DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.
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DiTing：从宏基因组和宏转录组数据推断和比较生物地球化学途径的管道
DOI：
10.3389/fmicb.2021.698286
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发表时间：
2021
影响因子：
5.2
通讯作者：
Zhang XH
中科院分区：
文献类型：
--
作者：
Xue CX;Lin H;Zhu XY;Liu J;Zhang Y;Rowley G;Todd JD;Li M;Zhang XH
宏基因组学和元转录组学是揭示自然生态系统中驱动生物地球化学循环的关键微生物和过程的有力方法。致力于从宏基因组/元转录组数据描述生物地球化学途径（例如，二甲基磺基丙酸酯（DMSP），这是一种丰富的有机硫化合物的代谢）的数据库很少见到。此外，一个公认的标准化模型，以估计相对丰度和环境的重要性，从宏基因组和元转录组数据的途径还没有组织的日期。这些限制影响了将关键微生物驱动的生物地球化学过程与环境条件差异准确联系起来的能力。因此，迫切需要一种易于使用的专门工具，可以推断和直观地比较包括DMSP循环在内的非地球化学过程的潜力。为了解决这些问题，我们开发了DiTing，这是一种基于京都基因和基因组百科全书（KEGG）和手动创建的DMSP循环基因数据库的工具包装器，用于一步推断和比较一组给定的宏基因组或元转录组读数之间的生物化学途径。为100多个途径开发了准确和具体的公式，以计算它们的相对丰度。输出报告以文本和图形格式详细说明地球化学途径的相对丰度。将DiTing应用于模拟宏基因组数据，并导致模拟基准基因组数据的遗传特征一致。随后，当应用于热液喷口和塔拉海洋项目的自然宏基因组和宏转录组数据时，DiTing预测的功能概况与环境条件变化相关。DiTing现在可以自信地应用于更广泛的宏基因组和元转录组数据集，并且可以在https://github.com/xuechunxu/DiTing上获得。
Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.
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DOI：
10.1038/ismej.2017.148
发表时间：
2018-01
期刊：
The ISME journal
影响因子：
--
作者：
Eyice Ö;Myronova N;Pol A;Carrión O;Todd JD;Smith TJ;Gurman SJ;Cuthbertson A;Mazard S;Mennink-Kersten MA;Bugg TD;Andersson KK;Johnston AW;Op den Camp HJ;Schäfer H
通讯作者：
Schäfer H
影响因子：
2.2
作者：
Forouzan, Esmaeil;Shariati, Parvin;Yakhchali, Bagher
通讯作者：
Yakhchali, Bagher
影响因子：
5.1
作者：
Fortunato, Caroline S.;Larson, Benjamin;Huber, Julie A.
通讯作者：
Huber, Julie A.
影响因子：
64.8
作者：
Denger, Karin;Weiss, Michael;Schleheck, David
通讯作者：
Schleheck, David
影响因子：
3.5
作者：
Bork, C;Schwenn, JD;Hell, R
通讯作者：
Hell, R