灵活的高通量培养方案,用于评估个体肠道微生物群对饮食、药物和宿主相关因素的反应。

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-03-12 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae035
Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin
{"title":"灵活的高通量培养方案,用于评估个体肠道微生物群对饮食、药物和宿主相关因素的反应。","authors":"Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin","doi":"10.1093/ismeco/ycae035","DOIUrl":null,"url":null,"abstract":"<p><p>The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of <i>ex vivo</i> cultures and donor microbiota while limiting the bloom of <i>Enterobacteriaceae</i>. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported <i>in vivo.</i> This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1000,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982853/pdf/","citationCount":"0","resultStr":"{\"title\":\"A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.\",\"authors\":\"Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin\",\"doi\":\"10.1093/ismeco/ycae035\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of <i>ex vivo</i> cultures and donor microbiota while limiting the bloom of <i>Enterobacteriaceae</i>. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported <i>in vivo.</i> This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.</p>\",\"PeriodicalId\":73516,\"journal\":{\"name\":\"ISME communications\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.1000,\"publicationDate\":\"2024-03-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982853/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ISME communications\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/ismeco/ycae035\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q1\",\"JCRName\":\"ECOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ISME communications","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/ismeco/ycae035","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q1","JCRName":"ECOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

厌氧培养粪便微生物群是研究肠道微生物群落如何对特定肠道条件和干扰做出反应的一种很有前景的方法。在此,我们介绍一种使用 96 深孔板培养粪便衍生肠道微生物群的灵活方案。我们的方案旨在弥补厌氧室高通量培养的不足。我们描述了气相对培养基化学和微生物生理学的影响,并引入了模块化培养基制备流程,以便同时测试多种条件。此外,我们还确定了一种培养基配方,既能最大限度地提高体内外培养物和供体微生物群的成分相似性,又能限制肠杆菌的繁殖。最后,我们验证了该方案,证明培养的粪便微生物群对膳食纤维(抗性糊精、可溶性淀粉)和药物(环丙沙星、5-氟尿嘧啶)的反应与体内报道的相似。这种高通量培养方案有望促进依赖培养的研究,加快发现肠道微生物群-饮食-药物-宿主之间的相互作用,并为以微生物群为中心的个性化干预铺平道路。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.

The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
自引率
0.00%
发文量
0
期刊最新文献
Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession. Introduction into natural environments shifts the gut microbiome of captivity-raised filter-feeding bivalves. Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments. Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis. Rhizospheric miRNAs affect the plant microbiota.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1