Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, USA
Appl Environ Microbiol. 2020 Jul 2;86(14). doi: 10.1128/AEM.00489-20.
The gut microbiome has far-reaching effects on host organism health, so understanding the processes that underlie microbial community assembly in the developing gut is a current research priority. Here, a holothurian (also known as sea cucumber; phylum Echinodermata) host is explored as a promising model system for studying the assembly of the gut microbiome. Holothurians have a unique capacity for evisceration (expulsion of the internal organs), followed by rapid regeneration of the gut, decoupling host ontogeny from gut tissue development and permitting experimental manipulation of the gut microbiome in mature host individuals. Here, evisceration was induced in the sea cucumber , and regenerating stomach and intestine microbiomes were characterized before and on days 0, 13, 17, and 20 after evisceration using Illumina sequencing of 16S rRNA genes. Regenerating stomach and intestine tissues had microbial communities significantly different from those of mature tissues, with much higher alpha diversity and evenness of taxa in regenerating tissues. Despite immersion in a diverse pool of sediment and seawater microbes in flowthrough seawater aquaria, regenerating gut microbiomes differed at each stage of regeneration and displayed a highly similar community structure among replicates, providing evidence for deterministic host selection of a specific microbial consortium. Moreover, regenerating gut tissues acquired a microbiome that likely conferred energetic and immune advantages to the sea cucumber host, including microbes that can fix carbon and degrade invading pathogens. The gut microbiome is pertinent to many aspects of animal health, and there is a great need for natural but tractable experimental systems to examine the processes shaping gut microbiome assembly. Here, the holothurian (sea cucumber) was explored as an experimental system to study microbial colonization in the gut, as individuals have the ability to completely eviscerate and rapidly regenerate their digestive organs. After induced evisceration, microbial community assembly was characterized over 20 days in regenerating animals. This study demonstrated that colonization of the sea cucumber gut was deterministic; despite immersion in a diverse consortium of environmental microbes, a specific subset of microbes proliferated in the gut, including taxa that likely conferred energetic and immune advantages to the host. Sea cucumbers have the potential to revolutionize our understanding of gut microbiome assembly, as rapid and repeatable gut tissue regeneration provides a promising and tractable experimental system.
肠道微生物组对宿主的健康有着深远的影响，因此，了解微生物群落在发育中的肠道中组装的基础过程是当前的研究重点。在这里，我们探索了一种海参（也称为海参；棘皮动物门）作为研究肠道微生物组组装的有前途的模型系统。海参具有独特的内脏排空（排出内部器官）能力，随后肠道迅速再生，使宿主个体的发育与肠道组织的发育脱钩，并允许对成熟宿主个体的肠道微生物组进行实验操作。在这里，通过诱导海参内脏排空，并使用 Illumina 16S rRNA 基因测序，在排空后 0、13、17 和 20 天，对再生的胃和肠道微生物组进行了特征描述。与成熟组织相比，再生的胃和肠道组织具有明显不同的微生物群落，再生组织中的分类单元具有更高的α多样性和均匀度。尽管在流动海水水族馆中浸入了各种沉积物和海水微生物中，但在每个再生阶段，再生肠道微生物组都有所不同，并且在重复样本中显示出高度相似的群落结构，这为宿主对特定微生物联合体的确定性选择提供了证据。此外，再生肠道组织获得了一种可能赋予海参宿主能量和免疫优势的微生物组，包括能够固定碳和降解入侵病原体的微生物。肠道微生物组与动物健康的许多方面都有关联，因此迫切需要自然但易于处理的实验系统来检查塑造肠道微生物组组装的过程。在这里，我们探索了海参（海参）作为研究肠道微生物定植的实验系统，因为个体具有完全排空和快速再生消化器官的能力。在诱导内脏排空后，在 20 天内对再生动物的微生物群落组装进行了特征描述。这项研究表明，海参肠道的定植是确定性的；尽管浸入了各种环境微生物的联合体中，但肠道中仍有特定的微生物亚群大量繁殖，包括可能赋予宿主能量和免疫优势的类群。海参有可能彻底改变我们对肠道微生物组组装的理解，因为快速且可重复的肠道组织再生提供了一个有前途的、易于处理的实验系统。
