PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes
Abstract Background Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganism...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-07-01
|
| Series: | Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40168-022-01292-1 |
| _version_ | 1818158577234214912 |
|---|---|
| author | Jiaxiong Zeng Qichao Tu Xiaoli Yu Lu Qian Cheng Wang Longfei Shu Fei Liu Shengwei Liu Zhijian Huang Jianguo He Qingyun Yan Zhili He |
| author_facet | Jiaxiong Zeng Qichao Tu Xiaoli Yu Lu Qian Cheng Wang Longfei Shu Fei Liu Shengwei Liu Zhijian Huang Jianguo He Qingyun Yan Zhili He |
| author_sort | Jiaxiong Zeng |
| collection | DOAJ |
| description | Abstract Background Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database. Results In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments. Conclusions We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract |
| first_indexed | 2024-12-11T15:32:18Z |
| format | Article |
| id | doaj.art-65d2b40b621048058ad5f4cf2d496c14 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-11T15:32:18Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-65d2b40b621048058ad5f4cf2d496c142022-12-22T01:00:01ZengBMCMicrobiome2049-26182022-07-0110111610.1186/s40168-022-01292-1PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genesJiaxiong Zeng0Qichao Tu1Xiaoli Yu2Lu Qian3Cheng Wang4Longfei Shu5Fei Liu6Shengwei Liu7Zhijian Huang8Jianguo He9Qingyun Yan10Zhili He11Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityInstitute of Marine Science and Technology, Shandong UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityEnvironmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen UniversityAbstract Background Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database. Results In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments. Conclusions We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstracthttps://doi.org/10.1186/s40168-022-01292-1Phosphorus cycling gene/microorganismDatabaseAccuracyComprehensivenessMetagenome sequencing data |
| spellingShingle | Jiaxiong Zeng Qichao Tu Xiaoli Yu Lu Qian Cheng Wang Longfei Shu Fei Liu Shengwei Liu Zhijian Huang Jianguo He Qingyun Yan Zhili He PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes Microbiome Phosphorus cycling gene/microorganism Database Accuracy Comprehensiveness Metagenome sequencing data |
| title | PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes |
| title_full | PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes |
| title_fullStr | PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes |
| title_full_unstemmed | PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes |
| title_short | PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes |
| title_sort | pcycdb a comprehensive and accurate database for fast analysis of phosphorus cycling genes |
| topic | Phosphorus cycling gene/microorganism Database Accuracy Comprehensiveness Metagenome sequencing data |
| url | https://doi.org/10.1186/s40168-022-01292-1 |
| work_keys_str_mv | AT jiaxiongzeng pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT qichaotu pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT xiaoliyu pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT luqian pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT chengwang pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT longfeishu pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT feiliu pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT shengweiliu pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT zhijianhuang pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT jianguohe pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT qingyunyan pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes AT zhilihe pcycdbacomprehensiveandaccuratedatabaseforfastanalysisofphosphoruscyclinggenes |