Yusheng Lu

During weaning, piglets are exposed to multiple nutritional, environmental, pathogenic, and psychological stressors and are therefore susceptible to structural and functional intestinal injury. The resulting damage can lead to diarrhea, impaired growth, and increased susceptibility to disease, seriously compromising piglet health and the efficiency of pig production. Establishing stable and reliable experimental models that match specific research objectives is essential for elucidating the mechanisms of intestinal injury in piglets and for evaluating nutritional interventions and prevention and control strategies. Current research on porcine intestinal injury uses a multilevel framework centered on porcine intestinal epithelial cells, porcine intestinal organoids, and in vivo piglet models. These models offer distinct advantages in experimental controllability, tissue-level physiological relevance, and whole-organism biological fidelity, respectively, while each has a defined scope of application. Focusing on intestinal injury in piglets, this review comprehensively summarizes the construction methods, injury-induction approaches, and evaluation systems used across these model levels and analyzes the key factors affecting model stability and the comparability of research findings. This review is intended to inform mechanistic studies of intestinal injury in piglets, model standardization, and the evaluation of nutritional intervention strategies. On this basis, the review concludes that porcine intestinal epithelial cell lines are most appropriate for high-throughput mechanistic screening, organoids for questions that require epithelial diversity and donor- or region-specific context, and in vivo piglet models for confirming physiological and production relevance. Because model reproducibility depends strongly on challenge dose, animal or donor age, culture conditions, and assessment endpoints, a coordinated sequence from cell lines to organoids and finally to in vivo validation should be combined with standardized reporting of model parameters.

Nitrogen loss during manure composting reduces the fertilizer value of the final product and increases its environmental burden. This study evaluated whether semi-permeable membrane covering could reduce gaseous emissions and promote mineral-N retention during the co-composting of swine manure and spent mushroom substrate. Conventional aerobic composting (AC) and semi-permeable membrane-covered aerobic composting (MCAC) were conducted for 35 d. Compared with AC, MCAC reduced the estimated cumulative emissions of NH₃, N₂O, and CH₄ by 53.1%, 34.1%, and 45.7%, respectively, and lowered the estimated direct global warming potential of direct CH₄ and N₂O emissions by 37.5%. On day 35, MCAC had higher NH₄⁺-N (530.5 vs. 172.0 mg kg⁻¹) and NO₃⁻-N concentrations (80.1 vs. 42.6 mg kg⁻¹) than AC. Total nitrogen concentration decreased by 14.98% in MCAC and 17.82% in AC from day 1 to day 35. Composting stage explained 33.95% of bacterial community variation, versus 5.71% for membrane covering. Metagenomic nitrogen-cycling profiles varied mainly over time, with higher ammonia-oxidation potential in MCAC on day 10. Profiles covaried mainly with moisture and inorganic nitrogen. Overall, semi-permeable membrane covering maintained thermophilic composting while reducing gaseous emissions. The lower NH₃ and N₂O emissions, together with the higher final NH₄⁺-N and NO₃⁻-N concentrations, indicate reduced gaseous N release and greater mineral-N retention under MCAC.

Published syntheses showed that straw return generally benefits crop production and soil quality. However, direct evidence is still needed to determine whether these benefits are consistent and how they vary among regions and cropping systems. The analysis included 379 treatment-comparator records from 24 monitoring sites in a national field experimental network covering six major agricultural regions of China. Specifically, 2800 outcome-specific effect sizes, each expressed as the ratio of the straw return treatment to its paired straw removal comparator, were compiled for crop yield and nine soil indicators. Compared with straw removal, straw return was associated with 3.6% higher crop yield (95% CI, 0.9% to 6.5%); pooled estimates were also higher for soil organic matter (11.5%), total nitrogen (5.7%), available phosphorus (9.0%), available potassium (14.7%), volumetric soil water content (6.1%), water-stable aggregates (17.8%), and plough-layer thickness (16.4%). Heterogeneity among agricultural regions was detected for crop yield, available phosphorus, available potassium, water-stable aggregates, and plough-layer thickness; because agricultural region is strongly confounded with cropping system in this network, these differences are region-associated rather than attributable to geography itself, and several regional strata were represented by only two or three monitoring sites. Among cropping systems, heterogeneity was detected for available potassium, water-stable aggregates, and plough-layer thickness, but not for crop yield. The shorter-duration category had a larger available phosphorus response, whereas the longer-duration category had larger aggregate and plough-layer responses but did not show an additional mean yield benefit. The observed profiles suggest that P-K balance and soil structure monitoring merit priority in rice paddies in southern China. Similarly, residue placement in Northeast China, soil test-based K management in North China, and coordinated water and nutrient management in Northwest and Southwest China are indicated as monitoring priorities rather than as validated prescriptions. Overall, straw return was associated with higher crop yield and with higher values of multiple soil properties, although the response profiles differed among regions. These patterns indicate a need for locally validated, region-specific strategies if the national benefits of straw return for both crop yield and soil quality are to be realized.

