Changes in chemical composition, structural and functional microbiome during alfalfa (Medicago sativa) ensilage with Lactobacillus plantarum PS-8

Responses of microbial community composition and CAZymes encoding gene enrichment in ensiled Elymus nutans to altitudinal gradients in alpine region

High-throughput metagenomic sequence technology was employed to evaluate changes in microbial community composition and carbohydrate-active enzymes encoding gene enrichment status in Elymus nutans silages to altitudinal gradients in the world's highest alpine region of Qinghai-Tibetan Plateau (QTP). E. nutans were collected from three different altitudes in QTP: 2,600 m (low altitude), 3600 m (moderate altitude), and 4,600 m [high (H) altitude], and ensiled for 7, 14, 30, and 60 d. Results indicated an improvement in silage quality with the increasing altitude, although the acetic acid concentration and dry matter loss were greater in H altitude silages after 30 d of ensiling. Harmful bacteria or potential pathogens predominated in the microbial community on d 7 and 14 of fermentation, while genera belonging to lactic acid bacteria gradually became the main microorganisms with the increasing altitude on d 30 and 60 of ensiling. The abundance of carbohydrate-active enzymes genes responsible for macromolecular carbohydrate degradation in silage increased with increasing altitude, and those genes were mainly carried by Lactiplantibacillus and Pediococcus at 30 and 60 d of ensiling. The abundance of key enzymatic genes associated with glycolysis and organic acid production in carbohydrate metabolism pathway was higher in H altitude silages, and Lactiplantibacillus and Pediococcus were also the main hosts after 30 d of silage fermentation, except for the fact that acetic acid production was also related to genera Leuconostoc, Latilactobacillus, and Levilactobacillus.

IMPORTANCE

The fermentation quality of Elymus nutans silage was getting better with the increase of altitude in the Qinghai-Tibetan Plateau. The abundance of hosts carrying carbohydrate-active enzymes genes and key enzyme genes related to organic acid production increased with increasing altitude during the later stages of fermentation. Lactiplantibacillus and Pediococcus were the core microorganisms responsible for both polysaccharide hydrolysis and silage fermentation in the late stage of ensiling. This study provided insights on the influence of different altitudes on the composition and function of silage microbiome in the Qinghai-Tibetan Plateau, and provided a reference approach for improving the quality and controllability of silage production in high altitude areas of the Qinghai-Tibetan Plateau.

Effects of temperature and lactic acid Bacteria additives on the quality and microbial community of wilted alfalfa silage

This study investigated the influence of different temperatures (35℃ High temperature and average indoor ambient temperature of 25℃) and lactic acid bacterial additives (Lactiplantibacillus plantarym, Lentilactobacillus buchneri, or a combination of Lactiplantibacillus plantarym and Lentilactobacillus buchneri) on the chemical composition, fermentation quality, and microbial community of alfalfa silage feed. After a 60-day ensiling period, a significant interaction between temperature and additives was observed, affecting the dry matter (DM), crude protein (CP), acid detergent fiber (ADF), and neutral detergent fiber (NDF) of the silage feed (p < 0.05). Temperature had a highly significant impact on the pH value of the silage feed (p < 0.0001). However, the effect of temperature on lactic acid, acetic acid, propionic acid, and butyric acid was not significant (p > 0.05), while the inoculation of additives had a significant effect on lactic acid, acetic acid, and butyric acid (p > 0.05). As for the dynamic changes of microbial community after silage, the addition of three kinds of bacteria increased the abundance of lactobacillus. Among all treatment groups, the treatment group using complex bacteria had the best fermentation effect, indicating that the effect of complex lactic acid bacteria was better than that of single bacteria in high temperature fermentation. In summary, this study explained the effects of different temperatures and lactic acid bacterial additives on alfalfa fermentation quality and microbial community, and improved our understanding of the mechanism of alfalfa related silage at high temperatures.

