The cyclic oligonucleotide (CO)-based anti-phage signaling system (CBASS), an innate immune system widely distributed in bacteria, is composed of oligonucleotide cyclases cGAS/DncV-like nucleotidyltransferases (CD-NTases), CD-NTase-associated protein (Cap), and accessory proteins. When bacteria are infected by phages, CD-NTases generate COs to amplify signals. Subsequently, effectors are activated by COs, inducing cell death through multiple mechanisms such as damaging cell membranes, degrading DNA, and depleting essential metabolites. Accessory proteins are responsible for regulating the CBASS, ultimately inhibiting phage infection. This review introduces the composition and classification of CBASS and further discusses the process by which CD-NTases recognize and bind to phage RNA to activate the synthesis of the second messenger CO. Effectors encoded by Cap effector genes mediate cell killing by binding to COs, while accessory proteins encoded by Cap auxiliary genes are involved in regulating the activity of CBASS. In addition, the immune evasion of phages from CBASS is also discussed. This review helps to understand the detailed mechanisms and biological significance of the interactions between phages and their host bacteria from the perspective of CBASS.

Objective Bacteria of Pseudomonas are the main cause of food-borne and clinical infections. At present, mass spectrometry and 16S rRNA gene are widely used to identify Pseudomonas, while the facilities relied on are expensive and require cumbersome operation. Internationally, the numerical identification products require manual single-sample loading procedures, which are cumbersome. This study aims to develop a numerical identification kit for Pseudomonas with high accuracy and simple operation. Methods On the basis of the existing biochemical reaction data of Pseudomonas, we developed a numerical identification model via the branching diagram method and designed and optimized 11 biochemical matrix formulas for microquantization. We then used the kit to identify the standard strains and isolates of Pseudomonas and compared the results with those from mass spectrometry and PCR to evaluate the performance of the kit. Results A numerical identification kit was developed, and it was capable of identifying 10 species of Pseudomonas with just one sample addition. The accuracy rate of the kit in the identification for 5 standard strains and 135 isolates reached 97.04%, and the accuracy rate in actual samples was 97.74%. The biochemical test was stable and reproducible, and the identification cost (25 CNY/sample) of the kit was only 10% of that (240 CNY/sample) of the comparable product from bioMérieux (France). Conclusion The numerical identification kit developed in this study for Pseudomonas has simple operation, a low price, and high accuracy, which can be used in clinical diagnosis and food detection.

Objective The mucosal microbiota of large yellow croaker (Larimichthys crocea) plays a vital role in host health and environmental adaptation. However, differences in the mucosal microbiota composition between wild and cultured populations of large yellow croaker, as well as their assembly mechanisms, remain unclear. This study compared the microbiota composition and characteristics in the skin, gill, and intestine of wild and cultured large yellow croaker, aiming to elucidate the impacts of aquaculture environments on host-microbiota interactions. Methods We employed 16S rRNA gene high-throughput sequencing to analyze the microbiota characteristics in the skin, gill, intestine, and surrounding seawater of wild and cultured large yellow croaker. Key bacterial strains were isolated and characterized. Results Significant divergence of mucosal microbiota was observed between cultured and wild populations. (1) Cultured fish exhibited homogenized mucosal microbiota across the skin, gill, and intestine, whereas wild fish maintained strong tissue-specific microbial signatures. (2) Cultured fish had more unique taxa in the skin (156 vs. 93) and gill (171 vs. 50) but fewer unique taxa in the intestine (118 vs. 253) than wild counterparts. (3) LEfSe revealed enrichment of potential opportunistic pathogens (e.g., Vibrio and Photobacterium) in the skin/gill of wild fish, while myxobacteria (e.g., Haliangium) were specifically enriched in the intestine of cultured fish. (4) Co-occurrence networks demonstrated predominantly cooperative interactions in both groups, yet wild fish microbiota displayed stronger competitive relationships. (5) Lysinibacillus sp. isolated from the mucosal tissue of large yellow croaker demonstrated cross-tissue colonization in cultured populations, exhibiting broad-spectrum antibiotic susceptibility and potential probiotic properties. Conclusion The aquaculture environment significantly reshaped the mucosal microbiota composition, diversity, and interaction networks in large yellow croaker, resulting in reduced microbiota stability and impaired metabolic processes, immune competence, and environmental adaptability of the host. These findings provide critical insights for refining aquaculture practices, developing probiotic resources, and mitigating microbiota dysbiosis in large yellow croaker.

