Effects of the supplementation of plant-based formulations on microbial fermentation and predicted metabolic function in vitro

Effect of Diet Supplementation with Two Yeast Cultures on Rumen Fermentation Parameters and Microbiota of Fattening Sheep In Vitro

Yeast culture can improve ruminant health and reduce economic losses in intensive farming, but as a non-standardized product in China, its quality and efficacy vary significantly. In this study, a self-developed yeast culture was compared with a commercially available product using in vitro rumen fermentation and amplicon-based high-throughput sequencing to evaluate its effects on rumen fermentation parameters, microbial diversities, and community compositions in Hu sheep. The aim was to validate the efficacy and mechanisms of the self-developed yeast culture, produced with simplified raw materials and processes, on rumen function. The experiment was divided into four groups. In each 60 mL fermentation solution, the following treatments were added: 0.00 g high-concentrate diet (CK1 group, blank control), 0.40 g high-concentrate diet (CK2 group, basal diet control), 0.40 g high-concentrate diet supplemented with 5% XP yeast culture (XP group), and 0.40 g high-concentrate diet supplemented with 5% YC yeast culture (YC group). Gas production was measured every 4 h during fermentation. At the end of fermentation, pH, ammonia nitrogen, microbial protein, volatile fatty acids, and ruminal microbiota were determined. The results demonstrated the following. Compared to the CK2 group, both the XP and YC groups exhibited a significant increase (p < 0.05) in cumulative gas production and microbial protein content, while a significant decrease (p < 0.05) was observed in acetic acid content and the acetate-to-propionate ratio. The microbial protein content in the YC group was significantly higher (p < 0.05) than that in the XP group. Additionally, the content of valeric acid and isobutyric acid in the XP group was significantly higher (p < 0.05) compared to the other groups. The microbial community sequencing results revealed that the addition of yeast culture did not affect the alpha diversity index of rumen bacteria (p > 0.05); however, the addition of XP significantly reduced (p < 0.05) the richness of rumen fungal communities. At the phylum and genus levels, the relative abundance of multiple functional bacteria improved after adding YC. In summary, under the conditions of in vitro rumen fermentation with high-concentrate diets, adding 5% XP and YC yeast cultures both promoted rumen fermentation. The rumen fermentation type changed from the acetic acid type to the propionic acid type, which regulated rumen microbial composition and thereby improved dietary digestion efficiency. Notably, YC significantly increased the relative abundance of functional microbial communities compared to XP. These findings provide a theoretical and practical foundation for optimizing the large-scale breeding of Hu sheep.

Effects of increasing levels of rubber seed cake on growth performance, nutrient digestion metabolism, serum biochemical parameters, and rumen microbiota of Hu sheep

This study aimed to reveal the effects of increasing levels of rubber seed cake (RSC) on growth performance, nutrient digestion metabolism, serum biochemical parameters, and rumen microbiota in Hu sheep. In this study, 48 Hu sheep, weighing 17.01 ± 0.57 kg at 3 months of age, were randomly divided into four treatments: 0% rubber seed cake (RSC0%), 6% rubber seed cake (RSC6%), 12% rubber seed cake (RSC12%) and 18% rubber seed cake (RSC18%), with 12 sheep per group. Compared to the RSC0%, the ADG and DMI of the RSC6% and RSC12% were increased (P > 0.05). The apparent digestibility of OM and EE quadratically (P < 0.05) changed with the increase of RSC supplementation, with the greatest apparent digestibility of OM and EE observed in the RSC6% diet. With increased RSC supplementation, the N intake and fecal N increased linearly (P < 0.05), and the apparent digestibility of N reduced linearly (P < 0.05). As the increase of RSC supplementation, the serum levels of IgA, IgM, IgG, IL-4, T-AOC, and GSH-Px increased linearly (P < 0.05), and the serum level of IL-6 reduced linearly (P < 0.05). The serum level of IL-1β reduced quadratically (P < 0.05) with the increased RSC dose, and the serum level of SOD increased quadratically (P < 0.05) with the increased RSC dose. The ruminal NH3-N and the relative abundance of norank_Muribaculaceae quadratically (P < 0.05) changed with increased RSC supplementation, and the greatest relative abundance of norank_Muribaculaceae was observed in the RSC6% diet. In general, incorporating RSC into the diet of Hu sheep did not adversely affect growth performance and rumen fermentation characteristics. Supplementing with 6% RSC enhanced the relative abundance of norank_Muribaculacea in the rumen fluid and the immune and antioxidant capabilities. However, supplementing with 12 and 18% RSC might have negatively impacted nutrient digestion and metabolism. Therefore, this study recommended replacing corn and soybean meal with 6% RSC in the diet of Hu sheep.

