The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics
The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics
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DOI：
10.1007/s10096-012-1787-3
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发表时间：
2013-05-01
影响因子：
4.5
通讯作者：
Raoult, D.
中科院分区：
文献类型：
--
作者：
Dubourg, G.;Lagier, J. C.;Raoult, D.
肠道微生物群由每克粪便10（10）个细菌组成。许多抗生素治疗方案会导致肠道植物群的多样性和丰富度降低。我们分析了一个病人的粪便样本收集耐药结核分枝杆菌治疗，最终死于肺炎链球菌肺炎10个月后。我们进行了显微镜观察，使用了70种培养条件（微生物培养组学），并通过基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF）和16 S rRNA扩增和测序、焦磷酸测序以及18 S rRNA扩增和克隆测序进行鉴定。电子显微镜和光学显微镜观察显示存在酵母菌，但没有观察到细菌物种。通过培养，只鉴定出39种细菌，包括一种新的物种，以及三种以前在人类肠道中未观察到的物种。焦磷酸测序仅显示18种细菌类型，检测到的细菌种类数量低于培养技术。只有两种类型的研究与文化组学重叠。此外，通过对真核生物的特异性分子检测，还发现了3种真菌。我们第一次在肠道细菌负荷低的患者中回收了比不可培养的细菌种类更多的可培养细菌种类，证明了焦磷酸测序的深度偏倚。我们认为该患者肠道菌群的荒漠化是全身菌群的反映，可能是导致S.肺炎。这一发现表明，在使用广谱抗生素治疗患者时应谨慎，并应采取预防措施，以避免侵入性感染。
Gut microbiota consists of 10(10) bacteria per gram of stool. Many antibiotic regimens induce a reduction in both the diversity and the abundance of the gut flora. We analyzed one stool sample collected from a patient treated for drug-resistant Mycobacterium tuberculosis and who ultimately died from pneumonia due to a Streptococcus pneumoniae 10 months later. We performed microscopic observation, used 70 culture conditions (microbial culturomics) with identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA amplification and sequencing, pyrosequencing, and 18S rRNA amplification and clone sequencing. Electron and optical microscopic observations revealed the presence of yeast, but no bacterial species were observed. By culture, only 39 bacterial species were identified, including one new species, as well as three species that have not been previously observed in the human gut. The pyrosequencing showed only 18 phylotypes, detecting a lower number of bacterial species than the culture techniques. Only two phylotypes overlapped with culturomics. In contrast, an amount of chloroplasts was found. Additionally, specific molecular eukaryote detection found three fungal species. We recovered, for the first time, more cultivable than non-cultivable bacterial species in a patient with a low bacterial load in the gut, demonstrating the depth bias of pyrosequencing. We propose that the desertification of gut microbiota in this patient is a reflection of the total body microbiota and may have contributed to the invasive infection of S. pneumoniae. This finding suggests that caution should be applied when treating patients with broad-spectrum antibiotics, and preventive measures should be taken in order to avoid invasive infection.