Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing.
Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing.
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利用宏基因组文库生成和鸟枪法测序揭示波多黎各科阿莫温泉的微生物和功能多样性。
DOI：
10.1016/j.gdata.2016.12.010
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发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Ríos-Velázquez,Carlos
中科院分区：
文献类型：
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作者：
Padilla-DelValle,Ricky;Morales-Vale,LuisR;Ríos-Velázquez,Carlos
在波多黎各，科阿莫温泉 (ThS) 的微生物多样性从未使用宏基因组学进行过研究。我们研究的重点是从波多黎各 Coamo 的 ThS 中生成宏基因组文库，并探索微生物和功能多样性。 ThS 水域的宏基因组文库是通过直接 DNA 分离生成的。高分子量 (40 kbp) DNA 经过末端修复、电洗脱并连接至 fosmid 载体 (pCCFOS1)；然后使用T1噬菌体转入大肠杆菌EPI300-T1R。该文库由大约 6000 个克隆组成，其中 90% 含有宏基因组 DNA。下一代测序技术 (Illumina MiSeq) 用于处理 ThS 宏基因组。去除克隆载体后，使用 MG-RAST 在线服务器对 122,026 个大小为 33.10 Mbps、G + C 含量为 64% 的序列进行注释和分析。细菌是最丰富的结构域（95.84%），其次是未知序列（2.28%）、病毒（1.67%）、真核生物（0.15%）和古细菌（0.01%）。最丰富的门是变形菌门(95.03%)，其次是未鉴定门(2.28%)、未分类病毒门(1.74%)、厚壁菌门(0.20%)和放线菌门(0.18%)。最丰富的物种是大肠杆菌、食萘极单胞菌、Albidiferax ferrireducens 和 Acidvoraxsp。子系统功能分析表明，20% 的基因属于转座元件，10% 属于基于聚类的子系统，8% 属于辅助因子的产生。使用 NOG 注释进行的功能分析表明，82.79% 的蛋白质特征描述很差，表明新的微生物功能的可能性以及潜在的生物医学和生物技术应用。宏基因组数据以登录号 SAMN06131862 存入 NCBI 数据库。
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced intoEscherichia coliEPI300-T1Rusing T1 bacteriophages. The library consisted of approximately 6000 clones, 90% containing metagenomic DNA. Next-Generation-Sequencing technology (Illumina MiSeq) was used to process the ThS metagenome. After removing the cloning vector, 122,026 sequences with 33.10 Mbps size and 64% of G + C content were annotated and analyzed using the MG-RAST online server. Bacteria showed to be the most abundant domain (95.84%) followed by unidentified sequences (2.28%), viruses (1.67%), eukaryotes (0.15%), and archaea (0.01%). The most abundant phyla wereProteobacteria(95.03%), followed by unidentified (2.28%), unclassified from viruses (1.74%),Firmicutes(0.20%) andActinobacteria(0.18%). The most abundant species wereEscherichia coli,Polaromonas naphthalenivorans,Albidiferax ferrireducensandAcidovoraxsp. Subsystem functional analysis showed that 20% of genes belong to transposable elements, 10% to clustering-based subsystems, and 8% to the production of cofactors. Functional analysis using NOG annotation showed that 82.79% of proteins are poorly characterized indicating the possibility of novel microbial functions and with potential biomedical and biotechnological applications. Metagenomic data was deposited into the NCBI database under the accession number SAMN06131862.