Microbial Communities, Metabolites, Fermentation Quality and Aerobic Stability of Whole-Plant Corn Silage Collected from Family Farms in Desert Steppe of North China

Characterization of the eukaryotic microbial communities in the chicken ileum in cage-free and conventional commercial housing systems

The current shift from conventional cage (CC) hen housing facilities towards cage-free (CF) hen housing in the egg industry has left many questions regarding how level of fecal exposure and exposure to other hens may influence the hen intestinal microbiota. In a previous publication we reported differences in the bacterial ileal communities and ileal morphology between hens in CC and CF production environments at a single commercial site. Here, we present the first 18S rRNA gene amplicon sequencing-based characterization of the eukaryotic ileal microbiota of adult layer hens, and their associations with intestinal health parameters and the bacterial microbiota. DNA was extracted from the ileal digesta of hens (n = 32 CC, n = 48 CF) using the Qiagen Powerlyzer Powersoil kit, followed by amplification of the V9 region of the 18S rRNA gene. Paired end sequencing was performed with the Illumina MiSeq platform, and the resulting reads were processed according to the Mothur MiSeq protocol in Mothur v1.43.0. De novo operational taxonomic unit (OTU) clustering was performed in mothur with a 99% similarity threshold, and OTUs were taxonomically classified with the SILVA SSU v138 reference database. OTUs classified as vertebrate, plant, or arthropod were removed, resulting in 3,136,400 high quality reads and 1,370 OTUs. Associations between OTUs and intestinal parameters were calculated using PROC GLIMMIX. PERMANOVA over Bray-Curtis distances revealed differences between CC and CF eukaryotic ileal microbiota at the whole community level, but no OTUs were differentially abundant after correcting for false discovery (P > 0.05; q > 0.1). Kazachstania and Saccharomyces, closely related genera of yeast, represented 77.1% and 9.7% of sequences respectively. Two Kazachstania OTUs and 1 Saccharomycetaceae OTU were positively correlated with intestinal permeability (r² ≥ 0.35). Eimeria accounted for 7.6% of sequences across all samples. Intriguingly, 15 OTUs classified as Eimeria were inversely associated with intestinal permeability (r² ≤ -0.35), suggesting Eimeria may play a more complex role in the microbiota of healthy birds than has been observed in disease challenges.

Fermentation weight loss, fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria at different silo densities

Sweet sorghum is an important forage in arid and semi-arid climatic regions. This study aimed to reveal the fermentation weight loss (FWL), fermentation quality, and bacterial community of ensiling of sweet sorghum with lactic acid bacteria LAB; (Lactiplantibacillus plantarum and Lentilactobacillus buchneri) at different silo densities. For this study, sweet sorghum was harvested at the first spikelet of inflorescence stage and ensiled without or with LAB (CK or L) in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at densities of 650 (CK_650 and L_650), 700 (CK_700 and L_700), and 750 kg/m3 (CK_750 and L_750), respectively. The FWL, fermentation quality, microbial counts, and bacterial community of the silage were assessed after 100 days of ensiling. L_750 had a lower FWL than CK_650, _700, and _750 after 100 days of ensiling (P < 0.005), and the FWL was affected by silo density and inoculating LAB (P < 0.005). All silages had low pH (<4.0) and ammonia nitrogen content (<50 g/kg total nitrogen) and did not contain propionic and butyric acids; moreover, inoculating LAB increased lactic and acetic acids (P < 0.005). Bacterial communities in inoculated and uninoculated silages were clustered together, respectively, and clearly separated from each other. The total abundance of Lactiplantibacillus and Lentilactobacillus in fresh forage was <1%. Lactiplantibacillus had the highest abundance in all silages (from 71.39 to 93.27%), followed by Lentilactobacillus (from 3.59 to 27.63%). Inoculating LAB increased the abundance of Lentilactobacillus in each silo density (P < 0.005) and decreased Lactiplantibacillus in the silage in densities of 700 and 750 kg/m3 (P < 0.005); moreover, increasing silo density decreased Lactiplantibacillus abundance and increased Lentilactobacillus abundance in inoculated silages (P < 0.005). Overall, sweet sorghum silage showed satisfactory fermentation quality, with a density of no <650 kg/m3, and inoculating LAB improved fermentation quality and reduced FWL. Lactiplantibacillus and Lentilactobacillus presented as minor taxa in fresh sweet sorghum and dominated the bacterial community of all silages. Inoculating LAB was the main factor affecting the bacterial community of sweet sorghum silage. Moreover, inoculating LAB and increasing silo density can contribute to the decreasing Lactiplantibacillus abundance and increasing Lentilactobacillus abundance.

