The efficient conversion of lignocellulosic biomass is at the core of ensuring the economic feasibility of biorefineries, where the comprehensive utilization of xylose serves as a determinant of overall conversion efficiency. Pichia kudriavzevii has demonstrated significant potential in industrial bioprocessing owing to its tolerance to low pH, high temperatures, and environmental stressors. However, its innate deficiency in xylose assimilation severely restricts its application in biomass valorization. [Objective] To elucidate the molecular mechanisms underlying the silencing of xylose metabolism in P. kudriavzevii E1, thereby providing a theoretical basis for the bioconversion of lignocellulosic feedstocks. [Methods] The xylose assimilation capacity of P. kudriavzevii E1 was evaluated, and its genome was analyzed to identify the genes and metabolic bottlenecks associated with xylose assimilation. Comparative transcriptomics was employed to characterize the differential expression of metabolic genes before and after the introduction of a xylose transporter. Furthermore, the heterologous expression of genes involved in efficient xylose metabolism was performed to verify specific rate-limiting steps within the pathway. [Results] Bioinformatics analysis, coupled with the functional restoration of xylose uptake via heterologous transporter expression, confirmed that the lack of high-affinity xylose transporters was the primary limiting factor for xylose assimilation in P. kudriavzevii E1. Although three genes—PkXYL1, PkXYL2, and PkXKS1—encoding core enzymes of the xylose redox pathway were natively present in the P. kudriavzevii E1 genome, in vitro enzymatic assays revealed that the low relative activity of PkXR was a critical cause of substrate accumulation and slow xylose metabolism. Comparative transcriptomics of the engineered strain P. kudriavzevii E1-Xpg4562 indicated that yeast cells underwent profound metabolic reprogramming in xylose-containing media, preferentially activating ribosome biogenesis and oxidative phosphorylation. However, the significant downregulation of TAL1 and the insufficient transcriptional response of genes in the pentose phosphate pathway (PPP) resulted in inefficient PPP flux. This prevented the effective redirection of carbon flux into glycolysis, thereby obstructing downstream xylose metabolism. Finally, quantification of the expression of key xylose metabolism genes identified by transcriptomics further demonstrated that the uncoordinated transcriptional regulation of essential downstream genes hindered overall metabolic efficiency. [Conclusion] The silencing of xylose metabolism in P. kudriavzevii E1 results from the combined effects of deficient substrate transport, low endogenous catalytic activity, and uncoordinated transcriptional regulation. This study provides a crucial theoretical foundation for the precision engineering of xylose metabolic pathways in non-conventional industrial yeasts.

Microbial fertilizers are an important component of green agricultural inputs, playing a key role in reducing chemical fertilizer use, improving arable land quality, and mitigating agricultural emissions. Using the registration certificate data of microbial fertilizers in China from 2000 to 2025, this paper systematically analyzes the structural characteristics and regional patterns of China’s microbial fertilizer industry and takes Guangdong Province as a case to examine the development bottlenecks of this industry in Guangdong. The study finds that China’s microbial fertilizer industry has gone through three stages: slow start, steady growth, and explosive expansion, forming a clustered pattern centered on Shandong, Hebei, Heilongjiang, and Henan provinces. However, three major structural contradictions are becoming increasingly prominent. Specifically, the products are highly concentrated in microbial inoculants, bioorganic fertilizers, and compound microbial fertilizers; microbial strain resources are highly homogenized; and enterprises are scattered, small, and weak. The number of registration certificates in Guangdong Province (334) accounts for only 2.83% of the national total (11 813) and is merely 13.82% of that of Shandong Province (2 416), which ranks first in China. Nearly 40% of enterprises are in a state of one certificate for one product, indicating a severe mismatch between the industrial scale and Guangdong’s status as a major agricultural province. In response to the above problems, this paper proposes recommendations from six aspects: elevating the policy position of microbial fertilizers, mining and protecting microbial strain resources, reforming registration management, optimizing the enterprise ecosystem, bridging the gap in technology transfer, and exploring the paths tailored for Guangdong, aiming to provide a reference for the high-quality development of the microbial fertilizer industry in China and especially Guangdong Province.

