Abstract
The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.
Highlights
D1 40.20 ± 1.20a 13.50 ± 1.92a 0.34 ± 0.04a 5.00 ± 1.01a 0.06 ± 0.01c 18.06 ± 0.42c 146.19 ± 8.55c have demonstrated the applicability of using such molecular techniques in quantifying certain silage-specific species under a wide variety of conditions
The silage bacterial microbiota profiles described by the previous studies are restricted to the genus precision due to the relatively low taxonomical resolution of the traditional DNA sequencing technique that could only determine the partial sequence of the 16S rRNA gene
The Pacific Biosciences (PacBio) single molecule, real-time sequencing technology (SMRT) is able to depict the bacterial profile of target samples to species level precision because of its power in generating long sequence reads[11,12]
Summary
D1 40.20 ± 1.20a 13.50 ± 1.92a 0.34 ± 0.04a 5.00 ± 1.01a 0.06 ± 0.01c 18.06 ± 0.42c 146.19 ± 8.55c have demonstrated the applicability of using such molecular techniques in quantifying certain silage-specific species under a wide variety of conditions. The silage bacterial microbiota profiles described by the previous studies are restricted to the genus precision due to the relatively low taxonomical resolution of the traditional DNA sequencing technique that could only determine the partial sequence of the 16S rRNA gene. The Pacific Biosciences (PacBio) single molecule, real-time sequencing technology (SMRT) is able to depict the bacterial profile of target samples to species level precision because of its power in generating long sequence reads[11,12]. Apart from analyzing the silage quality using conventional indicators like pH, organic acid contents, and mycotoxin formation, we focused on detecting and comparing the bacterial microbiota composition of M. sativa silages produced by adding four different lactic acid bacteria (LAB) additives using the PacBio SMRT method. Our data have demonstrated that the SMRT sequencing platform is suitable for assessing the quality of silage
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