Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women
Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.
Authors
- Tinja Kanerva
- Tiina Holster (ORCID: https://orcid.org/0000-0003-0257-1256)
- Rebecka Ventin-Holmberg (ORCID: https://orcid.org/0000-0001-9890-1066)
- Schahzad Saqib (ORCID: https://orcid.org/0000-0002-0844-2124)
- Ilkka Kalliala (ORCID: https://orcid.org/0000-0002-7664-0587)
- Anne Salonen (ORCID: https://orcid.org/0000-0002-6960-7447)
- Pekka Nieminen (ORCID: https://orcid.org/0000-0001-5671-8685)
- Seppo Virtanen (ORCID: https://orcid.org/0000-0003-0261-8958)
Institutions
- University of Helsinki (FI)
- Helsinki University Hospital (FI)
- Folkhälsans Forskningscentrum (FI)
- Kemira (Finland) (FI)
- Imperial College London (GB)
Publication Details
- Journal
- Microbiome
- Published
- 2024-12-27
- DOI
- https://doi.org/10.1186/s40168-024-01993-9
- Citations
- 5
- Primary Topic
- Gut microbiota and health
- Type
- article
- Field-Weighted Citation Impact
- 1.17
Funders
- Helsingin Yliopisto
- Karolinska Institutet
- China Scholarship Council