[Objective] To efficiently express and purify wild-type and three active site-deleted variants (ENO1-M1, ENO1-M2, and ENO1-M3) of ENO1 through the insect cell/baculovirus expression system, thus providing a theoretical basis for subsequent functional research, antibody development, and inhibitor screening. [Methods] Wild-type and active site-deleted genes of ENO1 with a C-terminal 6×His tag were cloned into the pFastBac-HTB vector via molecular cloning and then transformed into DH10Bac competent cells to obtain recombinant Bacmid through screening. Recombinant baculovirus particles were transfected into ExpiSf9 insect cells to generate the P0 virus stock, which was then amplified to produce high-titer P1 virus for target protein expression. Expression products were purified by affinity chromatography (e.g., nickel column) and identified by SDS-PAGE, Coomassie Brilliant Blue staining, and Western blotting. The anti-ENO1 monoclonal antibody, single-chain antibody, and chimeric antibody were used for specific detection by Western blotting. On the basis of the conversion of 2-phosphoglycerate to phosphoenolpyruvate (PEP) under the catalysis by ENO1, the specific activity of ENO1 was measured by UV spectrophotometry at 240 nm. [Results] All recombinant plasmids and bacmids were successfully constructed, and high-level expression of recombinant proteins was achieved in insect cells. High-purity recombinant proteins were obtained, and Western blotting analysis confirmed their reactivity. The deletion of active sites of the enzyme did not affect the immunoreactivity. The specific activity of wild-type ENO1 was 691.28 U/mg, while those of the three deletion variants were significantly reduced. ENO1-M2 (with deletion of GSHAGNK at residues 156-162) and ENO1-M3 (with deletion of SPDPSRYI at residues 262-270) exhibited particularly pronounced losses of enzyme activity. [Conclusion] We successfully expressed and purified both wild-type and active site-deleted ENO1 proteins with retained reactivity by using the baculovirus expression vector system. The results confirm that GSHAGNK and SPDPSRYI are two key active sites of this enzyme, laying both theoretical and material foundations for further exploring the functions of ENO1 and developing its specific inhibitors.

Litopenaeus vannamei is one of the crustacean species with the highest production and economic value in the global aquaculture industry. Its health status is closely linked to the community succession and balance of the microbiota in the aquaculture system, and the stable supply of seeds is one of the fundamental and core components of the high-quality development of the shrimp aquaculture industry. Characterizing the pattern of bacterial community succession during the early developmental stages of shrimp is an essential prerequisite for achieving microbiome-based regulation in larviculture. [Objective] To establish a standardized bacterial community dataset covering the entire cycle of L. vannamei larviculture, thereby providing data support for systematic investigations on the microbial communities during shrimp larvae development. [Methods] Focusing on the complete developmental stages of L. vannamei larvae, larval shrimps and rearing water samples were collected from the larviculture system of the Zhejiang Mariculture Research Institute following standardized sampling and laboratory processing protocols. Bacterial community datasets were constructed by high-throughput 16S rRNA gene amplicon sequencing combined with the standard Dix-seq amplicon analysis pipeline. [Results] This dataset encompassed the raw paired-end sequencing reads from 102 samples (48 larval samples and 54 rearing water samples) across the entire cycle of shrimp larviculture, comprising a total of 204 fastq.gz files and 4 709 988 raw paired-end reads. After quality control, 4 255 994 effective sequences and 202 505 zero-radius operational taxonomic units (ZOTUs) were obtained. Data generation strictly followed standardized protocols, with multi-point composite sampling ensuring sample representativeness of microbial samples, and unified sample collection and nucleic acid extraction procedures were employed. All analytical parameters were publicly disclosed through the parameter card mechanism of the Dix-seq pipeline, guaranteeing the reproducibility and reliability of the data analyses. [Conclusion] The samples in this dataset cover the key developmental nodes of L. vannamei larvae, achieving synchronous monitoring of the bacterial communities throughout the entire larviculture period. It provides fundamental data for exploring bacterial community succession and host-environment interaction mechanisms during the early developmental stages of shrimp, thereby facilitating the development of green larviculture technologies based on microbiome regulation. Additionally, it serves as a benchmark for the standardized management and analysis of similar high-throughput sequencing data, which is of great significance for enhancing the standardization and operability of microbiome research in agricultural ecosystems.

Bovine mastitis is a key factor restricting the high-quality development of China’s dairy industry, while the prevalence of antimicrobial-resistant bacteria and recurrent infections have become severe challenges for the current prevention and control system. Although long-term antibiotic selection pressure may temporarily alleviate clinical symptoms, it significantly accelerates the evolution and dissemination of multidrug-resistant (MDR) pathogens, leading to rising treatment failure rates and a transition toward chronic disease. Epidemiological data indicate that the pathogen spectrum of bovine mastitis in China is dominated by Staphylococcus aureus, Streptococcus spp., and Enterobacteriaceae, with resistance genes propagating across species and regions through horizontal gene transfer (HGT) mediated by plasmids, transposons, and integrons. Furthermore, mechanisms such as biofilm formation, efflux pump activation, target modification, and intracellular escape interact with the mammary microenvironment to establish a robust defense barrier against host immune clearance and antimicrobial agents. Incorporating the principles of endogenous inflammation and metabolic dysregulation mediated by the “gut-mammary axis”, this paper systematically reviews the regional prevalence and molecular dissemination mechanisms of resistant pathogens in China. It provides an in-depth analysis of the pathological basis of recurrence and prospectively proposes comprehensive management strategies—ranging from precision diagnosis to alternative therapies—aiming to provide a theoretical foundation for the scientific control of bovine mastitis.

