scholarly journals Additives Altered Bacterial Communities and Metabolic Profiles in Silage Hybrid Pennisetum

2022 ◽  
Vol 12 ◽  
Author(s):  
Hanchen Tian ◽  
Yanchen Zhu ◽  
Mengxue Dai ◽  
Tong Li ◽  
Yongqing Guo ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Nutrient Composition ◽  
Control Group ◽  
Metabolic Profiles ◽  
Fresh Matter ◽  
Positive Effects ◽  
Fermentation Quality ◽  
Hybrid Pennisetum

This study was conducted to investigate the effects of different additives on the fermentation quality, nutrient composition, bacterial communities, and metabolic profiles of the silage of hybrid Pennisetum. The experiment was conducted using five treatments, i.e., CK, control group, MA, 1% malic acid of fresh matter (FM) basis, GL, 1% glucose of FM basis, CE, 100 U/g FM cellulase, and BS, 106 cfu/g FM Bacillus subtilis, with six replicates each treatment. After a 120-day fermentation, 30 silage packages were opened for subsequent determination. As a result, all four additives had positive effects on the fermentation quality and nutrient composition of the silage of hybrid Pennisetum. The high-throughput sequencing of V3–V4 regions in 16S rRNA was performed, and results showed that Firmicutes and Proteobacteria were the dominant phyla and that Aquabacterium and Bacillus were the dominant genera. MA, GL, CE, and BS treatment resulted in 129, 21, 25, and 40 differential bacteria, respectively. The four additives upregulated Bacillus smithii but downregulated Lactobacillus rossiae. Metabolic profiles were determined by UHPLC-Q/TOF-MS technology and the differential metabolites caused by the four additives were 47, 13, 47, and 18, respectively. These metabolites played antioxidant, antibacterial, and anti-inflammatory functions and involved in pathways, such as the citrate cycle, carbon fixation in photosynthetic organisms, and glyoxylate and dicarboxylate metabolism. In conclusion, silage additives promoted fermentation quality and nutrient composition by altering bacterial communities and metabolic profiles. This study provided potential biomarkers for the improvement of silage quality.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

scholarly journals Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

2020 ◽  
Author(s):  
Zongfu Hu ◽  
Deying Ma ◽  
huaxin Niu ◽  
Jie Chang ◽  
Jianhua Yu ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Communities ◽  
Crude Protein ◽  
High Throughput Sequencing ◽  
Ammonium N ◽  
Enzyme Combination ◽  
Fermentation Quality ◽  
Dominant Bacteria

Abstract This study aimed to evaluate the effects of enzymes (cellulase combined with galactosidase),, and the combination of these enzymes with Lactobacillus plantarum (LP) on bacterial diversity using high-throughput sequencing. Alfalfa forages were treated without or with cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), ɑ-galactosidase + LP (GALP). After 56 days of ensiling, All the treated silages exhibited improved fermentation quality as reflecting by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage. Enzymatic treatment improved nutrients value by increased the level of crude protein and decreased the neutral detergent fibre (NDF) level. Treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. LAB dominated the bacterial community of the treated silage after ensiling. The dominant bacteria from Garciella, Enterococcus, Lactobacillus and Pediococcus in control silage changed to Lactobacillus and Pediococcus in CEGA silage, and Lactobacillus in CELP and GALP silages. Collectively, enzymes and enzyme in combination with inoculants both greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus in enzymes only silge (CEGA) and Lactobacillus in enzyme combination with inoculants silage (CELP and GALP).

scholarly journals Dynamics of the Fermentation Products, Residual Non-structural Carbohydrates, and Bacterial Communities of Wilted and Non-wilted Alfalfa Silage With and Without Lactobacillus plantarum Inoculation

2022 ◽  
Vol 12 ◽  
Author(s):  
Fengyuan Yang ◽  
Yanping Wang ◽  
Shanshan Zhao ◽  
Changsong Feng ◽  
Xiaomiao Fan
Keyword(s):  
Bacterial Community ◽  
Lactobacillus Plantarum ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Water Soluble ◽  
Soluble Carbohydrates ◽  
Fermentation Products ◽  
Fermentation Quality ◽  
Alfalfa Silage

