Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.

中文翻译：

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富含文化的群落分析提高了脊椎动物肠道微生物群的分辨率

脊椎动物拥有包含数百种细菌的肠道微生物群落，其中大部分从未在实验室中培养或分离过。缺乏来自脊椎动物肠道微生物群的培养代表限制了对这些群落的描述和实验询问。在这里，我们表明，在栅栏蜥蜴、家鼠、黑猩猩和人类的肠道微生物群中，通过不依赖于培养的测序检测到的超过 50% 的细菌属的代表是在混合培养物中从接种在九个面板上的冷冻粪便样本中回收的单一生长条件下的培养基。此外，培养捕获的 > 100 个稀有细菌属被不依赖于培养物的测序所忽视，使检测到的细菌序列变异总数增加了一倍以上。我们的方法从 23 个以前未培养的候选细菌属中恢复了代表，其中 12 个未通过培养非依赖性测序检测到。结果确定了肠道微生物群的不加选择和选择性培养策略，这些策略可在脊椎动物物种间复制。对来自野生黑猩猩的 161 个细菌菌落进行分离，然后进行全基因组测序，从而发现了与人类机会性病原体密切相关的候选新物种艰难梭菌和Hungatella hathewayi。这项研究建立了培养方法，可以改善库存并促进从多种脊椎动物物种中分离肠道微生物群成分。