Dietary curcumin alleviates intestinal damage induced by ochratoxin A in juvenile grass carp (Ctenopharyngodon idella): Necroptosis and inflammatory responses

Ochratoxin A (OTA) is one of the most common pollutants in aquatic feed. As a first line of defense, intestinal barriers could be utilized against OTA in order to prevent disorders. Natural product supplementation is one of the most popular strategies to alleviate toxicity induced by mycotoxins, but there is a lack of knowledge about how it functions in the teleost intestine. In this study, 720 juvenile grass carp of about 11 g were selected and four treatment groups (control group, OTA group, curcumin [Cur] group, and OTA + Cur group) were set up to conduct a 60-day growth test. After the test, the growth performance and intestinal health related indexes of grass carp were investigated. The addition of dietary Cur could have the following main results: (1) inhibit absorption and promote efflux transporters mRNA expression, reducing the residuals of OTA, (2) decrease oxidative stress by reducing oxidative damage and enhancing the expression of antioxidant enzymes, (3) promote mitochondrial fusion proteins to inhibit the expression of mitotic proteins and mitochondrial autophagy proteins and enhance mitochondrial function, (4) reduce necroptosis-related gene expression through inhibiting the tumor necrotic factor receptor-interacting protein kinase/mixed lineage kinase domain-like pathway, (5) reduce the expression of pro-inflammatory factors by inhibiting the Toll-like receptor 4/nuclear factor-κB signaling pathway to alleviate the intestinal inflammatory response. In summary, the results suggested that Cur could alleviate OTA-induced intestinal damage by enhancing antioxidant capacity and mitochondrial function as well as reducing necroptosis and inflammation in the grass carp intestine. This study provided a theoretical basis and production implications for dietary Cur that could improve growth performance and alleviate the intestinal damage induced by OTA in fish.

The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly

Symbiosis with arbuscular mycorrhizal (AM) fungi improves plant nutrient capture from the soil, yet there is limited knowledge about the diversity, structure, functioning, and assembly processes of AM fungi-related microbial communities. Here, 16S rRNA gene sequencing and metagenomic sequencing were used to detect bacteria in the rhizosphere of Lotus japonicus inoculated with and without AM fungi, and the L. japonicus mutant ljcbx (defective in symbiosis) inoculated with AM fungi in southern grassland soil. Our results show that AM symbiosis significantly increased bacterial diversity and promoted deterministic processes of bacterial community construction, suggesting that mycorrhizal symbiosis resulted in the directional enrichment of bacterial communities. AM fungi promoted the enrichment of nine bacteria, including Ohtaekwangia, Niastella, Gemmatimonas, Devosia, Sphingomonas, Novosphingobium, Opitutus, Lysobacter, Brevundimonas, which are positively correlated with NPK-related parameters. Through a functional identification experiment, we found that six of these genera, including Brevundimonas, Lysobacter, Ohtaekwangia, Sphingomonas, Devosia, and Gemmatimonas, demonstrated the ability to mineralize organophosphate and dissolve inorganic phosphorus, nitrogen, and potassium. Our study revealed that AM fungi can regulate rhizosphere bacterial community assembly and attract specific rhizosphere bacteria to promote soil nutrient turnover in southern grasslands.

Varieties and ensiling: Impact on chemical composition, fermentation quality and bacterial community of alfalfa

Introduction

Six species of alfalfa commonly found in northern China were collected in the present study.

Methods

The chemical composition and epiphytic microbial communities during the ensiling were analyzed; and their effects on fermentation quality and silage bacterial communities were assessed. The effects of physicochemical characteristics of alfalfa on the bacterial community were also investigated in terms of nutritional sources of microbial growth and reproduction.

Results and discussion

The results showed that the chemical composition was significantly different in various alfalfa varieties, yet, the dominant genera attached to each variety of alfalfa was similar, except for pantoea (p<0.05). After ensiling, both the fermentation quality and microbial community changed obviously (p<0.05). Specifically, ZM2 had lower pH and ammonia nitrogen (NH₃-N) content but higher LA content than other varieties of alfalfa silage. Beneficial bacteria such as Lentilactobacillus and Lactiplantibacillus were predominant in ZM2, which accounted for the higher fermentation quality. Significant correlations between the chemical composition of silage, fermentation quality and bacterial communities composition were observed. Moreover, variations in bacteria community structure during the fermentation of alfalfa were mainly influenced by water-soluble carbohydrates (36.79%) and dry matter (21.77%).

Conclusion

In conclusion, this study revealed the influence of chemical composition on microbial community and fermentation quality, laying the groundwork for future studies on high-quality silage.