The aim of this study was to investigate effects of wilting and Lactobacillus plantarum inoculation on the dynamics of the fermentation products, residual non-structural carbohydrates, and bacterial communities in alfalfa silage. Fresh and wilted alfalfa were ensiled with and without L. plantarum for 10, 30, 60, and 90 days. A high-throughput sequencing method for absolute quantification of 16S rRNA was adopted to determine the bacterial community composition at different ensiling periods. For the wilted silage, the bacterial community, pH value, and ammonia nitrogen concentration remained stable in the silage at 30 days. L. plantarum inoculation accelerated lactic acid fermentation and altered the predominant genus in the wilted silage as compared with the non-inoculated group. For the non-wilted group, fast consumption of water-soluble carbohydrates (WSCs) was observed at 10 days in the non-inoculated silage along with rapid growth of undesirable Hafnia. L. plantarum inoculation inhibited growth of Hafnia at 10 days in the non-wilted silage. Clostridia fermentation occurred in the non-wilted silage at 90 days, as indicated by an increased pH, formation of butyric acid (BA), and apparent abundance of genera belonging to Clostridia. L. plantarum inoculation inhibited BA accumulation and growth of Garciella in the non-wilted silage at 90 days as compared with the non-wilted silage without inoculation, but had little effect on the growth of Clostridium sensu stricto. Overall, the high moisture content of the non-wilted alfalfa silage led to rapid consumption of WSCs and growth of harmful microorganisms at the early stage of ensiling, resulting in poor fermentation quality. Wilting and L. plantarum inoculation both improved fermentation quality and inhibited the growth of spoilage microorganisms in alfalfa silage, while L. plantarum inoculation alone failed to achieve optimum fermentation quality of non-wilted alfalfa silage.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

scholarly journals Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zongfu Hu ◽  
Deying Ma ◽  
Huaxin Niu ◽  
Jie Chang ◽  
Jianhua Yu ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Crude Protein ◽  
High Throughput Sequencing ◽  
Protein Levels ◽  
Nutrient Value ◽  
Ammonium N ◽  
Fermentation Quality ◽  
Dominant Bacteria

AbstractThe goal of the present study was to evaluate the effects of enzymes (cellulase combined with galactosidase) and their combination with Lactobacillus plantarum (LP) on bacterial diversity in alfalfa silages using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage (P < 0.05). Enzymatic treatment improved nutrient value by increasing crude protein levels and decreasing neutral detergent fibre (NDF) levels (P < 0.05). Silage treatment significantly altered the bacterial community, as determined by PCoA (P < 0.05). Lactic acid bacteria (LAB) dominated the bacterial community of the treated silage after ensiling. The dominant bacteria changed from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage to Lactobacillus and Pediococcus in the CEGA silage and Lactobacillus in the CELP and GALP silages. Collectively, these results suggest that treatment with both enzymes alone and in combination with inoculants greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus observed in the silage treated with enzymes alone (CEGA) and Lactobacillus observed in the silage treated with a combination of enzymes and inoculants (CELP and GALP).

scholarly journals Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

2020 ◽  
Author(s):  
Zongfu hu ◽  
Deying Ma ◽  
Huaxin Niu ◽  
Jie Chang ◽  
Jianhua Yu ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Communities ◽  
Crude Protein ◽  
High Throughput Sequencing ◽  
Nutrient Value ◽  
Ammonium N ◽  
Fermentation Quality ◽  
Dominant Bacteria

Abstract This study aimed to evaluate the effects of enzymes (cellulase combined with galactosidase), and the combination of these enzymes with Lactobacillus plantarum (LP) on bacterial diversity using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all the treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage. Enzymatic treatment improved nutrient value by increasing the level of crude protein and decreasing the neutral detergent fibre (NDF) level. Treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. LAB dominated the bacterial community of the treated silage after ensiling. The dominant bacteria from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage changed to Lactobacillus and Pediococcus in the CEGA silage, and Lactobacillus in the CELP and GALP silages. Collectively, enzymes and enzymes in combination with inoculants both greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus in the silage with enzymes only (CEGA) and Lactobacillus in the silage with a combination of enzymes and inoculants (CELP and GALP).