Objective To screen the biocontrol bacterial isolates with antagonistic activity against root rot pathogens of Panax notoginseng from the rhizosphere of Bletilla striata in a P. notoginseng-B. striata rotation system, identify the isolates, and evaluate their control effects, thereby providing a scientific basis for the application of P. notoginseng-B. striata rotation in alleviating continuous cropping obstacles and screening biocontrol strains from the rhizosphere of the plants for rotation rather than from that of target plants in the plant rotation system for controlling soil-borne diseases in the field. Methods The dilution plate method was employed to isolate culturable microorganisms from the rhizosphere soil of B. striata. The antagonistic activities of the isolates against root rot pathogens of P. notoginseng were evaluated via the dual culture assay. Molecular identification was performed based on the 16S rRNA gene sequence. In pot experiments, antagonistic bacteria were inoculated, and then the ability of antagonistic bacteria to control root rot was evaluated based on the root rot incidence of P. notoginseng. Results The rotation with B. striata significantly reduced the incidence and disease index of P. notoginseng root rot compared with continuous cropping. A total of 200 bacterial strains were isolated from the rhizosphere soil of B. striata, from which 25 strains exhibiting antagonistic activities against the root rot pathogens including Ilyonectria destructans RS6, Fusarium solani F3, and Fusarium oxysporum Z5 of P. notoginseng were screened out. The isolation efficiency of antagonistic bacteria was 12.5%. The 25 strains were identified as 12 species belonging to 5 genera, demonstrating rich diversity. There were 14 strains of Bacillus sp., including 4 strains of B. subtilis, 2 strains of B. velezensis, 6 strains of B. amyloliquefaciens, 1 strain of B. cereus, and 1 strain of B. toyonensis. There were 5 strains of Acinetobacter, including 2 strains of A. johnsonii, 2 strains of A. junii, and 1 strain of A. pittii. There were 4 strains of Pseudomonas, including 3 strains of P. putida and 1 strain of P. fulva. In addition, 1 strain of Enterobacter asburiae and 1 strain of Aeromonas caviae with antagonistic activities were isolated. Four strains (B. amyloliquefaciens BJ1, B. subtilis BJ7, B. amyloliquefaciens BJ8, and A. johnsonii YB10) antagonistic to all the three pathogens were applied to continuous cropping soil. They significantly reduced the root rot incidence and enhanced the fresh weight of P. notoginseng. Conclusion The rhizosphere soil of B. striata in rotation with P. notoginseng harbors diverse biocontrol strains against the root rot pathogens of P. notoginseng. This study lays a theoretical foundation for the rotation of P. notoginseng with B. striata to alleviate continuous cropping obstacles.

Objective To elucidate and compare the diversity, structure, and functional characteristics of gut microbiota in sympatric fish species from a perspective of microbial ecology and explore the role of gut microbiota in feeding habit and ecological niche differentiation. Methods Foregut, midgut, and hindgut samples from Gymnocypris eckloni and Schizopygopsis pylzovi, along with their aquatic environmental samples, were collected from the upper Yellow River. The gut microbiota and potential functions were compared by 16S rRNA gene high-throughput sequencing and multiple bioinformatics approaches. Results Microbial alpha diversity followed the trend of aquatic environment>S. pylzovi>G. eckloni (P<0.05). In G. eckloni, alpha diversity was highest in the foregut, whereas in S. pylzovi, it decreased progressively from the foregut to the midgut and then to the hindgut. Beta diversity analysis based on clustering and CPCoA demonstrated that microbial communities derived from different gut segments of the same species were more similar to each other than those derived from the same gut segment of different species, indicating that the differences attributable to species were greater than those attributable to gut segments (P<0.001). Pseudomonadota accounted for over 50.00% of the gut microbiota in all sample types, while Bacillota comprised more than 25.00% in the guts of both fish species, which was significantly higher than that (3.80%) observed in the aquatic environment. Fusobacteriota and Cetobacterium were nearly absent in water and S. pylzovi but showed high abundance in the midgut and hindgut of G. eckloni. Enterococcus was specifically enriched in the hindgut of G. eckloni, while Lactococcus were predominantly found in the hindgut of S. pylzovi. PICRUS2 functional prediction revealed that gut microbiota of both species primarily enriched amino acid and carbohydrate metabolism pathways. The enriched metabolic pathways varied significantly across different gut segments of S. pylzovi, while significant differences in signaling molecules and interaction, cardiovascular diseases, and metabolism of terpenoids and polyketides were noted for the same gut segments between the two species. Conclusion There were significant differences in the microbiota composition and diversity in the gut between the two fish species and their aquatic environments, with distinct gut microbiota functions for each species. This study establishes a micrological foundation for research on the feeding habit and ecological niche differentiation of fish and provides theoretical support for exploitation of gut microbial resources and conservation and resource management of plateau fish species.

