死细菌——人类肠道菌群的培养盲区?
创作:周旸 审核:周旸 03月31日
  • 将来自8个健康人的粪便细菌菌群,通过荧光激活细胞分选技术(FACS)分为活细菌、受损细菌和死亡细菌,与58种培养条件下的培养组检测结果比对;
  • FACS结合16S扩增子测序检测,发现了1020 个细菌OTUs,其中735个OTUs来自活细菌,涵盖42%已知菌种,单个人粪便菌群中87%的细菌来自于该735个OTUs;
  • 培养组方法分离出495株细菌菌株;
  • 肠道中存在无法培养菌株的原因,不仅是培养条件受限,也可能是菌株丰度低,或者菌体在远端肠道死亡、受损。
主编推荐语
周旸
尽可能多地分离培养肠道细菌,对于研究肠道微生态以及进行有效干预具有重要意义;但是受限于目前技术条件,人体肠道中存在大量不可培养细菌菌株。Gut Microbes近期发表一项研究,通过联合使用荧光激活细胞分选技术、高通量测序和培养组技术,发现培养技术的局限性并不是部分菌株难以培养的唯一原因,标本的来源很可能对肠道菌株的活性具有重要影响。该研究不仅建立了宏基因组-培养组联用的新型分析方法,也为肠道菌株培养技术提供了理论和技术参考。
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Gut Microbes [IF:7.74]

Running after ghosts: are dead bacteria the dark matter of the human gut microbiota?

暗夜追灵:死去的细菌是人类肠道菌群的暗物质吗?

10.1080/19490976.2021.1897208

03-23, Article

Abstract & Authors:展开

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The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract. We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics. We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured. Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.

First Authors:
Sara Bellali

Correspondence Authors:
Didier Raoult,Jacques Bou Khalil

All Authors:
Sara Bellali,Jean-Christophe Lagier,Matthieu Million,Hussein Anani,Gabriel Haddad,Rania Francis,Edmond Kuete Yimagou,Saber Khelaifia,Anthony Levasseur,Didier Raoult,Jacques Bou Khalil

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