数字农科院2.0

Exploring the ruminal microbiota of dairy cows for probiotic strains

文献类型： 外文期刊

作者： Duan, Xiaowei;Ma, Rui;Vigors, Stafford;Ma, Lu;Gu, Jingang;Bu, Dengpan

作者机构：

关键词： rumen;culturomics;amplicon;probiotics

期刊名称： CABI AGRICULTURE & BIOSCIENCE

ISSN：

年卷期： 2025 年 6 卷 1 期

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收录情况： ESCI（2025版）

摘要： The rumen ecosystem is complex and dynamic, with bacteria playing crucial roles in nutrient breakdown and utilization. In this study, we aimed to establish a strain-level database that will enable targeted screening of functional probiotic strains for future applications in the ruminant industry. We examine the rumen bacterial community using a combined approach of culturomics and amplicon sequencing, utilizing six dairy cows as rumen fluid donors. To isolate both facultative and strict anaerobic strains, we employed 15 culture conditions, which included nine different media and two gas conditions. MALDI-TOF mass spectrometry, 16S rRNA gene amplicon sequencing, and phylogenetic analysis were combined to identify specific strains. A total of 1047 isolates were assigned to 203 strains, accounting for 7.62% of the OTUs found in the rumen microbiota. The strains were assigned to three phyla (Firmicutes, Proteobacteria, and Actinobacteria), three classes, six orders, 10 families, 16 genera, and 32 species, including eight potential new species (belonging to five genera). At the genus level, Escherichia, Limosilactobacillus, Ligilactobacillus, Streptococcus, Enterococcus, Bacillus, Klebsiella, Staphylococcus, Kurthia, Microbacterium, Brevibacillus, Lacticaseibacillus, Pediococcus, Weissella, Pseudomonas, and Propionibacterium were identified in the ruminal culturome. Of them, a group of previously identified probiotic strains, including LAB (Limosilactobacillus, Ligilactobacillus, Enterococcus, Lacticaseibacillus, Pediococcus, and Weissella) and Bacillus (B. safensis, B. subtilis, and B. tequilensis), was identified and based on function having potential as ruminant feed additives. Culturomics played a pivotal role in mining the five genera of Propionibacterium, Lacticaseibacillus, Microbacterium, Brevibacillus, and Kurthia, which accounted for 2.38% of bacterial genera, complementing the discovery made by the 16S rRNA gene amplicon sequencing results in this study, the Hungate 1000 project, and two other published ruminal culture datasets. Wilkins-Chalgren broth was the most efficient medium for isolating ruminal bacteria under both aerobic and anaerobic conditions, respectively. Among the 203 representative strains, 43 were strictly aerobic, seven were strictly anaerobic, and 152 were facultative anaerobes. This study confirms the key role of culturomics in exploring the complex microbiota of the rumen and provides a valuable probiotic resource for fermented feed and direct-fed microbes in the ruminant industry.

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