Streptococcus pneumoniae is a common opportunistic pathogen that can cause various infectious diseases, including acute otitis media, bronchitis, sinusitis, community-acquired pneumonia, septicemia, and purulent meningitis. Autophagy, a lysosome-dependent intracellular degradation pathway, plays a dual regulatory role in both bacterial infection and host defense against pathogens. During S. pneumoniae infection, host cells can activate xenophagy to eliminate invading bacteria. However, this pathogen has evolved multiple evasion strategies, such as interfering with autophagosome maturation, escaping autophagic encapsulation, and even hijacking the autophagy pathway to promote intracellular survival and dissemination. Recent years have witnessed significant progress in understanding the molecular mechanisms underlying the dynamic interplay between S. pneumoniae and host autophagy systems during bacterial infection, yet a systematic review synthesizing these findings remains unavailable. This review focuses on the interaction network and key mechanisms of S. pneumoniae with host cell autophagy, aiming to provide theoretical foundations and research perspectives for developing novel targeted therapeutic strategies against S. pneumoniae infections.

With the development of human industrial activities, nitrogen (N) emissions and atmospheric N deposition have increased significantly. When atmospheric N deposition exceeds the critical load that plants can bear, it may exert a negative effect on plants and lead to a decrease in species abundance. As an important biotic factor affecting species abundance, mycorrhizae can affect plant diversity and community structure through nutrient supply and hyphal network mechanism. Objective To compare the critical load of N deposition of understory herbaceous plants with different mycorrhizal types and explore how mycorrhizal types affect the responses of understory herbaceous plants to N deposition. Methods According to the database of long-term N deposition critical load of forest herbaceous plants, and the published literature, critical load database of herbaceous plants under different mycorrhizal types of forest forests in response to N deposition was established. We identified three mycorrhizal types of forest dominant species, which included arbuscular mycorrhiza (AM), ectomycorrhiza (ECM), and AM+ECM. The effects of mycorrhizal types on the critical load of N deposition of understory herbaceous plants were investigated. Results The critical load of N deposition of understory herbaceous plants varied in forests of different mycorrhizal types (P<0.05). The critical load of N deposition was the highest [9.28 kg N/(ha·a)] in the forest of the AM+ECM type, the second [8.41 kg N/(ha·a)] in the forest of the ECM type, and the lowest [7.19 kg N/(ha·a)] in the forest of the AM type. In forests of different mycorrhizal types, the critical loads of understory herbaceous plants of different functional groups (gramineous and non-gramineous) in response to N precipitation were consistent with the responses of all understory herbaceous plants of different mycorrhizal types. N deposition caused changes in the abundance of understory herbaceous plants. The species abundance of understory herbaceous plants in the forest of the AM type showed an increasing trend, while that in the forest of the ECM type mainly decreased. Conclusion Mycorrhizal types affect the critical load of N deposition of understory herbaceous plants (P<0.05), which is related to the niche differentiation, N concentration of litter, and N acquisition strategies of different mycorrhizal types of plants. In addition, the abundance of understory herbaceous plants will also vary due to different mycorrhizal types.