scholarly journals Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

2020 ◽  
Author(s):  
zongfu hu ◽  
Deying Ma ◽  
huaxin Niu ◽  
Jie Chang ◽  
Jianhua Yu ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Crude Protein ◽  
High Throughput Sequencing ◽  
Protein Levels ◽  
Nutrient Value ◽  
Ammonium N ◽  
Fermentation Quality ◽  
Dominant Bacteria

Abstract The goal of the present study was to evaluate the effects of enzymes (cellulase combined with galactosidase) and their combination with Lactobacillus plantarum (LP) on bacterial diversity in alfalfa silages using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage (P < 0.05). Enzymatic treatment improved nutrient value by increasing crude protein levels and decreasing neutral detergent fibre (NDF) levels (P < 0.05). Silage treatment significantly altered the bacterial community, as determined by PCoA (P < 0.05). Lactic acid bacteria (LAB) dominated the bacterial community of the treated silage after ensiling. The dominant bacteria changed from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage to Lactobacillus and Pediococcus in the CEGA silage and Lactobacillus in the CELP and GALP silages. Collectively, these results suggest that treatment with both enzymes alone and in combination with inoculants greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus observed in the silage treated with enzymes alone (CEGA) and Lactobacillus observed in the silage treated with a combination of enzymes and inoculants (CELP and GALP).

scholarly journals Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Xueshan Wang ◽  
Hai Du ◽  
Yan Zhang ◽  
Yan Xu
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Metabolic Profiles ◽  
Microbial Succession ◽  
Chinese Liquor ◽  
Content Type ◽  
Target Analysis ◽  
Metabolite Target Analysis

ABSTRACT Many microorganisms in the environment participate in the fermentation process of Chinese liquor. However, it is unknown to what extent the environmental microbiota influences fermentation. In this study, high-throughput sequencing combined with multiphasic metabolite target analysis was applied to study the microbial succession and metabolism changes during Chinese liquor fermentation from two environments (old and new workshops). SourceTracker was applied to evaluate the contribution of environmental microbiota to fermentation. Results showed that Daqu contributed 9.10 to 27.39% of bacterial communities and 61.06 to 80.00% of fungal communities to fermentation, whereas environments (outdoor ground, indoor ground, tools, and other unknown environments) contributed 62.61 to 90.90% of bacterial communities and 20.00 to 38.94% of fungal communities to fermentation. In the old workshop, six bacterial genera ( Lactobacillus [11.73% average relative abundance], Bacillus [20.78%], Pseudomonas [6.13%], Kroppenstedtia [10.99%], Weissella [16.64%], and Pantoea [3.40%]) and five fungal genera ( Pichia [55.10%], Candida [1.47%], Aspergillus [10.66%], Saccharomycopsis [22.11%], and Wickerhamomyces [3.35%]) were abundant at the beginning of fermentation. However, in the new workshop, the change of environmental microbiota decreased the abundances of Bacillus (5.74%), Weissella (6.64%), Pichia (33.91%), Aspergillus (7.08%), and Wickerhamomyces (0.12%), and increased the abundances of Pseudomonas (17.04%), Kroppenstedtia (13.31%), Pantoea (11.41%), Acinetobacter (3.02%), Candida (16.47%), and Kazachstania (1.31%). Meanwhile, in the new workshop, the changes of microbial community resulted in the increase of acetic acid, lactic acid, malic acid, and ethyl acetate, and the decrease of ethyl lactate during fermentation. This study showed that the environmental microbiota was an important source of fermentation microbiota and could drive both microbial succession and metabolic profiles during liquor fermentation. IMPORTANCE Traditional solid-state fermentation of foods and beverages is mainly carried out by complex microbial communities from raw materials, starters, and the processing environments. However, it is still unclear how the environmental microbiota influences the quality of fermented foods and beverages, especially for Chinese liquors. In this study, we utilized high-throughput sequencing, microbial source tracking, and multiphasic metabolite target analysis to analyze the origins of microbiota and the metabolic profiles during liquor fermentation. This study contributes to a deeper understanding of the role of environmental microbiota during fermentation.