Alzheimer’s disease (AD) is a complex neurodegenerative disorder characterized by progressive cognitive impairment. In recent years, the “gut-brain axis” has been recognized to play an important role in the pathogenesis of AD, with the gut microbiota-derived metabolites serving as key mediators of gut-brain communication. This review systematically summarizes the alterations and underlying molecular mechanisms of five classes of key metabolites—short-chain fatty acids, bile acids, indole derivatives, trimethylamine N-oxide, and lipopolysaccharides—during the progression of AD. This review not only provides new perspectives for understanding the pathological processes of AD but also lays a theoretical foundation for the development of diagnostic and therapeutic strategies based on microbiota modulation.

Neurodegenerative diseases, a group of highly prevalent central nervous system disorders, are closely linked to gut microbiota dysbiosis and impaired gut-brain axis function. The emerging gut-brain axis theory offers a novel perspective to explain how microbes exert remote, cross-organ regulation over the central nervous system. Recent studies have indicated that butyrate-producing bacteria, a core functional component of the gut microbiota, exhibit dynamic changes temporally and spatially correlated with the onset and progression of these diseases. These bacteria are thought to modulate the central nervous system microenvironment and disease pathology via the gut-brain axis. This article systematically reviews the bidirectional signaling mechanisms between the gut microbiota and the brain, analyzing the complex, multidimensional relationship between butyrate-producing bacteria and neurodegenerative diseases. This analysis encompasses population heterogeneity in patients with diverse clinical features and the dynamic evolution of these bacterial communities across different disease stages. We summarize the key mechanisms by which butyrate-producing bacteria regulate disease progression, including barrier protection, immunomodulation, metabolic regulation, and epigenetic modification. Furthermore, we explore their clinical potential as predictive biomarkers and therapeutic targets. We propose that future research should prioritize the development of targeted intervention strategies for gut-derived butyrate-producing bacteria. This review aims to provide a theoretical foundation and novel insights to advance both the fundamental investigation and clinical translation of these bacteria in the context of neurodegenerative diseases.

Coronavirus infections pose a serious threat to human health and have resulted in substantial economic losses to the livestock industry. Coronaviruses invade host cells primarily through two pathways: cell surface membrane fusion and endosomal membrane fusion. During viral entry, the spike protein subunit 1 (S1) recognizes and binds to cellular receptors, while the spike protein subunit 2 (S2) facilitates membrane fusion between the viral envelope and host cell membrane. Due to its high sequence conservation across different coronaviruses, S2 represents an attractive target for the development of broad-spectrum antiviral agents. Blocking S2-mediated membrane fusion can effectively inhibit viral infection. This review summarizes recent advances in understanding the mechanisms of coronavirus entry into host cells, the structure and function of the spike protein, and the development of membrane fusion inhibitors. In addition, this paper discusses the challenges and future prospects in targeting S2 for antiviral drug development, aiming to provide insights for coronavirus prevention and the discovery of novel antiviral therapeutics.

Salicylic acid (SA) is an important phenolic compound that plays a key role in plant defenses and is widely used in pharmaceuticals, cosmetics, and personal care products due to its significant anti-inflammatory and antimicrobial activities. Currently, the production of SA mainly relies on plant extraction and chemical synthesis, which suffers from complex processes, severe environmental pollution, and high dependence on petrochemical resources. With the rapid development of synthetic biology, metabolic engineering, and artificial intelligence (AI) technologies, the green synthesis of SA through intelligently designed microbial cell factories, empowered by machine learning algorithms and automated platforms, has become an important research direction to replace conventional production methods. This review systematically summarizes the microbial biosynthetic pathways of SA. With a focus on the intelligent design theme, this paper highlights the application of AI and synthetic biology tools in the discovery and utilization of natural SA-producing microbial resources and the rational reconstruction and optimization of the SA biosynthetic pathway in model microorganisms via intelligent metabolic engineering strategies. Furthermore, it introduces the key intelligent technologies for enhancing yields and the challenges faced. Finally, it discusses the future trends in this field.

Streptococcus suis is a major zoonotic pathogen that can infect both pigs and humans, causing severe diseases such as meningitis in humans. Its pathogenicity depends on the ability to rapidly adapt to environmental stress and host immune responses. Serine/threonine kinases and their corresponding phosphatases constitute a eukaryotic-like signal transduction system in bacteria and play a key regulatory role in S. suis serotype 2, closely related to its biological characteristics and pathogenic mechanisms. Through precise regulation of the phosphorylation and dephosphorylation of downstream substrates, serine/threonine kinases/phosphatases form complex signaling networks, thereby influencing various physiological and pathogenic processes of the bacterium. This article systematically reviews the currently known substrates of serine/threonine kinases in S. suis serotype 2, with a focus on elucidating how these kinases precisely regulate bacterial growth and division, capsule synthesis, stress tolerance, adhesion, invasion, and pathogenicity by modulating the phosphorylation status of functional substrates. This review aims to provide new perspectives for deciphering the pathogenic mechanism of S. suis serotype 2 and the development of novel antibacterial strategies.