Metagenomics analysis reveals the performance of homo- and heterofermentative lactic acid bacteria in alfalfa silage fermentation, bacterial community, and functional profiles

Alfalfa (Medicago sativa L.) is a kind of roughage frequently utilized as an animal feed but challenging to be ensiled due to its low water-soluble carbohydrate (WSC), high water content, and elevated buffering capacity, thus requiring the application of lactic acid bacteria (LAB) to improve its fermentation. This study employed high-throughput metagenomic sequence technology to reveal the effects of homofermentative LAB, Lactobacillus plantarum (Lp), or Pediococcus pentosaceus (Pp), and heterofermentative LAB, L. buchneri (Lb), or their combinations (LbLp or LbPp) (applied at 1.0 × 109 colony forming units (cfu) per kilogram of alfalfa biomass fresh material) on the fermentation, microbial community, and functional profiles of alfalfa silage after 7, 14, 30, and 60 ensiling days. The results indicated a reduction (P < 0.05) in glucose and pH and higher (P < 0.05) beneficial organic acid contents, xylose, crude protein, ammonia nitrogen, and aerobic stability in Lb-, LbPp-, and LbLp-inoculated alfalfa silages after 30 and 60 d. Also, higher (P < 0.05) WSC contents were recorded in LbLp-inoculated alfalfa silages after 30 d (10.84 g/kg dry matter [DM]) and 60 d (10.92 g/kg DM). Besides, LbLp-inoculated alfalfa silages recorded higher (P < 0.05) LAB count (9.92 log10 cfu/g) after 60 d. Furthermore, a positive correlation was found between the combined LAB inoculants in LbLp-inoculated alfalfa silages and dominant LAB genera, Lactobacillus and Pediococcus, with fermentation properties after 30 and 60 d. In addition, the 16S rRNA gene-predicted functional analyses further showed that the L. buchneri PC-C1 and L. plantarum YC1-1-4B combination improved carbohydrate metabolism and facilitated further degradation of polysaccharides in alfalfa after 60 d of ensiling. These findings reveal the significant performance of L. buchneri and L. plantarum in combination with dominant LAB species in suppressing the growth of Clostridia, molds, and yeasts and improving the fermentation characteristics and functional carbohydrate metabolism of alfalfa after 60 d ensiling, thus suggesting the need for further studies to uncover the diverse performance of the LAB combination and their consortium with other natural and artificial inoculants in various kinds of silages.

A meta-analysis to observe silage microbiome differentiated by the use of inoculant and type of raw material

Silage fermentation is naturally carried out by lactic acid bacteria (LAB) to mainly produce lactic acid (LA) and other organic acids as preservatives. Along with fermentation time, the growth of LAB will replace and suppress undesirable microorganisms. This meta-analysis study aimed to explore silage microbiome differentiated by LAB inoculants and type of raw materials. A total of 37 articles with 185 studies and 475 datasets were used for building up the meta-database. Data were subjected to the mixed model methodology. The parameters observed were silage quality and silage microbiome post-ensiling process. Results revealed that four bacterial genera along with Weissella dominated the post-ensiling process. The addition of lactic acid inoculants in the silage has increased the abundance of Lactobacillus spp. and decreased the Shannon index significantly. Moreover, the abundance of both L. plantarum and L. buchneri increased, and subsequently, Weissella, Pseudomonas, Proteobacteria, pH value, ammoniacal nitrogen (NH₃-N), coliforms, and the yeasts were decreased significantly due to the addition of LAB inoculants in silage (p < 0.05). Environmental factors such as temperature affected the existence of Pseudomonas, Exiguobacterium, and Acinetobacter. However, the dry matter, LA, acetic acid (AA), the ratio of LA to AA, and the LAB population were enhanced significantly (p < 0.05). Among the LAB types, the lowest abundance of Pseudomonas was due to the LAB group, while the lowest abundance of Weissella and Proteobacteria was due to the addition of the combined LAB group. In conclusion, the addition of LAB is effectively enhancing the silage microbiome and silage quality by altering bacterial diversity and the metabolic products of the silage materials for safe preservation.

