Strategies to improve reference databases for soil microbiomes.
Strategies to improve reference databases for soil microbiomes.
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DOI：
10.1038/ismej.2016.168
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发表时间：
2017-04
期刊：
影响因子：
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通讯作者：
Howe A
中科院分区：
文献类型：
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作者：
Choi J;Yang F;Stepanauskas R;Cardenas E;Garoutte A;Williams R;Flater J;Tiedje JM;Hofmockel KS;Gelder B;Howe A
土壤中的微生物种群对我们的生活至关重要。土壤微生物组有助于种植食物、滋养和保护植物，同时还提供重要的生态服务，例如侵蚀防护、水过滤和气候调节。我们越来越意识到巨大的微生物多样性对土壤健康具有重要作用；然而，尽管我们付出了巨大努力从土壤中分离出微生物，但我们只获得了土壤生物多样性的一小部分。即使采用新的细胞分离技术，仍有 1-50% 的土壤物种被耕种（Janssen 等人，2002 年；Van Pham 和 Kim，2012 年）。宏基因组测序加速了我们对环境微生物的获取，使我们能够表征土壤群落，而无需首先培养分离株。然而，我们注释和表征检索到的基因的能力取决于信息丰富的参考基因或基因组数据库的可用性。当前的基因组数据库不能代表土壤微生物组。对现有数据库的贡献很大程度上源于人类健康和生物技术研究工作，并且可能会误导源自土壤微生物组的基因注释（例如，与土壤中的生命明显不相容的注释）。土壤微生物学家并不是第一个面临参考数据库有限问题的人。 NIH 人类微生物组计划 (HMP) 认识到对精心策划的参考基因组数据集的迫切需求
Microbial populations in the soil are critical in our lives. The soil microbiome helps to grow our food, nourishing and protecting plants, while also providing important ecological services such as erosion protection, water filtration and climate regulation. We are increasingly aware of the tremendous microbial diversity that has a role in soil heath; yet, despite significant efforts to isolate microbes from the soil, we have accessed only a small fraction of its biodiversity. Even with novel cell isolation techniques, o1–50% of soil species have been cultivated (Janssen et al., 2002; Van Pham and Kim, 2012). Metagenomic sequencing has accelerated our access to environmental microbes, allowing us to characterize soil communities without the need to first cultivate isolates. However, our ability to annotate and characterize the retrieved genes is dependent on the availability of informative reference gene or genome databases.The current genomic databases are not representative of soil microbiomes. Contributions to the existing databases have largely originated from human health and biotechnology research efforts and can mislead annotations of genes originating from soil microbiomes (for example, annotations that are clearly not compatible with life in soil). Soil microbiologists are not the first to face the problem of a limited reference database. The NIH Human Microbiome Project (HMP) recognized the critical need for a well-curated reference genome dataset