旨在构建哺乳纲（Mammalia）皮肤微生物组基线数据集，并探究物种、采样地点、卫生状况、身体部位以及生物性别对皮肤微生物组的影响。本研究共采集了187只非人类哺乳动物与20名人类受试者的背部、躯干及大腿内侧皮肤样本，涵盖10个哺乳纲目、38个物种的代表类群。样本来源涵盖本地农场、动物园、家庭饲养以及野生环境中的动物。所有样本均通过V3-V4区16S rRNA基因进行扩增，并采用MiSeq（Illumina）平台完成测序。基于香农指数（Shannon index）分析结果显示，人类皮肤微生物组的多样性显著低于所有其他哺乳纲目（6.54 vs 3.96，p < 0.001）。置换多元方差分析（PERMANOVA）结果显示，对所有样本的微生物群落变异解释度最高的因素为宿主是否为人类（F=37.8，p < 0.001；图2）。通过整合所有样本开展分析，随机森林建模结果显示，人类与动物皮肤样本的正确区分率可达98.51%。本研究是目前规模最大的哺乳动物皮肤微生物组研究项目，同时也是首次针对32个不同物种的皮肤微生物群进行解析的研究。此外，本研究首次证实人类皮肤微生物组不仅区别于其他灵长目（Primates）类群，同时也与本次采样涵盖的全部10个哺乳纲目均存在显著差异。哺乳动物皮肤微生物组的基线数据，可为兽医研究与保护策略制定提供科学依据，同时也为解析哺乳动物的演化历史提供了重要参考。