Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics
Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics
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DOI：
10.1016/j.ijantimicag.2014.04.020
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发表时间：
2014-08-01
影响因子：
10.8
通讯作者：
Raoult, Didier
中科院分区：
文献类型：
--
作者：
Dubourg, Gregory;Lagier, Jean Christophe;Raoult, Didier
目前，人类肠道菌群已通过分子技术得到广泛表征。微生物培养组学（使用 MALDI-TOF 或 16S rRNA 鉴定菌落的大规模培养条件）是细菌培养重生的一部分，由环境微生物学家发起，用于临床微生物学中细胞内细菌的无菌培养设计。对接受大规模抗生素治疗的患者的四份粪便样本进行了培养组学，以与其他依赖培养的研究进行比较，评估其肠道菌群的多样性。还对 V6 区域进行了焦磷酸测序并与对照组进行了比较。还通过显微镜观察后的细菌计数来估计肠道丰富度。总共测试了 77 种培养条件，产生了 32,000 个不同的菌落；鉴定出 190 种细菌，其中 9 种在本研究之前尚未从人类肠道中分离出来，7 种是在人类中新描述的，8 种是全新的。在四个粪便样本中的两个样本中观察到多样性急剧下降，其中抗生素治疗时间延长且不间断。细菌总数总体上保持不变，表明原始种群被取代但规模保持不变。文化和焦磷酸测序生物多样性生物标志物之间的不一致凸显了分子研究的深度偏差。研究的粪便样本显示细菌多样性急剧减少。考虑到肠道中抗生素浓度的变化，物种数量的减少可能与特定细菌（例如乳杆菌属）在上消化道中产生细菌素有关。 (C) 2014 年 Elsevier B.V. 和国际化疗协会。版权所有。
The human gut flora is currently widely characterised using molecular techniques. Microbial culturomics (large-scale culture conditions with identification of colonies using MALDI-TOF or 16S rRNA) is part of the rebirth of bacterial culture that was initiated by environmental microbiologists for the design of axenic culture for intracellular bacteria in clinical microbiology. Culturomics was performed on four stool samples from patients treated with large-scale antibiotics to assess the diversity of their gut flora in comparison with other culture-dependent studies. Pyrosequencing of the V6 region was also performed and was compared with a control group. Gut richness was also estimated by bacterial counting after microscopic observation. In total, 77 culture conditions were tested and 32,000 different colonies were generated; 190 bacterial species were identified, with 9 species that had not been isolated from the human gut before this study, 7 newly described in humans and 8 completely new species. A dramatic reduction in diversity was observed for two of the four stool samples for which antibiotic treatment was prolonged and uninterrupted. The total number of bacteria was generally preserved, suggesting that the original population was replaced but was sustained in size. Discordances between culture and pyrosequencing biodiversity biomarkers highlight the depth of bias of molecular studies. Stool samples studied showed a dramatic reduction in bacterial diversity. Considering the variable antibiotic concentration in the gut, this reduction in the number of species is possibly linked to the production of bacteriocin in the upper digestive tract by specific bacteria, such as Lactobacillus spp. (C) 2014 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.