细菌培养是一套从复杂的微生物生态系统中分离和鉴定活细菌的技术。尽管它有可能彻底改变微生物组研究,由于其劳动密集型性质,细菌培养物应用于人类肠道微生物组研究具有重大挑战。因此,我们建立了一种简化的培养方法,以最少的培养条件进行粪便样品预培养。我们基于16SrRNA基因扩增子分析评估了非选择性培养基候选物在30天孵育期内维持微生物多样性的适用性。随后,我们应用了四种培养条件(有氧/厌氧环境下的两种预孵育培养基),从8个健康人的粪便样本中大规模分离肠道细菌。我们鉴定了8141个分离株,分为263种细菌,包括12个新的候选物种。我们对培养效率的分析表明,在每种条件下,7天的有氧和10天的厌氧培养捕获了大约91%和95%的已识别物种。分别,当选择的预孵育培养基组合时,具有协同作用。此外,与16SrRNA基因扩增子测序结果相比,我们的文化遗传学发现扩大了肠道微生物多样性的覆盖范围.总之,这项研究证明了流线型文化方法从人类粪便样本中有效分离肠道细菌的潜力。这种方法可能为在人类肠道微生物组研究中更广泛地采用文化遗传学铺平道路。最终导致对这个复杂的微生物生态系统的更全面的了解。
Bacterial culturomics is a set of techniques to isolate and identify live bacteria from complex microbial ecosystems. Despite its potential to revolutionize microbiome research, bacterial culturomics has significant challenges when applied to human gut microbiome studies due to its labor-intensive nature. Therefore, we established a streamlined culturomics approach with minimal culture conditions for stool sample preincubation. We evaluated the suitability of non-selective
medium candidates for maintaining microbial diversity during a 30-day incubation period based on 16S rRNA gene amplicon analysis. Subsequently, we applied four culture conditions (two preincubation media under an aerobic/anaerobic atmosphere) to isolate gut bacteria on a large scale from eight stool samples of healthy humans. We identified 8141 isolates, classified into 263 bacterial species, including 12 novel species candidates. Our analysis of cultivation efficiency revealed that seven days of aerobic and ten days of anaerobic incubation captured approximately 91% and 95% of the identified species within each condition, respectively, with a synergistic effect confirmed when selected preincubation media were combined. Moreover, our culturomics findings expanded the coverage of gut microbial diversity compared to 16S rRNA gene amplicon sequencing results. In conclusion, this study demonstrated the potential of a streamlined culturomics approach for the efficient isolation of gut bacteria from human stool samples. This approach might pave the way for the broader adoption of culturomics in human gut microbiome studies, ultimately leading to a more comprehensive understanding of this complex microbial ecosystem.