Data for: The source of microbial transmission influences niche colonization and microbiome development

Early life microbial colonizers shape and support the immature vertebrate immune system. Microbial colonization relies on the vertical route via parental provisioning and the horizontal route via environmental contribution. Vertical transmission is mostly a maternal trait making it hard to determine the source of microbial colonization in order to gain insight in the establishment of the microbial community during crucial development stages. The evolution of unique male pregnancy in pipefishes and seahorses enables the disentanglement of both horizontal and vertical transmission, but also facilitates the differentiation of maternal vs. paternal provisioning ranging from egg development, to male pregnancy and early juvenile development. Using 16s rRNA amplicon sequencing and source-tracker analyses, we revealed how the distinct origins of transmission (maternal, paternal & horizontal) shaped the juvenile internal and external microbiome establishment in the broad-nosed pipefish Syngn..., Sample collection: 
Adult Syngnathus typhle were caught in Orth on Fehmarn (54°26'N 11°02'E) and brought to our aquaria facilities at GEOMAR Kiel, for breeding. Fish were kept in a flow-through aquaria system at 18°C with 18h day/6h night light regime and fed with live Artemia salina and frozen Mysidae spp. twice a day. In each aquarium three males and three females were kept together to allow mating. After the onset of breeding, fish were randomly sampled, regarding their sex and gravity stages, on five days between the end of May 2019 and end of June 2019. We sampled 89 mature S. typhle (18 females, 16 early pregnant males, 19 mid pregnant males, 18 late pregnant males and 19 non-pregnant males). Pregnancy stages (early, mid and late pregnancy) were defined according to (56). In order to detect microbial transfer from parental gonads and pouch tissue to the juveniles, we sampled testes and endometrial inner pouch lining tissue as well as fertilized larvae from the three pregnancy stag...,

生命早期的微生物定殖者可塑造并支撑未成熟脊椎动物的免疫系统。微生物定殖依赖于通过亲本供给实现的垂直传播途径，以及通过环境贡献达成的水平传播途径。垂直传播大多属于母系特性，这使得研究者难以明确微生物定殖的来源，从而难以深入理解关键发育阶段微生物群落的构建过程。海龙鱼和海马所演化出的独特雄性妊娠特性，不仅能够厘清水平与垂直传播路径，还有助于区分从卵子发育、雄性妊娠到幼体早期发育各个阶段的母系与父系供给差异。本研究通过16S核糖体RNA（16S rRNA）扩增子测序与源追踪（source-tracker）分析，揭示了不同传播来源（母系、父系与水平途径）如何塑造宽吻海龙鱼（*Syngn*...）幼体的体内与体外微生物群落构建过程。

样本采集：
实验用成年粗吻海龙（*Syngnathus typhle*）捕获于费马恩岛的Orth海域（北纬54°26'，东经11°02'），随后被转运至基尔GEOMAR海洋研究中心的水族养殖设施中开展繁育实验。实验鱼饲养于流通式水族系统中，水温维持18℃，光照周期设置为18小时光照/6小时黑暗，每日投喂两次鲜活卤虫（*Artemia salina*）与冻存的糠虾科（*Mysidae* spp.）生物。每个水族箱内饲养3尾雄性与3尾雌性个体，以保障自然交配。繁殖活动启动后，研究团队于2019年5月末至6月末的5个采样日中，按照个体性别与妊娠阶段对实验鱼进行随机采样。本次共采集89尾成熟粗吻海龙样本，其中雌性18尾、早期妊娠雄性16尾、中期妊娠雄性19尾、晚期妊娠雄性18尾以及非妊娠雄性19尾。妊娠阶段（早期、中期与晚期）的划分依据参考文献[56]。为检测亲本性腺与育儿袋组织向幼体的微生物传递过程，我们从三个妊娠阶段的个体中采集了精巢、育儿袋内层内膜组织以及受精幼体样本……