Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.

IF 5 2区 生物学 Q1 MICROBIOLOGY mSystems Pub Date : 2024-11-19 Epub Date: 2024-10-23 DOI:10.1128/msystems.00682-24
Yuan Wang, Yunlei Sun, KeXin Huang, Yu Gao, Yufan Lin, Baojie Yuan, Xin Wang, Gang Xu, Luiz Gustavo Nussio, Fuyu Yang, Kuikui Ni
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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.

Importance: Silage 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.

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多组学分析揭示了苜蓿青贮发酵过程中的核心微生物群和营养降解的生物标志物。
紫花苜蓿(Medicago sativa L.)是全球最广泛种植的饲料作物之一,其营养质量对奶牛的生产率有着至关重要的影响。青贮发酵被认为是保存新鲜饲草的关键技术,可确保保留其重要营养成分。然而,人们对青贮发酵过程中的微生物成分及其功能还不完全了解。本研究将大规模微生物培养与高通量测序相结合,深入研究了苜蓿青贮中的微生物群落结构,并通过元基因组分析探索了营养降解的潜在途径。研究结果表明,青贮饲料中的微生物多样性丰富,这体现在扩增子序列变异的鉴定上。值得注意的是,大规模培养方法回收了大量高通量测序无法检测到的独特微生物。根据其丰度和普遍性,确定了主要菌属,如乳杆菌属(Lactiplantibacillus)、白念珠菌属(Leuconostoc)、扁豆乳杆菌属(Lentilactobacillus)、魏氏菌属(Weissella)和液乳杆菌属(Liquorilactobacillus)。此外,还发现了与肠杆菌科相关的基因,这些基因可能参与了氨-N 和丁酸的生产途径。总之,这项研究全面揭示了青贮发酵的微生物生态学,为利用微生物联合体提高发酵质量提供了有价值的信息:青贮发酵是一种微生物驱动的厌氧发酵过程,可有效地将各种基质转化为反刍动物易于吸收和代谢的营养物质。这项研究结合了培养组学和元基因组学,成功鉴定了参与青贮发酵的核心微生物,包括低丰度微生物。这一发现对于有针对性地培养特定微生物以优化发酵过程至关重要。此外,我们的研究还发现了在养分代谢中起关键作用的特征微生物,极大地推动了我们对青贮发酵过程中微生物群落与养分降解之间错综复杂关系的理解。
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来源期刊
mSystems
mSystems Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
10.50
自引率
3.10%
发文量
308
审稿时长
13 weeks
期刊介绍: mSystems™ will publish preeminent work that stems from applying technologies for high-throughput analyses to achieve insights into the metabolic and regulatory systems at the scale of both the single cell and microbial communities. The scope of mSystems™ encompasses all important biological and biochemical findings drawn from analyses of large data sets, as well as new computational approaches for deriving these insights. mSystems™ will welcome submissions from researchers who focus on the microbiome, genomics, metagenomics, transcriptomics, metabolomics, proteomics, glycomics, bioinformatics, and computational microbiology. mSystems™ will provide streamlined decisions, while carrying on ASM''s tradition of rigorous peer review.
期刊最新文献
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