Among Live and Dead Bacteria, the Optimization of Sample Collection and Processing Remains Essential in Recovering Gut Microbiota Components
Among Live and Dead Bacteria, the Optimization of Sample Collection and Processing Remains Essential in Recovering Gut Microbiota Components
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DOI：
10.3389/fmicb.2019.01606
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发表时间：
2019-07-10
影响因子：
5.2
通讯作者：
Khalil, Jacques Bou
中科院分区：
文献类型：
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作者：
Bellali, Sara;Lagier, Jean-Christophe;Khalil, Jacques Bou
人体肠道微生物群在人体健康中起着重要作用。培养和培养肠道微生物在微生物学中仍然至关重要。文化组学方法与测序策略相结合，为肠道微生物群组分的研究提供了新的见解。然而，我们离描述所有的微生物还很远。回收尽可能多的细菌涉及许多因素。最重要的因素之一是样品的制备和保存。本工作的目的是评估三种不同类型的粪便样本调理，主要是研究空气中的氧气对细菌的生存力和培养能力的影响。使用非培养方法（流式细胞术）和培养依赖性方法（平板接种技术）对来自8个不同健康个体的粪便样本进行定量分析。我们发现，培养的细菌达到50%的产量时，样品暴露于氧气为120分钟，没有任何保护剂的培养基，而在抗氧化剂的存在下，可培养性的百分比增加到67%。更重要的是，当样品暴露于氧气中小于2min时，结合厌氧室下的工作，未发现两种计数技术之间的不一致性，可培养性提高到87%。我们的研究证实了样品调节对保持样品中细菌活力的重要性，特别是对于氧敏感的肠道细菌。
The human gut microbiota plays an important role in human health. Accessing and culturing the gut microbes remains critical in microbiology. The culturomics approach, combined with sequencing strategies, provides new insights in the study of gut microbiota components. However, we are still far from having described all the microbes. Many factors are involved in recovering as much bacteria as possible. One of the most important factors is sample preparation and conservation. The aim of the present work was to evaluate three different types of stool sample conditioning by mainly studying the effect of atmospheric oxygen on bacterial viability and culturability. Quantitative analysis of fecal samples from eight different healthy individuals was carried out using a culture-independent method (flow cytometry) and a culture-dependent method (plating technique). We found that the cultured bacteria reached a 50% yield when the samples were exposed to oxygen for 120 min without any protectant medium, while the percentage of culturability increased to 67% in the presence of antioxidants. More importantly, when samples were exposed to oxygen for less than 2 min, combined with the work under the anaerobic chamber, no discordance was found between the two counting techniques and the culturability increased to 87%. Our study confirmed the importance of sample conditioning to preserve the bacterial viability in samples, especially for oxygen-sensitive intestinal bacteria.