The study of the human gut microbiome is essential in microbiology and infectious diseases as specific alterations in the gut microbiome might be associated with various pathologies, such as chronic inflammatory disease, intestinal infection and colorectal cancer. To identify such dysregulations, several strategies are being used to create a repertoire of the microorganisms composing the human gut microbiome. In this study, we used the “microscomics” approach, which consists of creating an ultrastructural repertoire of all the cell-like objects composing stool samples from healthy donors using transmission electron microscopy (TEM). We used TEM to screen ultrathin sections of 8 resin-embedded stool samples. After exploring hundreds of micrographs, we managed to elaborate ultrastructural categories based on morphological criteria or features. This approach explained many inconsistencies observed with other techniques, such as metagenomics and culturomics. We highlighted the value of our culture-independent approach by comparing our microscopic images to those of cultured bacteria and those reported in the literature. This study helped to detect “minimicrobes” Candidate Phyla Radiation (CPR) for the first time in human stool samples. This “microscomics” approach is non-exhaustive but complements already existing approaches and adds important data to the puzzle of the microbiota.

中文翻译：

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完整序列比较构成人类肠道微生物组的微观对象与经过测序和培养的群落。

人类肠道微生物组的研究对于微生物学和传染病至关重要，因为肠道微生物组的特定改变可能与多种病理相关，例如慢性炎性疾病，肠道感染和结肠直肠癌。为了识别这种失调，正在使用几种策略来创建构成人类肠道微生物组的微生物库。在这项研究中，我们使用了“显微术”方法，该方法包括使用透射电子显微镜（TEM）创建构成健康捐献者粪便样本的所有细胞样物体的超微结构库。我们使用TEM筛选了8个树脂包埋的粪便样品的超薄切片。在探究了数百张显微照片之后，我们设法根据形态学标准或特征精心制定了超微结构类别。该方法解释了其他技术（例如宏基因组学和文化学）观察到的许多不一致之处。通过比较显微镜图像与培养细菌的图像以及文献报道的图像，我们突出了我们的文化独立方法的价值。这项研究有助于人类粪便样品中首次检测到“微型微生物”候选门脉辐射（CPR）。这种“微生物学”方法不是穷尽性的，而是对现有方法的补充，并为微生物群的难题增加了重要数据。这项研究首次在人粪便样品中检测到了“微型微生物”候选门脉辐射（CPR）。这种“微生物学”方法不是穷尽性的，而是对现有方法的补充，并为微生物群的难题增加了重要数据。这项研究首次在人粪便样品中检测到了“微型微生物”候选门脉辐射（CPR）。这种“微生物学”方法不是穷尽性的，而是对现有方法的补充，并为微生物群的难题增加了重要数据。