Effects of Isolated LAB on Chemical Composition, Fermentation Quality and Bacterial Community of Stipa grandis Silage

This study aimed to screen and identify lactic acid bacteria (LAB) strains from the Stipa grandis and naturally fermented silage, and assess their effects on the silage quality and bacterial community of Stipa grandis after 60 days of the fermentation process. A total of 38 LAB were isolated, and strains ZX301 and YX34 were identified as Lactiplantibacillus plantarum and Pediococcus pentosaceus using 16S rRNA sequences; they can normally grow at 10−30 °C, with a tolerance of pH and NaCl from 3.5 to 8.0 and 3 to 6.5%, respectively. Subsequently, the two isolated LAB and one commercial additive (Lactiplantibacillus plantarum) were added to Stipa grandis for ensiling for 60 days and recorded as the ZX301, YX34, and P treatments. The addition of LAB was added at 1 × 105 colony-forming unit/g of fresh weight, and the same amount of distilled water was sprayed to serve as a control treatment (CK). Compared to the CK treatment, the ZX301 and YX34 treatments exhibited a positive effect on pH reduction. The water-soluble carbohydrate content was significantly (p < 0.05) increased in ZX301, YX34, and P treatments than in CK treatment. At the genus level, the bacterial community in Stipa grandis silage involves a shift from Pantoea to Lactiplantibacillus. Compared to the CK treatment, the ZX301, YX34, and P treatments significantly (p < 0.05) increase the abundance of Pediococcus and Lactiplantibacillus, respectively. Consequently, the results indicated that the addition of LAB reconstructed microbiota and influenced silage quality. The strain ZX301 could improve the ensiling performance in Stipa grandis silage.

Current approaches on the roles of lactic acid bacteria in crop silage

Lactic acid bacteria (LAB) play pivotal roles in the preservation and fermentation of forage crops in spontaneous or inoculated silages. Highlights of silage LAB over the past decades include the discovery of the roles of LAB in silage bacterial communities and metabolism and the exploration of functional properties. The present article reviews published literature on the effects of LAB on the succession, structure, and functions of silage microbial communities involved in fermentation. Furthermore, the utility of functional LAB in silage preparation including feruloyl esterase-producing LAB, antimicrobial LAB, lactic acid bacteria with high antioxidant potential, pesticide-degrading LAB, lactic acid bacteria producing 1,2-propanediol, and low-temperature-tolerant LAB have been described. Compared with conventional LAB, functional LAB produce different effects; specifically, they positively affect animal performance, health, and product quality, among others. In addition, the metabolic profiles of ensiled forages show that plentiful probiotic metabolites with but not limited to antimicrobial, antioxidant, aromatic, and anti-inflammatory properties are observed in silage. Collectively, the current knowledge on the roles of LAB in crop silage indicates there are great opportunities to develop silage not only as a fermented feed but also as a vehicle of delivery of probiotic substances for animal health and welfare in the future.

Multi-Omics-Based Functional Characterization of Hybrid Fermented Broussonetia papyrifera: A Preliminary Study on Gut Health of Laying Hens

More attention has been paid in recent times to the application of Broussonetia papyrifera (BP) silage in ruminants, owing to its nutritional value. This study aimed to characterize the functionality of fermented BP and preliminarily explore its dietary effects on the gut health of laying hens. In this study, we characterized the antioxidant and antibacterial activities, bioactive compound profile, and bacterial community in Lactobacillus plantarum-fermented BP (FBP), as well as its dietary effects on intestinal morphology, microbiota and gene expression of laying hens. Improved contents of protein, total polyphenol and flavonoids as well as antioxidant and antibacterial activities were found after fermentation of BP. Untargeted metabolomics displayed more abundant apigenin, luteolin, diosmetin, and quercetin within the FBP, which may contribute to its functionality. Microbiome demonstrated increased abundance of Firmicutes at the expense of Cyanobacteria phylum, accompanied with raised levels of Lactobacillus genus. The results of a feeding trial showed dietary FBP supplementation increased the serum superoxide dismutase, but down-regulated gene expression of aryl hydrocarbon receptor (AhR), mucin2, and ZO-2, without obviously affecting the intestinal morphology and colonic microbiota. These findings suggest that FBP warrants further investigation as it may serve as a functional dietary supplement in laying hen feed.

Antimicrobial resistance determinants in silage

Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer's body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.