The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization–time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.

中文翻译：

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人类微生物群文化的最新进展：新的兴趣和策略

过去 5 年见证了肠道微生物群研究的转折点，依赖培养的肠道微生物群研究方法重生。已经开发出高通量方法来研究细菌多样性的培养条件，旨在通过在厌氧工作站中使用 YCFA（酵母提取物、酪蛋白水解物、脂肪酸）和岐阜厌氧培养基等富培养基以及培养基来模拟肠道环境富含瘤胃、血液和共培养物，以模拟肠道微生物群的共生关系。其他培养条件针对细菌物种的表型和代谢特征，以促进它们的分离。已有的技术，如新一代测序和流式细胞术，也已被用于开发创新方法，以分离以前未培养的细菌或探索感兴趣样本的生存能力。这些技术已应用于隔离 CPR（候选门辐射）以及其他更经典的方法。与细菌培养相比，产甲烷古菌和真菌培养提出了不同的挑战。通过共培养系统改进可用于古菌生长的系统的努力已经取得成功。对于更容易从人类微生物群中分离出来的真菌，挑战在于分离菌的鉴定，这已经通过将基质辅助激光解吸电离 - 飞行时间质谱技术应用于真菌来解决。细菌疗法代表了未来医学中不可忽视的途径，以纠正生态失调并改善健康或对治疗的反应。尽管在过去 5 年中取得了长足的进步，但仍需继续努力在细菌培养方面继续破译宏基因组学的暗物质，尤其是 CPR，并将这些方法扩展到古细菌和真菌。