scholarly journals Effects of Mixing Garlic Skin on Fermentation Quality, Microbial Community of High-Moisture Pennisetum hydridum Silage

2021 ◽  
Vol 12 ◽  
Author(s):  
Juncai Chen ◽  
Guohao Huang ◽  
Hanlin Xiong ◽  
Hao Qin ◽  
Haonan Zhang ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
Lactic Acid Production ◽  
Matter Content ◽  
Dry Matter Content ◽  
High Moisture ◽  
Fresh Matter ◽  
Microbial Characteristics ◽  
Fermentation Quality

Garlic skin, a by-product of garlic processing, was supposed to improve the fermentation quality of high-moisture silages because of its low moisture content and active compounds. Thus, fermentation and microbial characteristics of high-moisture Pennisetum hydridum ensiled with the addition of 0, 10, 20, and 30 wt% garlic skin (on a fresh matter basis) were analyzed during a 60-days fermentation. Results showed that the addition of garlic skin increased the dry matter content and lactic acid production, and decreased the pH and ammonia-N content of the silage. Adding garlic skin changed the relative abundance of bacterial communities with an increase in Lactobacillus and a decrease in Clostridium relative abundance. In conclusion, co-ensiling of high-moisture Pennisetum hydridum with garlic skin could be a simple approach to improve the silage quality and nutrients preservation.

scholarly journals Response of the Intertidal Microbial Community Structure and Metabolic Profiles to Zinc Oxide Nanoparticle Exposure

2020 ◽  
Vol 17 (7) ◽  
pp. 2253
Author(s):  
Yinghai Wu ◽  
Xinyu Rong ◽  
Cuiya Zhang ◽  
Renduo Zhang ◽  
Tao He ◽  
...  
Keyword(s):  
Zinc Oxide ◽  
Community Structure ◽  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Community Structure ◽  
High Throughput Sequencing ◽  
Control Group ◽  
Metabolic Profiles ◽  
Zno Nps

The toxicity of nanomaterials to microorganisms is related to their dose and environmental factors. The aim of this study was to investigate the shifts in the microbial community structure and metabolic profiles and to evaluate the environmental factors in a laboratory scale intertidal wetland system exposed to zinc oxide nanoparticles (ZnO NPs). Microbial assemblages were determined using 16S rRNA high-throughput sequencing. Community-level physiological profiles were determined using Biolog-ECO technology. Results showed Proteobacteria was the predominant (42.6%–55.8%) phylum across all the sediments, followed by Bacteroidetes (18.9%–29.0%). The genera Azoarcus, Maribacter, and Thauera were most frequently detected. At the studied concentrations (40 mg·L−1, 80 mg·L−1, 120 mg·L−1), ZnO NPs had obvious impacts on the activity of Proteobacteria. Adverse effects were particularly evident in sulfur and nitrogen cycling bacteria such as Sulfitobacter, unidentified_Nitrospiraceae, Thauera, and Azoarcus. The alpha diversity index of microbial community did not reflect stronger biological toxicity in the groups with high NP concentrations (80 mg·L−1, 120 mg·L−1) than the group with low NP concentration (40 mg·L−1). The average well color development (AWCD) values of periodically submersed groups were higher than those of long-term submersed groups. The group with NP concentration (40 mg·L−1) had the lowest AWCD value; those of the groups with high NP concentrations (80 mg·L−1, 120 mg·L−1) were slightly lower than that of the control group. The beta diversity showed that tidal activity shaped the similar microbial community among the periodically submerged groups, as well as the long-term submerged groups. The groups with high DO concentrations had higher diversity of the microbial community, better metabolic ability, and stronger resistance to ZnO NPs than the groups with a low DO concentration.

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