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Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters.

Bao W, Mi Z, Xu H, Zheng Y, Kwok LY, Zhang H, Zhang W - Sci Rep (2016)

Bottom Line: 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.Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.

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.

No MeSH data available.


Box plots of the silage bacterial abundances at species level.Each dot represents a specific sample.
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f3: Box plots of the silage bacterial abundances at species level.Each dot represents a specific sample.

Mentions: Using the RDP classifier, more than 960 species were identified from all samples; twelve of them had a relative abundance of >1%, namely Pediococcus acidilactici, Lactobacillus plantarum, Lactobacillus pobuzihii, Bacillus megaterium, Salmonella enterica, Enterobacter cloacae, Pantoea agglomerans, Ochrobactrum lupini, Weissella cibaria, Enterococcus durans, Bacillus cereus and Bacillus marisflavi. In fact, great variations were found among the species number (Fig. 3) and relative abundances of detected bacteria before and after fermentation (Fig. 4). Before fermentation, Bacillus megaterium was the most abundant species in the silage samples. After fermentation, P. acidilactici (41.18%) and L. plantarum (20.15%) appeared to be the dominant species in the silages (Fig. 4). Clearly, the prevalent species existed in the fermented silages were highly dependent on the original bacterial composition in the LAB additives. By PCoA analysis based on the weighted and unweighted UniFrac distances (Fig. 5), distinct clusters were identified in relation to the silage fermentation status.


Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters.

Bao W, Mi Z, Xu H, Zheng Y, Kwok LY, Zhang H, Zhang W - Sci Rep (2016)

Box plots of the silage bacterial abundances at species level.Each dot represents a specific sample.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920031&req=5

f3: Box plots of the silage bacterial abundances at species level.Each dot represents a specific sample.
Mentions: Using the RDP classifier, more than 960 species were identified from all samples; twelve of them had a relative abundance of >1%, namely Pediococcus acidilactici, Lactobacillus plantarum, Lactobacillus pobuzihii, Bacillus megaterium, Salmonella enterica, Enterobacter cloacae, Pantoea agglomerans, Ochrobactrum lupini, Weissella cibaria, Enterococcus durans, Bacillus cereus and Bacillus marisflavi. In fact, great variations were found among the species number (Fig. 3) and relative abundances of detected bacteria before and after fermentation (Fig. 4). Before fermentation, Bacillus megaterium was the most abundant species in the silage samples. After fermentation, P. acidilactici (41.18%) and L. plantarum (20.15%) appeared to be the dominant species in the silages (Fig. 4). Clearly, the prevalent species existed in the fermented silages were highly dependent on the original bacterial composition in the LAB additives. By PCoA analysis based on the weighted and unweighted UniFrac distances (Fig. 5), distinct clusters were identified in relation to the silage fermentation status.

Bottom Line: 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.Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China.

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.

No MeSH data available.