Colorectal cancer (CRC), one of the most common malignancies of the digestive system, is characterized by complex pathogenic mechanisms and an overall poor prognosis. The gut microbiota and its metabolites play a dual role in CRC by modulating various forms of programmed cell death (PCD), either promoting or inhibiting tumorigenesis and influencing the tumor responses to chemotherapy and immunotherapy. This review systematically summarizes recent advances in understanding how the gut microbiota regulates CRC initiation, progression, and responses to therapies through the modulation of apoptosis, autophagy, ferroptosis, and pyroptosis. Furthermore, it discusses the potential clinical-translational implications of these findings, aiming to provide a theoretical foundation for elucidating CRC pathogenesis and developing novel therapeutic strategies targeting the gut microbiota.

Objective The engineering of the reductive glycine pathway (rGlyP) in Komagataella phaffii (syn. Pichia pastoris) represents a promising strategy for the co-utilization of methanol and CO₂. However, the efficiency of this pathway is constrained by the insufficient supply of intracellular reduced nicotinamide adenine dinucleotide (NADH), as the native alcohol oxidase (AOX) pathway generates hydrogen peroxide rather than NADH, leading to energy loss and oxidative stress. To overcome this bottleneck, this study reconstructed the methanol oxidation pathway and employed a subcellular compartmentalization strategy to optimize the carbon flux and energy metabolism. Methods Five different sources of NAD⁺-dependent methanol dehydrogenase (MDH) were screened in an aox1/aox2-deficient strain by using the growth curve and methanol utilization rate as indicators to determine the optimal MDH, and the methanol induction concentration was optimized. Subsequently, a compartmentalization strategy was employed by fusing the peroxisomal targeting signal 1 (PTS1) to MDHN1T, which targeted the enzyme to the peroxisome to spatially couple methanol oxidation with formaldehyde detoxification. Results The MDHN1T derived from Cupriavidus necator had the best catalytic performance, and the optimum methanol induction concentration was optimized to be 0.6%. Under co-utilization conditions, the engineered strain achieved a methanol consumption rate of 28.98 mg/d, with the total intracellular NAD_total pool, NADH/NAD⁺ ratio, and biomass being 1.3, 1.2, and 2.2 folds, respectively, of those in the parental strain. Conclusion This study successfully alleviates the redox cofactor imbalance in the rGlyP and enhances co-utilization of methanol and CO₂ in K. phaffii, providing a robust chassis and a theoretical basis for the development of microbial cell factories utilizing one-carbon resources.

Objective To investigate changes in ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 (Agap2) expression during hepatic fibrosis progression following hepatitis E virus (HEV) infection and preliminarily explore the association between chronic HEV infection and Agap2 expression. Methods A BALB/c mouse model of HEV infection was established through inoculation in tail vein and subjected to RNA sequencing. HEV infection and Agap2 expression in the liver tissue were detected via immunohistochemistry, immunofluorescence assay, and real-time qPCR. Results Agap2 expression was upregulated following HEV infection (24 hpi group: P=0.000 3, 48 hip group: P=0.001 9). Chronic HEV infection induced hepatic fibrosis in mice, and Agap2 expression in the mouse liver was positively correlated with HEV load (r=0.797 4, P<0.000 1). Similarly, in vitro experiments demonstrated that Agap2 expression was upregulated in HEV-infected Huh 7.5.1 cells (r=0.968 3, P=0.002 4) and LX-2 cells (r=0.683 5, P=0.006 5), showing a positive correlation with HEV load. Conclusion The results demonstrate that Agap2 expression is positively correlated with HEV load during hepatic fibrosis progression after chronic HEV infection. Agap2 may serve as a potential molecular target for the treatment of HEV-associated hepatic fibrosis.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of secondary metabolites synthesized by the ribosomes of microorganisms and formed through a series of post-translational modifications. They have diverse structures, high stability, and antimicrobial, antiviral, anti-inflammatory or anti-tumor activities. Moreover, they are not prone to generating drug resistance, thus showcasing great potential to be applied in the fields of medicine, food, and agriculture. The genomes of microorganisms harbor a large number of biosynthetic gene clusters for RiPPs, while many of them require the producing strains to be cultivated in specific conditions or to interact with other environmental microorganisms, being the “dark matter” in the genome. Heterologous biosynthesis is an effective means to obtain novel RiPPs and make use of them. This article reviews the recent research progress in the diversity, bioactivity, genomic mining, and heterologous biosynthesis of RiPPs from microorganisms, with the expectation of providing a theoretical basis for a deeper understanding of the molecular structures and functions of RiPPs, as well as for the development and application of novel microbial active metabolites and their producers.

