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Comparative microbiota assessment of wilted Italian ryegrass, whole crop corn, and wilted alfalfa silage using denaturing gradient gel electrophoresis and next-generation sequencing

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Abstract

The microbiota of pre-ensiled crop and silage were examined using denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Wilted Italian ryegrass (IR), whole crop corn (WC), and wilted alfalfa (AL) silages stored for 2 months were examined. All silages contained lactic acid as a predominant fermentation product. Across the three crop species, DGGE detected 36 and 28 bands, and NGS identified 253 and 259 genera in the pre-ensiled crops and silages, respectively. The NGS demonstrated that, although lactic acid bacteria (LAB) became prevalent in all silages after 2 months of storage, the major groups were different between crops: Leuconostoc spp. and Pediococcus spp. for IR silage, Lactobacillus spp. for WC silage, and Enterococcus spp. for AL silage. The predominant silage LAB genera were also detected by DGGE, but the presence of diverse non-LAB species in pre-ensiled crops was far better detected by NGS. Likewise, good survival of Agrobacterium spp., Methylobacterium spp., and Sphingomonas spp. in IR and AL silages was demonstrated by NGS. The diversity of the microbiota described by principal coordinate analysis was similar between DGGE and NGS. Our finding that analysis of pre-ensiled crop microbiota did not help predict silage microbiota was true for both DGGE and NGS.

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Authors and Affiliations

  1. Department of Animal Science, Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan

    Kuikui Ni, Tang Thuy Minh, Tran Thi Minh Tu, Takeshi Tsuruta & Naoki Nishino

  2. Henan Provincial Key Laboratory of Ion Beam Bio-engineering, Zhengzhou University, Zhengzhou, China

    Kuikui Ni & Huili Pang

Authors
  1. Kuikui Ni
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  2. Tang Thuy Minh
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  3. Tran Thi Minh Tu
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  4. Takeshi Tsuruta
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  5. Huili Pang
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  6. Naoki Nishino
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Correspondence to Naoki Nishino.

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This work was supported by the Ministry of Agriculture, Forestry, and Fisheries of Japan (Grant No. 26081C).

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The authors declare that they have no competing interests.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Ni, K., Minh, T.T., Tu, T.T.M. et al. Comparative microbiota assessment of wilted Italian ryegrass, whole crop corn, and wilted alfalfa silage using denaturing gradient gel electrophoresis and next-generation sequencing. Appl Microbiol Biotechnol 101, 1385–1394 (2017). https://doi.org/10.1007/s00253-016-7900-2

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  • DOI: https://doi.org/10.1007/s00253-016-7900-2

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