Fermentation quality, bacterial community, and aerobic stability of ensiling Leymus chinensis with lactic acid bacteria or/and water after long-term storage

Leymus chinensis is a major forage resource for herbivores on typical steppe and meadow steppes in Northern China. This study aimed to reveal the fermentation quality, bacterial community, and aerobic stability of L. chinensis silage treated with lactic acid bacteria or/and water after long-term storage. Leymus chinensis was harvested at the heading stage and ensiled with lactic acid bacteria [LAB, 2.00 ml/kg fresh weight (FW) of LAB, L], water (100 ml/kg FW of distilled water, W), or a combination of both [2.00 ml/kg fresh weight (FW) of LAB and 100 ml/kg FW of distilled water, LW] in polyethylene laboratory-scale silos (diameter, 20 cm; height, 30 cm) at a density of 650 kg/m3. As a control silage (CK), untreated L. chinensis silage was also assessed. The samples were taken at 0 day of opening after 300 days of ensiling (CK_0d, L_0d, W_0d, and LW_0d) and at 10 days of opening (CK_10d, L_10d, W_10d, and LW_10d). The fermentation quality, microbial counts, bacterial community, and aerobic stability of the silage were assessed. The CK_0d contained higher pH and aerobic bacteria count, and lower LA and BC concentrations than L_0d, W_0d, and LW_0d (p < 0.05), and the LAB and yeasts were only detected in CK at 0 day of opening. Lactobacillus had the most abundance among bacterial genera in all silages at 0 day of opening. Just CK had 2°C above the ambient temperature during aerobic exposure (at 224 h). During aerobic exposure, the pH and microbial counts in CK increased (p < 0.05), and Lactobacillus in L and LW had decreasing abundance (p < 0.05). The CK_10d had higher pH and microbial counts, and lower lactic acid and buffering capacity than L_10d, W_10d, and LW_10d (p < 0.05). At 10 days of opening, the coliforms and yeasts were just detected in CK, and Lactobacillus also had the most abundance among bacterial genera in all silages at 10 days of opening. Overall, inoculating LAB and adding water improved the fermentation quality and the aerobic exposure of L. chinensis silage after long-term storage. The activities of coliforms and yeasts during aerobic exposure contributed to the aerobic deterioration of L. chinensis silage without any treating. Lactobacillus dominated the bacterial communities of all silage at 0 and 10 days of opening. During aerobic exposure, the abundance of Lactobacillus reduced in L. chinensis silage treated with LAB or water.

Effect of Bacillus Additives on Fermentation Quality and Bacterial Community during the Ensiling Process of Whole-Plant Corn Silage

The aim of this study was to evaluate the effects of a complex Bacillus subtilis additive on the fermentation quality and bacterial community during the ensiling process of whole-plant corn silage (WPCS). The pH values of WPCS treated with the B. subtilis inoculant decreased faster than those of the control without inoculant, and significantly higher contents of lactic acid (LA) and acetic acid (AA) were observed. After 45 days of ensiling, the LA contents reached 7.95% (w/w). In the treatment group, the neutral detergent fibre (NDF) and acid detergent fibre (ADF) contents decreased significantly compared to the control, and the degradation rates of the NDF and ADF were 26.52% and 27.34% after 45 days, respectively. The deoxynivalenol (DON) content in the treatment group decreased to 205.67 μg/kg, which was significantly lower than the content of 382.51 μg/kg in the control group. The results indicated the positive effect of the B. subtilis inoculant in improving WPCS fermentation, especially in terms of degrading linocellulose and removing DON. The analysis of the bacterial community indicated that the B. subtilis inoculant resulted in an increased abundance of Lactobacillus, which contributed to the enhancement of LA production. The increased abundance of Bacillus possibly played a role in the degradation of NDF and ADF and the reduction in DON. Therefore, the complex B. subtilis additive could be used for the production of high-quality WPCS.

Dynamics of Bacterial Community and Fermentation Quality in Leymus chinensis Silage Treated With Lactic Acid Bacteria and/or Water

This study aimed to reveal the bacterial community and fermentation quality of Leymus chinensis silage during the fermentation process. L. chinensis was harvested at the heading stage, and ensiled with lactic acid bacteria (LAB, L), water (W), or a combination of both (LW) in vacuum-sealed plastic bags. As a control silage, untreated L. chinensis silage was also assessed. The samples were taken at 0, 5, 15, 35, and 60 days after ensiling. The bacterial community structure was assessed by plate cultivation and Illumina sequencing, and the fermentation parameters were also analyzed. Fresh L. chinensis contained low moisture (509 g/kg) and LAB (3.64 log colony-forming units/g fresh weight). Control silage displayed higher pH and lower lactic acid (LA) than other treatments during ensilage (p < 0.05); moreover, LW-treatment had lower pH from 5 to 35 days and greater LA at 5 days than L- and W-treatments (p < 0.05). During the fermentation process, Lactobacillus in L- and LW-treatments was the most dominant bacterial genus (>97%), had higher abundance than that in control silage and W-treatment (p < 0.05), and correlated negatively with other main genera and pH, and positively with LA and acetic acid (p < 0.05). Moreover, Lactobacillus had considerable abundance in W-treatment from 5 to 15 days (81.38–85.86%). Enterobacteriaceae had the most abundance among bacteria in control silage during ensiling (49.31–69.34%), and in W-treatment from 35 to 60 days (47.49–54.15%). The L-, W-, and LW-treatments displayed the aggregated bacterial community at 5 and 15 days, with W-treatment diverging from L- and LW-treatments at 35 and 60 days. Overall, the low moisture and/or insufficient LAB in fresh L. chinensis led to Enterobacteriaceae dominating bacterial community and contributing to the high pH and low LA in control silage during the fermentation process. Applying L, W, or LW contributed to Lactobacillus succession, LA production, and pH reduction during early stage of fermentation; moreover, treating with L and LW displayed more efficiency. Lactobacillus dominated the entire ensilage process in L- and LW-treatments and the early stage of fermentation in W-treatment, and contributed to the satisfactory fermentation quality of L. chinensis silage. The L- and LW-treatments displayed a similar pattern of bacterial succession during ensiling.