Beneficial plant-associated microorganisms are key drivers of sustainable agriculture. However, their discovery and practical application remain insufficiently explored. Here, we present the first comprehensive comparative genomic analysis of a newly identified Sinomonas strain together with all publicly available genomes to assess its agronomic potential. Our results demonstrate that Sinomonas has an open pangenome and harbors multiple pathways for IAA biosynthesis, including a rare pathway found in only a limited number of bacterial taxa. The genus also contains genes involved in the synthesis of cytokinin analogues. In addition, genomic annotation identified ten genes putatively associated with phosphorus solubilization. A total of sixteen distinct biosynthetic gene clusters were identified, covering pathways for the biosynthesis of stenothricin, dactylocycline, aborycin, reveromycin, michiganin A, ikarugamycin, and peucechelin, all of which are compounds with reported antibacterial activity. In addition, Sinomonas carries multiple genes potentially involved in improving plant stress tolerance, including genes related to the biosynthesis of spermidine, 2,3-butanediol, acetoin, betaine, proline, and trehalose. Overall, these findings highlight the functional diversity of the Sinomonas genome and provide preliminary insights into its potential agricultural applications. The online version contains supplementary material available at 10.1186/s12866-026-05072-x.

A novel strain of the genus Sinomonas, designated G460-2 ^T, was isolated from rice paddy soil. The cells of strain G460-2 ^T were Gram-positive, aerobic, and non-motile rods. The optimal growth conditions for this strain were observed at 30 °C and a pH of 7.0. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain G460-2 ^T shared the highest sequence similarity (98.41%) with Sinomonas albida LC13^T. The genomic DNA of strain G460-2 ^T had a G + C content of 68.6 mol%. The genome size was determined to be 4.4 Mbp, and the average nucleotide identity (ANI) with the closest related reference strains was 86.39%, which is below the species delineation threshold of 95%. Digital DNA–DNA hybridization (dDDH) calculations yielded a relatedness value of 32.0% with the nearest neighbor. The predominant respiratory quinone identified in strain G460-2 ^T was MK-9(H2). The major fatty acids were C15:0 anteiso (44.8%), C17:0 anteiso (28.7%), C15:0 iso (11.6%), and C16:0 iso (10.1%).

Passiflora edulis Sims peel (Chinese name Baixiangguo, BXG) is a by-product with a high nutritional and economic value of Passiflora edulis Sims. In this study, corn was partly replaced with BXG to make feed for finishing pigs and the effects on the carcass traits, meat quality, muscle amino acid profile, and gene expression of finishing pigs were evaluated. A total of 20 healthy finishing pigs (Duroc × Landrace × Large) were randomly divided into two groups. The control group (CON) was fed the basal diet, and the experimental group (BXG) was fed a basal diet with BXG instead of 10% corn for a period of 43 d. Compared to the CON group, the carcass weight, intramuscular fat content, and marbling score were significantly increased, while the drip loss, b^* value, and shear force of the BXG group were significantly reduced (p < 0.05). Gene expression analysis showed that the mRNA expression of lipid synthesis and oxidative-type fiber related genes was significantly increased in the BXG group (p < 0.05). Proteomic research revealed that the metabolic pathways of the BXG and CON groups differed significantly. A total of 36 differentially expressed proteins were identified, mainly related to energy metabolism, fatty acid degradation, and endocrine regulation pathways. However, the contents of glutamine, glutamate, proline, and other amino acids in the BXG group were significantly reduced (p < 0.05). Overall, this study has a positive effect on improving meat quality, but the specific mechanism needs to be further explored, which offers practical guidance for the application of BXG in producing higher-quality pork and further promotes its commercial application.

