Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans.
Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans.
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DOI：
10.3791/64393
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发表时间：
2022-09-13
期刊：
影响因子：
--
通讯作者：
Shapira M
中科院分区：
文献类型：
--
作者：
Trang K;Bodkhe R;Shapira M
秀丽隐杆线虫是研究宿主与肠道微生物相互作用的分子机制的一个有用的模型。虽然具有良好特征的细菌或定义的细菌群落的实验可以促进分子机制的分析，但在其天然微生物环境中研究线虫对于探索此类机制的多样性至关重要。与此同时，从野外分离蠕虫并不总是可行的，即使可能，从野外取样也限制了对C. elegans研究。以下方案描述了一种微生物组研究方法，该方法利用堆肥微宇宙在微生物多样性和类似自然的环境中进行实验室内生长。当地来源的土壤可以富含农产品，以使蠕虫饲养的微生物群落多样化，并从中收获，洗涤和表面消毒用于随后的分析。代表性的实验证明了通过用不同的产品丰富普通土壤来调节微生物群落的能力，并进一步证明了在这些不同的环境中饲养的蠕虫组装了与其各自环境不同的相似的肠道微生物组，支持了物种特异性核心肠道微生物组的概念。总的来说，堆肥微生态系统为微生物组研究提供了类似自然的实验室环境，作为合成微生物群落或野生线虫隔离的替代方案。
The nematode Caenorhabditis elegans is emerging as a useful model for studying the molecular mechanisms underlying interactions between hosts and their gut microbiomes. While experiments with well-characterized bacteria or defined bacterial communities can facilitate the analysis of molecular mechanisms, studying nematodes in their natural microbial context is essential for exploring the diversity of such mechanisms. At the same time, the isolation of worms from the wild is not always feasible, and, even when possible, sampling from the wild restricts the use of the genetic toolkit otherwise available for C. elegans research. The following protocol describes a method for microbiome studies utilizing compost microcosms for the in-lab growth in microbially diverse and natural-like environments. Locally sourced soil can be enriched with produce to diversify the microbial communities in which worms are raised and from which they are harvested, washed, and surface-sterilized for subsequent analyses. Representative experiments demonstrate the ability to modulate the microbial community in a common soil by enriching it with different produce and further demonstrate that worms raised in these distinct environments assemble similar gut microbiomes distinct from their respective environments, supporting the notion of a species-specific core gut microbiome. Overall, compost microcosms provide natural-like in-lab environments for microbiome research as an alternative to synthetic microbial communities or to the isolation of wild nematodes.
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作者：
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通讯作者：
Shapira M
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48
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DOI：
10.1016/j.cub.2021.04.046
发表时间：
2021-06-21
期刊：
Current biology : CB
影响因子：
--
作者：
Zhang F;Weckhorst JL;Assié A;Hosea C;Ayoub CA;Khodakova AS;Cabrera ML;Vidal Vilchis D;Félix MA;Samuel BS
通讯作者：
Samuel BS
DOI：
10.1038/s41396-021-00910-4
发表时间：
2021-07
期刊：
The ISME journal
影响因子：
--
作者：
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通讯作者：
Gore J