Respiratory viral infections pose a severe threat to global public health security, and exploring effective strategies to prevent them is of clinical significance. The gut microbiota plays a crucial role in regulating anti-infective immunity by remodeling the immune microenvironment, maintaining the immune homeostasis and boosting antiviral defenses of the host. Conversely, dysbiosis of the gut microbiota can disrupt immune homeostasis, resulting in impaired innate immune responses and abnormal activation of adaptive immunity, thereby raising the risk of respiratory viral infections in the host. This study elaborates on the essential role of the gut microbiota in the antiviral immune response of the host across multiple aspects. (1) It thoroughly explains how the gut microbiota contributes to forming an immune defense barrier by performing physiological functions such as secreting antimicrobial peptides, metabolizing nutrients, preserving mucosal barrier integrity, and modulating immune homeostasis of the host. (2) It analyzes the antiviral immune regulatory network that involves the regulation of type I interferon responses and immune cell differentiation, all within the context of gut microbiota balance and dysbiosis. (3) It explores how probiotics exert antiviral effects through mechanisms such as inhibiting viral proliferation, improving the host’s immune response, reducing secondary infections, and restoring gut microbiota balance. Although breakthroughs have been made in understanding the ternary interaction network of the microbiota, the immune system, and viral infection, the molecular mechanisms behind its dynamic balance and precise regulation still urgently need detailed investigation. Specifically, the mechanisms of interactions between gut microbiota metabolites and host epigenetic regulation, along with the long-term protective strategies of microbiota-induced immune homeostasis against viral infection, remain to be systematically revealed through multi-omics technologies.

Microorganisms represent the largest untapped resource reservoir on the Earth, and breakthroughs in their isolation and cultivation are prerequisites for fundamental advances in the life sciences. This review focuses on recent progress in the isolation and screening technologies for bacteria, fungi, and archaea. It systematically elucidates how the development and application of cutting-edge isolation and screening technologies have enhanced the efficiency of isolating previously uncultivable and rare microbial taxa. By summarizing lineage-specific strategies—such as multi-omics targeting and single-cell precision localization for bacteria, metabolomics-guided screening and microfluidic technology for fungi, and co-culture systems coupled with extreme-condition cultivation for archaea—this review highlights the core value of interdisciplinary technology integration in bridging genomic data with in situ functional validation. Finally, the article prospectively addresses challenges in data integration and the construction of automated workflows, thereby outlining a strategic pathway for the systematic exploration of microbial resources.

Objective The effects of the helper strain (Priestia endophytica)1-112 on the growth of Ketogulonicigenium vulgare and the biotransformation of 2-keto-L-glonic acid (2-KLG) remain unclear. In this study, we cultured the helper strain in different media to study the mechanisms of the growth- and 2-KLG biotransformation-promoting effects of the helper strain on K. vulgare. Methods We used different media (minimal, mixed, and fementation media) to culture the helper strain and investigated the effects of the strain on the growth and 2-KLG biotransformation of K. vulgare. The differently expressed genes (DEGs) and associated metabolic pathways in the helper strain cultured in different media were analyzed by transcriptomics to screen the key factors in the co-culture system. The effects of key factors on the growth and 2-KLG biotransformation of K. vulgare were evaluated to explore their roles in the co-culture system. Results Strain 1-112 cultured in the minimal medium lost or reduced the ability to promote 2-KLG production, while it retained the ability to promote the growth of K. vulgare. This result indicated that the helper strain promoted 2-KLG biotransformation through two distinct mechanisms. There were 1 859 DEGs in strain 1-112 cultured in fermentation medium in comparison with the minimal medium, and the DEGs were significantly enriched in the pathways such as nicotinate and nicotinamide metabolism, carbon metabolism, arginine and proline metabolism, and amino acid biosynthesis. In addition, the helper strain cultured in the minimal medium containing some key factors could restore the ability to promote 2-KLG production. Glycine, proline, biotin, and nicotinic acid were found to be essential for promoting K. vulgare growth, whereas glycine, threonine, biotin, and nicotinic acid played critical roles in enhancing 2-KLG biotransformation. Conclusion The helper strain promoted the growth and 2-KLG biotransformation of K. vulgare through different mechanisms.

