RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing
Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. Howe...
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| Format: | Article |
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MDPI AG
2020-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/10/1563 |
| _version_ | 1797551362076049408 |
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| author | Zhikai Xing Yunting Zhang Meng Li Chongye Guo Shuangli Mi |
| author_facet | Zhikai Xing Yunting Zhang Meng Li Chongye Guo Shuangli Mi |
| author_sort | Zhikai Xing |
| collection | DOAJ |
| description | Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size. |
| first_indexed | 2024-03-10T15:43:38Z |
| format | Article |
| id | doaj.art-9aa26f52f22140179ff78f9b7692a2dd |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T15:43:38Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-9aa26f52f22140179ff78f9b7692a2dd2023-11-20T16:36:22ZengMDPI AGMicroorganisms2076-26072020-10-01810156310.3390/microorganisms8101563RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun SequencingZhikai Xing0Yunting Zhang1Meng Li2Chongye Guo3Shuangli Mi4Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, ChinaKey Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, ChinaKey Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, ChinaKey Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, ChinaKey Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, ChinaWhole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.https://www.mdpi.com/2076-2607/8/10/1563microbial communitymetagenome databasemetagenomic profilingmicrobial functiontype 2 diabetes mellitus (T2D)avian colibacillosis |
| spellingShingle | Zhikai Xing Yunting Zhang Meng Li Chongye Guo Shuangli Mi RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing Microorganisms microbial community metagenome database metagenomic profiling microbial function type 2 diabetes mellitus (T2D) avian colibacillosis |
| title | RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing |
| title_full | RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing |
| title_fullStr | RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing |
| title_full_unstemmed | RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing |
| title_short | RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing |
| title_sort | rbud a new functional potential analysis approach for whole microbial genome shotgun sequencing |
| topic | microbial community metagenome database metagenomic profiling microbial function type 2 diabetes mellitus (T2D) avian colibacillosis |
| url | https://www.mdpi.com/2076-2607/8/10/1563 |
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