Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus
Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus
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肠道微生物群对食源性细菌的反应取决于鱼类生长速度：养殖暗纹东方鲀幼鱼的快照调查
DOI：
10.1101/2020.08.24.265785
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发表时间：
2020-08
影响因子：
5.7
通讯作者：
Zhe Zhao
中科院分区：
文献类型：
--
作者：
Xingkun Jin;Ziwei Chen;Yan Shi;Jian-Fang Gui;Zhe Zhao
了解控制肠道微生物群聚集的生态过程成为更可持续水产养殖的必要先决条件。在这里，我们使用16 S rRNA扩增子测序来表征养殖暗纹东方鲀的后肠微生物群。与水和沉积物相比，肠道微生物群具有较低的α多样性，较大的β分散性和较高的平均16 S rRNA拷贝数，但远低于饲料。SourceTracker预测了肠道微生物群中饲料的显著来源特征。此外，不同程度的饲料相关细菌对肠道微生物群的组成，功能和系统发育多样性的影响。与此同时，在缓慢生长的河豚中观察到物种丰富度和饲料来源比例的显著增加，这意味着在饲料细菌干扰下肠道微生物群的稳定性降低。应用定量生态学分析框架，确定了群落迁移的生态过程。在较低程度的饲料干扰下，同质选择和扩散限制在很大程度上有助于群落的稳定性和宿主间的局部变异。虽然随着饲料干扰程度的增加，可变选择会导致肠道微生物群内的相互作用增强，从而导致群落不稳定和转变。总而言之，我们的研究结果说明了河豚肠道微生物群中明确的多样性-功能关系，并且它暗示了食源性细菌与宿主生长速率之间的强相关性。这些结果提供了一个新的见解河豚鱼和其他经济上重要的鱼类水产养殖，以及更好地了解宿主微生物在脊椎动物胃肠道的相互作用。环境细菌对鱼类肠道微生物群有很大的影响，但人们对鱼类在哪里获得肠道共生体以及肠道微生物群如何对环境细菌做出反应知之甚少。通过群落分析和源追踪的综合分析，我们发现饲料相关细菌可以对河豚肠道微生物区系产生强烈的干扰。结果，观察到缓慢生长河豚肠道微生物群的组成和功能的显著改变，这可能与宿主的生理条件如胃排空率相关。我们的研究结果强调了饲料和肠道微生物群之间的复杂联系，并强调了在得出微生物群比较分析结论之前解决饲料来源信号的重要性。我们的研究结果提供了一个更深入的了解河豚鱼和其他经济上重要的鱼类水产养殖，并有进一步的影响，以提高理解宿主微生物在脊椎动物胃肠道的相互作用。
Understanding the ecological processes in controlling the assemblage of gut microbiota becomes an essential prerequisite for a more sustainable aquaculture. Here we used 16S rRNA amplicon sequencing to characterize the hindgut microbiota from cultured obscure puffer Takifugu obscurus. The gut microbiota is featured with lower alpha-diversity, greater beta-dispersion and higher average 16S rRNA copy numbers comparing to water and sediment, but far less so to feed. SourceTracker predicted a notable source signature from feed in gut microbiota. Furthermore, effect of varying degrees of feed-associated bacteria on compositional, functional and phylogenetic diversity of gut microbiota were revealed. Coincidently, considerable increase of species richness and feed source proportions both were observed in slow growth fugu, implying a reduced stability in gut microbiota upon bacterial disturbance from feed. Moreover, quantitative ecological analytic framework was applied and the ecological processes underlying such community shift were determined. In the context of lower degree of feed disturbance, homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts. Whilst with the degree of feed disturbance increased, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Altogether, our findings illustrated a clear diversity-function relationships in fugu gut microbiota, and it has implicated in a strong correlation between feed-borne bacteria and host growth rate. These results provide a new insight into aquaculture of fugu and other economically important fishes, as well as a better understanding of host-microbe interactions in the vertebrate gastrointestinal tract. IMPORTANCE Environmental bacteria has a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon fugu gut microbiota. As a result, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, which is potentially correlated with the host physiological condition such as gastric evacuation rate. Our findings emphasized the intricate linkage between feed and gut microbiota, and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes, and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.
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影响因子：
2.4
作者：
M. Ruzauskas;I. Klimienė;J. Armalytė;E. Bartkienė;R. Šiugždinienė;Jūratė Skerniškytė;R. Krasauskas;E. Sužiedėlienė
通讯作者：
M. Ruzauskas;I. Klimienė;J. Armalytė;E. Bartkienė;R. Šiugždinienė;Jūratė Skerniškytė;R. Krasauskas;E. Sužiedėlienė
影响因子：
16.6
作者：
Cazares, Adrian;Moore, Matthew P.;Winstanley, Craig
通讯作者：
Winstanley, Craig
影响因子：
4.6
作者：
Giatsis C;Sipkema D;Smidt H;Heilig H;Benvenuti G;Verreth J;Verdegem M
通讯作者：
Verdegem M
影响因子：
9.8
作者：
Bordenstein SR;Theis KR
通讯作者：
Theis KR
影响因子：
4.9
作者：
T. Prest;Abigail K. Kimball;Jordan G. Kueneman;V. McKenzie
通讯作者：
T. Prest;Abigail K. Kimball;Jordan G. Kueneman;V. McKenzie