Objective To determine the cause of death of an adult crocodile in the Alligator sinensis Management Center in Anhui Province. Methods Bacteria were isolated from the heart, liver, lung, and spleen via the culture method, and the isolates were identified by morphological observation, biochemical tests, and molecular biological methods. Furthermore, the mucus phenotype was determined by means of the string test. Multilocus sequence typing (MLST) was conducted on the basis of seven housekeeping loci. Virulence gene analysis, pathogenicity test, drug resistance gene analysis, and antimicrobial susceptibility testing were conducted to clarify the pathogenicity and drug resistance of the isolates. Results The pathogenic bacteria isolated from the four organs were morphologically consistent Gram-negative bacilli. Through biochemical tests and 16S rRNA gene and khe sequencing, the isolates were identified as Klebsiella pneumoniae YZE01, capsular serotype K2. String test showed that the strain was hypermucinous K. pneumoniae, and MLST analysis showed that the strain belonged to sequence type 25 (ST25). The strain carried six virulence genes: fimH, entB, rmpA, rmpA2, mrkD, and wabG. Pathogenicity tests showed that some of the tested mice died within 24 h after infection with YZE01, and the same strain was isolated from the heart, liver, lung, and spleen. The lung tissue of infected mice showed hemorrhage and congestion lesions to different degrees. In addition, RT-qPCR revealed that the transcript levels of IL-1β, IL-6, IL-8, and TNF-α in the lung peaked at 12 h post-infection and then declined. The strain carried three drug resistance genes (blaSHV, armA, and ermB), and it was not sensitive to cephalexin, cefazolin, ampicillin, streptomycin, gentamicin, erythromycin, roxithromycin, and clindamycin. Conclusion The isolated strain K. pneumoniae YZE01 carries a variety of virulence genes and has strong pathogenicity and drug resistance. It is considered as a major cause of death in A. sinensis. The findings are conducive to the prevention and control of diseases in A. sinensis.

Objective The outer membrane protein CirA serves as a specific transporter for catecholate-type siderophores and is involved in the uptake of siderophores and other nutrients, playing a crucial role in bacterial physiology. However, its impact on bacterial antibiotic resistance remains unclear. This study aimed to investigate the role of ahcirA in the antibiotic resistance of Aeromonas hydrophila ATCC 7966 under antibiotic stress, thereby providing a theoretical basis for elucidating the molecular mechanism by which ahcirA regulates bacterial resistance. Methods With A. hydrophila ATCC 7966 as the model organism, an ahcirA knockout strain (ΔahcirA) was constructed, and its susceptibility to multiple quinolones and aminoglycosides was assessed. Quantitative proteomics was further employed to compare protein expression profiles of ΔahcirA with and without antibiotic stress. Bioinformatic approaches were adopted for the functional analysis of differentially expressed proteins. Results In the media containing enrofloxacin and norfloxacin, the growth of ΔahcirA was significantly impaired compared with that of the wild-type strain. In contrast, ΔahcirA exhibited enhanced growth in the media supplemented with kanamycin and streptomycin. Proteomic and bioinformatic analyses revealed that the deletion of ahcirA may alter bacterial antibiotic resistance by affecting the expression of proteins involved in multiple biological processes, such as small molecule metabolism, and by modulating the expression of antibiotic resistance genes. Conclusion CirA plays a significant role in the antibiotic resistance of A. hydrophila. Its absence influences bacterial susceptibility to different classes of antibiotics by regulating the expression of diverse functional proteins and antibiotic resistance genes.

Objective To establish a mouse model that effectively simulates the key clinical features of porcine Senecavirus A (SVA) infection, providing a crucial experimental tool for elucidating its pathogenesis and evaluating prevention and control products. Methods Five-week-old SPF C57BL/6J wild-type (WT) mice and type I interferon receptor-deficient (C57BL/6J ^IFNR-/- ) mice were inoculated via intraperitoneal, subcutaneous, and intramuscular routes. Blood and tissue samples were collected on days 1, 3, and 5 post-infection (dpi) for analysis of gross pathology, histopathology, viral load, and dynamic determination of inflammatory cytokines at the mRNA level. Results Compared with the mock-infected control group, both mouse strains developed gross lesions (e.g., swollen inguinal lymph nodes, yellowish livers, splenomegaly) and histopathological lesions (e.g., cortical disintegration of lymph nodes, hepatocellular necrosis, atrophy of splenic white pulp, and renal tubular necrosis). However, these lesions were more severe in C57BL/6J ^IFNR-/- mice. Viral RNA was widely distributed in tissues of both groups but was significantly higher in the C57BL/6J ^IFNR-/- group. Notably, viremia was undetectable in WT mice, whereas in C57BL/6J ^IFNR-/- mice, the virus was detected in whole blood as early as 1 dpi, peaked at 3 dpi, and then declined rapidly. Inflammatory cytokine analysis revealed significantly higher mRNA levels and protein levels of IL-1β and IL-6 in C57BL/6J ^IFNR-/- mice than in WT mice. Conclusion The C57BL/6J ^IFNR-/- mouse model successfully simulates, for the first time, the transient viremia characteristic of porcine SVA infection. It comprehensively replicates key features, including the multi-organ viral distribution, high viral load, and self-limiting recovery, providing a more effective animal model for delving into the pathogenic mechanism of SVA and evaluating vaccines and antiviral drugs.