Paddy fields are the main agricultural source of greenhouse gas methane (CH₄) emissions. To enhance rice yield, various fertilization practices have been employed in rice paddies. However, the key microbial and abiotic factors driving CH₄ emissions under different fertilization practices in paddy fields remain largely uncharted. This study conducted field experiments in a traditional double-cropping rice area in South China, utilizing five different fertilization practices to investigate the key factors influencing CH₄ emissions. High-throughput sequencing and PICRUSt2 functional prediction were employed to investigate the contributions of soil physicochemical properties, CH₄-metabolizing microorganisms (methanogens and methanotrophs), and key genes (mcrA and pmoA) on CH₄ emissions. The results showed that CH₄ emission fluxes exhibited seasonal variations, with consistent patterns of change observed across all treatments for both early- and late-season rice. Compared to the no-fertilization (NF) treatment, cumulative CH₄ emissions were lower in early-season rice with green manure (GM) and straw returning (SR) treatments, as well as in late-season rice with GM treatment, while rice yields were maintained at higher levels. High-throughput sequencing analysis revealed that potential methanogens were primarily distributed among four orders: Methanobacteriales, Methanocellales, Methanomicrobiales, and Methanosarcinales. Furthermore, there was a significant positive correlation between the relative abundance of the CH₄-related key gene mcrA and these microorganisms. Functional analysis indicated that these potential methanogens primarily produce methane through the acetoclastic and hydrogenotrophic pathways. Aerobic CH₄-oxidizing bacteria, predominantly from the genus Methylocystis, were detected in all the treatments, while the CH₄ anaerobic-oxidizing archaea ANME-1b was only detected in chemical fertilization (CF) and cow manure (CM) treatments. Our random forest analysis revealed that the relative abundance of two methanogens (Methanocellales and Methanosarcinales) and two environmental factors (pH and DOC) had significant impacts on the cumulative CH₄ emissions. The variance decomposition analysis highlighted the CH₄-metabolizing microorganisms explained 50% of the variance in the cumulative CH₄ emissions, suggesting that they are the key microbial factors driving CH₄ emissions. These findings provide guidance for the development of rational measures to reduce CH₄ emissions in paddy fields.

Phage therapy has the potential to alleviate plant bacterial wilt. However, the knowledge gap concerning the phage-agrochemical interaction impedes the broader application of phages in agriculture. This study characterized a phage isolate and investigated its interactions with agrochemicals. A novel species within the Ampunavirus genus was proposed, serving phage LPRS20 as a type phage with a broad lytic range and significant antibacterial activity against Ralstonia solanacearum strains infecting tobacco, chili, or tomato. Sensory evaluation of the morphology of tobacco leaves suggested that phage application resulted in negligible harm to plants. Investigations into phage-agrochemical interactions revealed synergisms when LPRS20 was delivered 4 h before thiodiazole-copper as well as LPRS20 in combination with low-concentration berberine. Overall, our findings reveal that phage LPRS20 represents a novel, effective, and eco-friendly biocontrol agent against tobacco bacterial wilt in vivo and in vitro and contributes to the potential integration of phages and agrochemicals for controlling soil-borne pathogens.

Bacillus velezensis is well known as a plant growth-promoting rhizobacteria (PGPR) and biocontrol agent. Nevertheless, there are very few reports on the study of B. velezensis on tomato early blight, especially the biocontrol effects among different inoculation concentrations. In this study, an IAA-producing strain, Bacillus velezensis YXDHD1-7 was isolated from the tomato rhizosphere soil, which had the strongest inhibitory effect against Alternaria solani. Inoculation with bacterial suspensions of this strain promoted the growth of tomato seedlings effectively. Furthermore, inoculations at 10⁶, 10⁷, and 10⁸ cfu/mL resulted in control efficacies of 100%, 83.15%, and 69.90%, respectively. Genome sequencing showed that it possesses 22 gene clusters associated with the synthesis of antimicrobial metabolites and genes that are involved in the production of IAA. Furthermore, it may be able to produce spermidine and volatile compounds that also enhance plant growth and defense responses. Our results suggest that strain YXDHD1-7 prevents early blight disease by promoting growth and enhancing the defense enzyme activities in tomato plants. This strain is a promising candidate for an excellent microbial inoculant that can be used to enhance tomato production.

Paenibacillus mucilaginosus has widely been reported as a plant growth-promoting rhizobacteria (PGPR). However, the important genomic insights into plant growth promotion in this species remain undescribed. In this study, the genome of P. mucilaginosus G78 was sequenced using Illumina NovaSeq PE150. It contains 8,576,872 bp with a GC content of 58.5%, and was taxonomically characterized. Additionally, a total of 7337 genes with 143 tRNAs, 41 rRNAs, and 5 ncRNAs were identified. This strain can prohibit the growth of the plant pathogen, but also has the capability to form biofilm, solubilize phosphate, and produce IAA. Twenty-six gene clusters encoding secondary metabolites were identified, and the genotypic characterization indirectly proved its resistant ability to ampicillin, bacitracin, polymyxin and chloramphenicol. The putative exopolysaccharide biosynthesis and biofilm formation gene clusters were explored. According to the genetic features, the potential monosaccharides of its exopolysaccharides for P. mucilaginosus G78 may include glucose, mannose, galactose, fucose, that can probably be acetylated and pyruvated. Conservation of the pelADEFG compared with other 40 Paenibacillus species suggests that Pel may be specific biofilm matrix component in P. mucilaginosus. Several genes relevant to plant growth-promoting traits, i.e., IAA production and phosphate solubilization are well conserved compared with other 40 other Paenibacillus strains. The current study can benefit for understanding the plant growth-promoting traits of P. mucilaginosus as well as its potential application in agriculture as PGPR.