Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation
ABSTRACT Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retenti...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-11-01
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| Series: | mSystems |
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00682-24 |
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| author | Yuan Wang Yunlei Sun KeXin Huang Yu Gao Yufan Lin Baojie Yuan Xin Wang Gang Xu Luiz Gustavo Nussio Fuyu Yang Kuikui Ni |
| author_facet | Yuan Wang Yunlei Sun KeXin Huang Yu Gao Yufan Lin Baojie Yuan Xin Wang Gang Xu Luiz Gustavo Nussio Fuyu Yang Kuikui Ni |
| author_sort | Yuan Wang |
| collection | DOAJ |
| description | ABSTRACT Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.IMPORTANCESilage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation. |
| format | Article |
| id | doaj-art-fe6ce7d43d2b4314a931566cc63a517f |
| institution | Kabale University |
| issn | 2379-5077 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj-art-fe6ce7d43d2b4314a931566cc63a517f2024-12-25T12:35:41ZengAmerican Society for MicrobiologymSystems2379-50772024-11-0191110.1128/msystems.00682-24Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentationYuan Wang0Yunlei Sun1KeXin Huang2Yu Gao3Yufan Lin4Baojie Yuan5Xin Wang6Gang Xu7Luiz Gustavo Nussio8Fuyu Yang9Kuikui Ni10College of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaDepartment of Animal Science, University of São Paulo, Piracicaba, BrazilCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaCollege of Grassland Science and Technology, China Agricultural University, Beijing, ChinaABSTRACT Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.IMPORTANCESilage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.https://journals.asm.org/doi/10.1128/msystems.00682-24silagemetagenomicsculturomicsammonia-Nbutyric acid |
| spellingShingle | Yuan Wang Yunlei Sun KeXin Huang Yu Gao Yufan Lin Baojie Yuan Xin Wang Gang Xu Luiz Gustavo Nussio Fuyu Yang Kuikui Ni Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation mSystems silage metagenomics culturomics ammonia-N butyric acid |
| title | Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation |
| title_full | Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation |
| title_fullStr | Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation |
| title_full_unstemmed | Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation |
| title_short | Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation |
| title_sort | multi omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation |
| topic | silage metagenomics culturomics ammonia-N butyric acid |
| url | https://journals.asm.org/doi/10.1128/msystems.00682-24 |
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