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

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.

Effect of ensiling corn stover with legume herbages in different proportions on fermentation characteristics, nutritive quality and in vitro digestibility on the Tibetan Plateau

“…This indicated the different conversion efficiency of WSC to LA by the epiphytic LAB in the corn stover silages mixed with various legume herbages. And this also indirectly confirmed the fact that the numbers and species of epiphytic LAB varied considerably among different herbages (Lin et al 1992;Ni et al 2016), though the common vetch and alfalfa were both the Leguminosae herbages.…”

Effects of inoculants and environmental temperature on fermentation quality and bacterial diversity of alfalfa silage

“…Ni et al . () examined the microbiota of three silages (wilted Italian ryegrass, whole crop corn, and wilted alfalfa) using DGGE and the Illumina Miseq sequencing method. In the three silages, DGGE detected 28 bands, while Illumina Miseq sequencing method identified 259 genera.…”

Rumen fluid, feces, milk, water, feed, airborne dust, and bedding microbiota in dairy farms managed by automatic milking systems

“…Bacterial pellets were obtained by centrifugation at 16,000× g for 2 min. For feed sample, a 10 g of silage was vigorously mixed with 90 ml of sterilized saline and the gauze‐filtered extract was centrifuged to obtain the pellet (Ni et al., ). For milk, water, and airborne dust samples, a 250 μL sample was centrifuged to collect the pellet.…”