Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis-associated bacteria emerge. Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later. Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development.

中文翻译：

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早期生活中的肠道营养不良与鸵鸟的青少年死亡率有关

脊椎动物的肠道微生物群落失衡（营养不良）与多种胃肠道疾病和自身免疫性疾病有关。但是，尚不清楚哪些分类单元与肠道营养不良有关，是否在个体发育过程中特定的肠道区域或特定时间段更易感。尽管人们越来越意识到肠道菌群对健康的重要性，但我们在非模式生物中对这一过程的了解却很少。在这里，我们检查了一只长寿的，具有高幼体死亡率的鸵鸟（鸵鸟（Struthio camelus））在胃肠道不同部位营养不良期间微生物组中发生的变化。我们评估了生命的前三个月内死于可疑小肠结肠炎的68名个体（患病者）的回肠，盲肠和结肠的16S rRNA基因组成，被安乐死作为年龄匹配的对照组的50名健康个体。我们将这些数据与纵向环境和粪便采样相结合，以确定潜在的病原细菌来源，并阐明与发育不良相关的细菌出现的发展阶段。在胃肠道的所有三个区域中，患病个体的微生物α多样性大大降低，并且其微生物β多样性与对照个体大不相同。在回肠的所有年龄段中，多样性低下与疾病之间的明确关系是一致的，但随着盲肠和结肠年龄的增加，这种关系逐渐减弱。一些分类单元与死亡率有关（肠杆菌科，Peptostreptococcaceae，卟啉单胞菌科，梭状芽孢杆菌），而其他一些分类则与健康有关（Lachnospiraceae，Ruminococcaceae，丹参科，Turicibacter，Roseburia）。环境样品没有证据表明食物，水或土壤基质中存在与营养不良相关的细菌。取而代之的是，重复的粪便采样显示病原体在孵化后不久就已经存在，并且在微生物多样性低的个体中扩散，导致数周后死亡率很高。查明新生儿病态交感神经的起源以及随后影响多样化肠道菌群建立的因素，可能是了解营养不良和宿主发育的关键。重复的粪便采样显示，病原体在孵化后不久就已经存在，并且在微生物多样性低的个体中扩散，导致数周后死亡率很高。识别新生儿病态交感神经的起源以及随后影响多元化肠道菌群建立的因素，可能是了解营养不良和宿主发育的关键。重复的粪便采样表明，病原菌在孵化后不久就已经存在，并且在微生物多样性低的个体中扩散，导致数周后死亡率很高。查明新生儿病态交感神经的起源以及随后影响多样化肠道菌群建立的因素，可能是了解营养不良和宿主发育的关键。