Bacterial glycoproteins, glycolipids, and polysaccharides are collectively known as glycans, which can serve as pivotal pathogenic factors leading to infection. Bacterial protein glycosylation mainly includes N-glycosylation, O-glycosylation, S-glycosylation, and arginine glycosylation. Glycolipids and polysaccharides are also important glycoconjugates, mainly including lipopolysaccharides, lipoarabinomannan, rhamnolipids, peptidoglycan, teichoic acids, and capsular polysaccharides. Bacterial glycoconjugates can promote host-pathogen interactions, influencing bacterial virulence, drug resistance, and biofilm formation, thereby facilitating bacterial infection. In addition, bacterial glycoconjugates can exert dual effects by modulating the host immune system: on one hand, aiding bacteria in achieving immune evasion and causing host infection; on the other, activating host immunity to help eliminate bacteria and suppress infection. This article provides an overview of bacterial glycans regarding the types, structural characteristics, roles in bacterial adhesion and colonization, and regulation of host immune responses and summarizes the effects of bacterial glycans on infection, aiming to offer a distinct perspective from glycoimmunology and an alternative strategy for clinical prevention and treatment of bacterial infectious diseases.

Objective The outbreaks of infectious bovine rhinotracheitis (IBR) have been reported in multiple regions across China. To systematically characterize the molecular features and biological properties of the predominant strains of infectious bovine rhinotracheitis virus (IBRV) and provide etiological insights for evidence-based prevention and control against IBR. Methods We collected the bovine lung tissue for detection of common bovine respiratory viruses by PCR. Viral isolation was performed with MDBK cells, and then metagenomic sequencing was conducted to determine and analyze complete genome sequences of the viruses. Viruses were purified via the plaque assay and subcultured to the 9th generation (F9) for determination of the 50% tissue culture infectious dose (TCID₅₀), monitoring of one-step growth kinetics, and observation of viral particle morphology via electron microscopy. Two IBRV-seronegative healthy adults of cattle were intranasally inoculated with the F9 suspension (2.5 mL/nostril), while one additional head of cattle was housed in close contact. The clinical manifestations were monitored, including body temperature fluctuations and viral shedding dynamics. Results PCR detection revealed the presence of both IBRV and bovine coronavirus (BCoV) in the bovine lung tissue. After inoculation into MDBK cells, obvious cytopathic effects were observed at the third passage. Metagenomic sequencing confirmed the virus as IBRV, with a whole genome length of 134 678 bp. This isolate was designated as IBRV GSLT/04/2024. The TCID₅₀ of F9 was 10^5.5 TCID₅₀/mL, and no mutation was detected in the gB, gC, gD, or gE gene. Based on the gC gene and whole genome sequences, this strain was classified into the IBRV 1.2b subtype lineage. Viral shedding began on day 5 post-inoculation in the inoculated cattle and on day 10 in the contact cattle, lasting for approximately 10 days. The amount of viral shedding followed the order of nasal swabs>oral swabs>rectal swabs>ocular swabs. On day 30 post-inoculation, IBRV genes were only detected in the colon tissue. IBR-specific antibodies were detected on approximately day 7 in the inoculated cattle and on day 10 in the contact cattle. Conclusion We successfully isolated a novel IBRV subtype 1.2b strain with high infectivity in adult cattle. The findings provide epidemiological and etiological evidence to trace the recent surge in IBRV prevalence across China.

Streptomyces are deeply studied and applied in the biocontrol of plant diseases. Streptomyces are widely distributed in soil, ocean and plant tissue. Streptomyces and the bioactive metabolites produced by Streptomyces exhibited antifungal, antibacterial, antivirus, nematicidal, pesticidal and herbicidal effects. The biocontrol mechanisms of Streptomyces against plant diseases, including antifungal activity, mycoparasitism, inducing resistance, enhancing plant growth, producing volatile organic compounds were summarized. The commercialized biocontrol agents developed based on Streptomyces were introduced. The research on Streptomyces-based biocontrol agents is limited in China, and the development and promotion of such agents could decrease the use of chemical fungicides and promote the environmental-friendly sustainable development of agriculture.