Effects of chili straw on rumen fermentation, meat quality, amino acid and fatty acid contents, and rumen bacteria diversity in sheep

Crop residues have shown promise as non-conventional feed sources to enhance animal health and growth. This study evaluated the effects of chili straw (CS) on rumen fermentation, meat quality, amino and fatty acid composition, and rumen microbial diversity in sheep. Fifty F1 Dorper×Hu lambs (29.58 ± 2.06 kg) were randomly assigned to five groups, fed pelleted feed with 0%, 5%, 10%, 15%, or 20% CS over a 63-day period, including a 7-day pre-test. Post-trial, rumen fluid was sampled to assess fermentation and microbial profiles, and slaughter performance and meat quality were evaluated. Key findings include: (1) No significant differences were observed in rumen pH, NH3-N, or acetic acid-to-propionic acid ratio across groups (P > 0.05). (2) Rumen microbial diversity indices did not vary significantly between groups (P > 0.05), though the relative abundance of Firmicutes and Proteobacteria increased, and Bacteroidota decreased in CS-fed groups, with specific genus-level changes. (3) Carcass weight decreased in the CS20% group (P < 0.01). (4) Cooking loss decreased in CS10%, 15%, and 20% groups (P < 0.05), and meat redness increased in CS15% and 20% groups (P < 0.01). (5) Saturated fatty acids decreased, while the PUFA/SFA ratio and amino acid profiles, including sulfur-containing amino acids (SAA), dibasic amino acids (DAA), essential amino acids (EAA), and total amino acids (TAA), increased with CS, with a significant rise in Gly content in the CS15% group (P < 0.05). In conclusion, incorporating CS into lamb diets can enhance meat quality without adversely affecting rumen fermentation, with recommended levels between 10% and 15%.

Quercetin Supplementation Improves Intestinal Digestive and Absorptive Functions and Microbiota in Rats Fed Protein-Oxidized Soybean Meal: Transcriptomics and Microbiomics Insights

To clarify the nutritional mechanisms of quercetin mitigation in the digestive and absorptive functions in rats fed protein-oxidized soybean meal, 48 three-week-old male SD rats were randomly allocated into a 2 × 2 factorial design with two soybean meal types (fresh soybean meal or protein-oxidized soybean meal) and two quercetin levels (0 or 400 mg/kg) for a 28-day feeding trial. The protein-oxidized soybean meal treatment decreased (p < 0.05) the relative weights of the pancreas, stomach, and cecum, duodenal villus height, pancreatic and jejunal lipase activities, apparent ileal digestibility of amino acids, and apparent total tract digestibility of dry matter, crude protein, and ether extract. The supplementation of quercetin in the protein-oxidized soybean meal diet reversed (p < 0.05) the decreases in the duodenal length, ileal villus height, lipase activity, apparent ileal digestibility of amino acids, and apparent total tract digestibility of dry matter, crude protein, and ether extract. Transcriptomics revealed that the "alanine transport" and "lipid digestion and absorption" pathways were downregulated by the protein-oxidized soybean meal compared with fresh soybean meal, while the "basic amino acid transmembrane transporter activity" and "lipid digestion and absorption" pathways were upregulated by the quercetin supplementation. Microbiomics revealed that the protein-oxidized soybean meal increased the protein-degrading and inflammation-triggering bacteria in the cecum, while the relative abundances of beneficial bacteria were elevated by the quercetin supplementation.

Leachate derived humic-like substances drive the variation in microbial communities in landfill-affected groundwater

Landfills are commonly used for waste disposal in many countries, and pose a significant threat of groundwater contamination. Dissolved organic matter (DOM) plays a crucial role as a carbon and energy source, supporting the growth and activity of microorganisms. However, the changes in the DOM signature and microbial community composition in landfill-affected groundwater and their bidirectional relationships remain inadequately explored. Herein, we showed that DOM originating from more recent landfills mainly comprises microbially produced substances resembling tryptophan and tyrosine. Conversely, DOM originating from older landfills predominantly comprises fulvic-like and humic-like compounds. Leachate leakage increases microbial diversity and richness and facilitates the transfer of foreign bacteria from landfills to groundwater, thereby increasing the vulnerability of the microbial ecosystem in groundwater. Deterministic processes dominated the assembly of the groundwater microbial community, while stochastic processes accounted for an increased proportion of the microbial community in the old landfills. The dominant phyla observed in groundwater were Proteobacteria, Bacteroidota, and Actinobacteriota, and humic-like substances play a crucial role in driving the variation in microbial communities in landfill-affected groundwater. Predictions using PICRUSt2 suggested significant associations between various metabolic pathways and microbial communities, with the Kyoto Encyclopedia of Genes and Genomes pathway "Metabolism" being the most predominant. The findings contribute to advancing our understanding of the transformation of DOM and its interplay with microbial communities and can serve as a scientific reference for decision-making regarding groundwater pollution monitoring and remediation.

