FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling
While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundan...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022002902 |
| _version_ | 1797978211219406848 |
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| author | Zixuan Xie Chaysavanh Manichanh |
| author_facet | Zixuan Xie Chaysavanh Manichanh |
| author_sort | Zixuan Xie |
| collection | DOAJ |
| description | While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundant fungal proteins) databases for the identification of fungi. Applied to more than 2,600 human metagenomic samples, the tool revealed fungal species associated with geography, body sites, and diseases. Correlation network analysis provided new insights into inter-kingdom interactions. With this pipeline and two of the most comprehensive fungal databases, we foresee a fast-growing resource for mycobiome studies. |
| first_indexed | 2024-04-11T05:19:23Z |
| format | Article |
| id | doaj.art-448412e46f304c768d4aaa5b08777a8c |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:23Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-448412e46f304c768d4aaa5b08777a8c2022-12-24T04:53:23ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012036853694FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profilingZixuan Xie0Chaysavanh Manichanh1Microbiome Lab, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Barcelona, SpainMicrobiome Lab, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain; Corresponding author at: Microbiome Lab, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundant fungal proteins) databases for the identification of fungi. Applied to more than 2,600 human metagenomic samples, the tool revealed fungal species associated with geography, body sites, and diseases. Correlation network analysis provided new insights into inter-kingdom interactions. With this pipeline and two of the most comprehensive fungal databases, we foresee a fast-growing resource for mycobiome studies.http://www.sciencedirect.com/science/article/pii/S2001037022002902MycobiomeFungal databasesTaxonomy and functionsShotgun metagenomicsInter-kingdom interactions |
| spellingShingle | Zixuan Xie Chaysavanh Manichanh FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling Computational and Structural Biotechnology Journal Mycobiome Fungal databases Taxonomy and functions Shotgun metagenomics Inter-kingdom interactions |
| title | FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling |
| title_full | FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling |
| title_fullStr | FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling |
| title_full_unstemmed | FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling |
| title_short | FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling |
| title_sort | funomic pipeline with built in fungal taxonomic and functional databases for human mycobiome profiling |
| topic | Mycobiome Fungal databases Taxonomy and functions Shotgun metagenomics Inter-kingdom interactions |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022002902 |
| work_keys_str_mv | AT zixuanxie funomicpipelinewithbuiltinfungaltaxonomicandfunctionaldatabasesforhumanmycobiomeprofiling AT chaysavanhmanichanh funomicpipelinewithbuiltinfungaltaxonomicandfunctionaldatabasesforhumanmycobiomeprofiling |