Advances in Microbial Fermentation Processes

In the food sector, fermentation processes have been the object of great interest in regard to enhancing the yield, the quality, and the safety of the final product [...]

Dynamics of Bacterial and Fungal Communities and Metabolites During Aerobic Exposure in Whole-Plant Corn Silages With Two Different Moisture Levels

The study was aimed to investigate the effect of moisture content on microbial communities, metabolites, fermentation quality, and aerobic stability during aerobic exposure in whole-plant corn silages preserved long time to improve the quality and aerobic stability of the silage during feed-out. Corn plants with two different moisture levels (high-moisture content, 680 g/kg; low-moisture content, 620 g/kg) were harvested at one-third and two-thirds milk-line stages, respectively, ensiled in laboratory-scale silos, and then sampled at 350 day after ensiling and at 2 and 5 day after opening to investigate bacterial and fungal communities, metabolites, and aerobic stability. High-moisture content increased aerobic stability and pH and decreased lactic acid and microbial counts in silages (P < 0.05). During aerobic exposure, the low-moisture silages had higher pH and lactic acid bacterial count and lower lactic acid than the high-moisture silages (P < 0.05); Acinetobacter sp. was the most main bacterial species in the silages; Candida glabrata and unclassified Candida had an increasing abundance and negatively correlation with aerobic stability of high-moisture silages (P < 0.05), while C. glabrata, Candida xylopsoci, unclassified Saccharomycetaceae, and unclassified Saccharomycetales negative correlated with aerobic stability of low-moisture silages (P < 0.05) with a rising Saccharomycetaceae; the silages had a reducing concentration of total metabolites (P < 0.05). Moreover, the high-moisture silages contained greater total metabolites, saturated fatty acids (palmitic and stearic acid), essential fatty acids (linoleic acid), essential amino acids (phenylalanine), and non-essential amino acids (alanine, beta-alanine, and asparagine) than the low-moisture silages at 5 day of opening (P < 0.05). Thus, the high-moisture content improved the aerobic stability. Acinetobacter sp. and Candida sp. dominated the bacterial and fungal communities, respectively; Candida sp. resulted in the aerobic deterioration in high-moisture silages, while the combined activities of Candida sp. and Saccharomycetaceae sp. caused the aerobic deterioration in low-moisture silages. The greater aerobic stability contributed to preserve the palmitic acid, stearic acid, linoleic acid, phenylalanine, alanine, beta-alanine, and asparagine during aerobic exposure.

Bacterial Succession Pattern during the Fermentation Process in Whole-Plant Corn Silage Processed in Different Geographical Areas of Northern China

Whole-plant corn silage is a predominant forage for livestock that is processed in Heilongjiang province (Daqing city and Longjiang county), Inner Mongolia Autonomous Region (Helin county and Tumet Left Banner) and Shanxi province (Taigu and Shanyin counties) of North China; it was sampled at 0, 5, 14, 45 and 90 days after ensiling. Bacterial community and fermentation quality were analysed. During fermentation, the pH was reduced to below 4.0, lactic acid increased to above 73 g/kg DM (p < 0.05) and Lactobacillus dominated the bacterial community and had a reducing abundance after 14 days. In the final silages, butyric acid was not detected, and the contents of acetic acid and ammonia nitrogen were below 35 g/kg DM and 100 g/kg total nitrogen, respectively. Compared with silages from Heilongjiang and Inner Mongolia, silages from Shanxi contained less Lactobacillus and more Leuconostoc (p < 0.05), and had a separating bacterial community from 14 to 90 days. Lactobacillus was negatively correlated with pH in all the silages (p < 0.05), and positively correlated with lactic and acetic acid in silages from Heilongjiang and Inner Mongolia (p < 0.05). The results show that the final silages had satisfactory fermentation quality. During the ensilage process, silages from Heilongjiang and Inner Mongolia had similar bacterial-succession patterns; the activity of Lactobacillus formed and maintained good fermentation quality in whole-plant corn silage.