Effects of Flammulina velutipes mushroom residues on growth performance, apparent digestibility, serum biochemical indicators, rumen fermentation and microbial of Guizhou black goat

Introduction

The primary objective of the current study was to evaluate the effects of Flammulina velutipes mushroom residue (FVMR) in a fermented total mixed ration (FTMR) diet on the fattening effect and rumen microorganisms in Guizhou black male goats.

Methods

A total of 22 Guizhou black male goats were allocated into two groups using the Randomized Complete Block Design (RCBD) experimental design. The average initial weight was 22.41 ± 0.90 kg and with 11 goats in each group. The control group (group I) was fed the traditional fermentation total mixed ration (FTMR) diet without FVMR. Group II was fed the 30% FVMR in the FTMR diet.

Results

The results showed that compared with group I, the addition of FVMR in the goat diet could reduce the feed cost and feed conversion ratio (FCR) of group II (p < 0.01). Notably, the apparent digestibility of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), and dry matter (DM) were higher in group II (p < 0.01). The levels of growth hormone (GH), immunoglobulin A (IgA), and immunoglobulin M (IgM) in group II were higher than that of group I (p < 0.01), which the level of glutamic oxalacetic transaminase (ALT) and interleukin-6 (IL-6) was noticeably lower than that of group I (p < 0.01). 30% FVMR in FTMR diets had no effect on rumen fermentation parameters and microbial composition at the phylum level of Guizhou black male goats (p > 0.05). However, at the genus level, the relative abundance of bacteroidal_bs11_gut_group, Christensenellaceae_R-7_group and Desulfovibrio in group II was lower than in group I (p < 0.05), and the relative abundance of Lachnospiraceae_ND3007_group was higher than in group I (p < 0.01).

Discussion

In conclusion, the results of the current study indicated that 30% FVMR in the FTMR diet improves rumen fermentation and rumen microbial composition in Guizhou black male goats, which improves growth performance, apparent digestibility, and immunity.

- Invited Review - Assessment of the gastrointestinal microbiota using 16S ribosomal RNA gene amplicon sequencing in ruminant nutrition

The gastrointestinal (GI) tract of ruminants contains diverse microbes that ferment various feeds ingested by animals to produce various fermentation products, such as volatile fatty acids. Fermentation products can affect animal performance, health, and well-being. Within the GI microbes, the ruminal microbes are highly diverse, greatly contribute to fermentation, and are the most important in ruminant nutrition. Although traditional cultivation methods provided knowledge of the metabolism of GI microbes, most of the GI microbes could not be cultured on standard culture media. By contrast, amplicon sequencing of 16S rRNA genes can be used to detect unculturable microbes. Using this approach, ruminant nutritionists and microbiologists have conducted a plethora of nutritional studies, many including dietary interventions, to improve fermentation efficiency and nutrient utilization, which has greatly expanded knowledge of the GI microbiota. This review addresses the GI content sampling method, 16S rRNA gene amplicon sequencing, and bioinformatics analysis and then discusses recent studies on the various factors, such as diet, breed, gender, animal performance, and heat stress, that influence the GI microbiota and thereby ruminant nutrition.

Responses of soil microbial communities to concentration gradients of antibiotic residues in typical greenhouse vegetable soils

To explore the responses of soil microbial communities to concentration gradients of antibiotic residues in soil, 32 soil samples were collected from a typical greenhouse vegetable production base in Northern China in 2019. The total concentrations of 26 antibiotic residues in these soil samples was 83.24-4237.93 μg·kg^-1, of which metabolites of tetracyclines were 23.34-1798.80 μg·kg^-1. The total concentrations in 32 samples were clustered into three levels (L: <100 μg·kg^-1, M: 100-300 μg·kg^-1, H: >300 μg·kg^-1) to elucidate the impacts of antibiotic residues on the diversity, structure, composition, function and antibiotic resistome of soil microbial community. Results showed that higher concentration of antibiotic residues in soil was prone to decrease the diversity and shift the structure and composition of soil microbial community. Antibiotic resistome occurred in soils with antibiotic residues exceeding 300 μg·kg^-1. Interactions among soil bacteria followed the order of H > L > M, consistent with the relative abundances of mobile genetic elements. Bacteroidetes and Firmicutes were the top attributors impacting the profile of antibiotics in soil. According to weighted comprehensive pollution index of risk quotient, in 28.1 % of soil samples the residual antibiotics presented high ecological risk, whereas in the rest of soil samples the ecological risk is medium. The results will enrich the database and provide references for antibiotic contamination control in soils of the region and alike.

