Metagenome-guided culturomics for the targeted enrichment of gut microbes
Abstract The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 gr...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55668-y |
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| author | Jeremy Armetta Simone S. Li Troels Holger Vaaben Ruben Vazquez-Uribe Morten O. A. Sommer |
| author_facet | Jeremy Armetta Simone S. Li Troels Holger Vaaben Ruben Vazquez-Uribe Morten O. A. Sommer |
| author_sort | Jeremy Armetta |
| collection | DOAJ |
| description | Abstract The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes. |
| format | Article |
| id | doaj-art-7add0b36c3ef48b9a55a363a7fe26035 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-7add0b36c3ef48b9a55a363a7fe260352025-01-19T12:32:08ZengNature PortfolioNature Communications2041-17232025-01-0116111410.1038/s41467-024-55668-yMetagenome-guided culturomics for the targeted enrichment of gut microbesJeremy Armetta0Simone S. Li1Troels Holger Vaaben2Ruben Vazquez-Uribe3Morten O. A. Sommer4Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Kgs.Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Kgs.Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Kgs.Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Kgs.Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Kgs.Abstract The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.https://doi.org/10.1038/s41467-024-55668-y |
| spellingShingle | Jeremy Armetta Simone S. Li Troels Holger Vaaben Ruben Vazquez-Uribe Morten O. A. Sommer Metagenome-guided culturomics for the targeted enrichment of gut microbes Nature Communications |
| title | Metagenome-guided culturomics for the targeted enrichment of gut microbes |
| title_full | Metagenome-guided culturomics for the targeted enrichment of gut microbes |
| title_fullStr | Metagenome-guided culturomics for the targeted enrichment of gut microbes |
| title_full_unstemmed | Metagenome-guided culturomics for the targeted enrichment of gut microbes |
| title_short | Metagenome-guided culturomics for the targeted enrichment of gut microbes |
| title_sort | metagenome guided culturomics for the targeted enrichment of gut microbes |
| url | https://doi.org/10.1038/s41467-024-55668-y |
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