Glucogenic and lipogenic diets affect in vitro ruminal microbiota and metabolites differently

This study was conducted to evaluate the effects of two glucogenic diets (C: ground corn and corn silage; S: steam-flaked corn and corn silage) and a lipogenic diet (L: sugar beet pulp and alfalfa silage) on the ruminal bacterial and archaeal structures, the metabolomic products, and gas production after 48 h in vitro fermentation with rumen fluid of dairy cows. Compared to the C and S diets, the L dietary treatment leaded to a lower dry matter digestibility (DMD), lower propionate production and ammonia-nitrogen concentration. The two glucogenic diets performed worse in controlling methane and lactic acid production compared to the L diet. The S diet produced the greatest cumulative gas volume at any time points during incubation compared to the C and L diet. The metabolomics analysis revealed that the lipid digestion especially the fatty acid metabolism was improved, but the amino acid digestion was weakened in the L treatment than in other treatments. Differences in rumen fermentation characteristics were associated with (or resulting from) changes in the relative abundance of bacterial and archaeal genera. The rumen fluid fermented with L diet had a significantly higher number of cellulolytic bacteria, including the genera of Ruminococcus, Butyrivibrio, Eubacterium, Lachnospira, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. The relative abundances of amylolytic bacteria genera including Selenomonas_1, Ruminobacter, and Succinivibrionaceae_UCG-002 were higher in samples for diets C and S. The results indicated that the two glucogenic diets leaded to a higher relative abundance of bacteria which functions in succinate pathway resulting in a higher propionate production. The steam-flaked corn diet had a higher gas production and lower level of metabolites in fatty acids and amino acids. Most highly abundant bacteria were observed to be not sensitive to dietary alterations of starch and fiber, except for several amylolytic bacteria and cellulolytic bacteria. These finding offered new insights on the digesting preference of ruminal bacteria, which can assist to improve the rumen functioning.

Shifts in Soil Microbial Community Composition, Function, and Co-occurrence Network of Phragmites australis in the Yellow River Delta

Soil microorganisms play vital roles in regulating biogeochemical processes. The composition and function of soil microbial community have been well studied, but little is known about the responses of bacterial and fungal communities to different habitats of the same plant, especially the inter-kingdom co-occurrence pattern including bacteria and fungi. Herein, we used high-throughput sequencing to investigate the bacterial and fungal communities of five Phragmites australis habitats in the Yellow River Delta and constructed their inter-kingdom interaction network by network analysis. The results showed that richness did not differ significantly among habitats for either the bacterial or fungal communities. The distribution of soil bacterial community was significantly affected by soil physicochemical properties, whereas that of the fungal community was not. The main functions of the bacterial and fungal communities were to participate in the degradation of organic matter and element cycling, both of which were significantly affected by soil physicochemical properties. Network analysis revealed that bacteria and fungi participated in the formation of networks through positive interactions; the role of intra-kingdom interactions were more important than inter-kingdom interactions. In addition, rare species acted as keystones played a critical role in maintaining the network structure, while NO3−−N likely played an important role in maintaining the network topological properties. Our findings provided insights into the inter-kingdom microbial co-occurrence network and response of the soil microbial community composition and function to different P. australis habitats in coastal wetlands, which will deepen our insights into microbial community assembly in coastal wetlands.

Microbial community composition and metabolic functions in landfill leachate from different landfills of China

Landfill leachate usually harbors complex microbial communities responsible for the decomposition of municipal solid waste. However, the diversity and metabolic functions of the microbial communities in landfill leachate as well as the factors that influence them are still not well understood. In this study, Illumina MiSeq high-throughput sequencing was used to investigate the microbial community composition and metabolic functions in landfill leachate from 11 cities in China. The microbial diversity and structure of different leachate samples exhibited obvious differences. In general, Bacteroidetes, Firmicutes and Proteobacteria were the three dominant microbial communities among the 26 bacterial phyla identified in landfill leachate, regardless of the geographical locations. Diverse bacterial genera associated with various functions such as cellulolytic bacteria (e.g., Sphaerochaeta and Defluviitoga), acidifying bacteria (e.g., Prevotella and Trichococcus) and sulfate-reducing bacteria (e.g., Desulfuromonas and Desulfobacterium) were detected abundantly in the landfill leachate. Moreover, the archaeal community in all leachate samples was dominated by the orders Methanomicrobiales and Methanosarcinales belonging to the Euryarchaeota phylum. Notably, the archaea-specific primer pair covered more diverse archaeal communities than the universal bacteria-archaea primer pair. Seventeen archaeal genera belonging to acetoclastic, hydrogenotrophic, and methylotrophic methanogens were identified, and the composition of the dominant genera in these samples varied greatly. The canonical correlation analysis indicated that landfill age, electrical conductivity, ammonia nitrogen, and total nitrogen were significantly correlated with the microbial community structure. Based on PICRUSt2, a total of 41 metabolic pathways belonging to six metabolic pathway groups were predicted, and the KEGG pathway Metabolism was the most abundant group across all leachate samples. This study provides an important insight into the composition and functional characteristics of the microbial communities in landfill leachate.