Abstract:Type 2 diabetes mellitus (T2DM) is a prevalent metabolic disease, yet its pathogenesis remains inconclusive. Recent studies have revealed a close relationship between the gut microbiota and T2DM, and specific gut microbiota structures and metabolic characteristics are associated with the onset and progression of T2DM. Exercise is an effective intervention for the prevention and management of T2DM, capable of reversing the dysbiosis induced by T2DM and regulating gut metabolites. However, the effects of exercise on the gut microbiota in T2DM patients still present many unresolved issues. Furthermore, the regulation of gut microbiota by exercise in T2DM patients is closely linked to multiple organs and can exert alleviation effects on T2DM via various gut-organ axis pathways. This paper reviews the characteristics of gut microbiota in T2DM and the effects of exercise on the gut microbiota in T2DM, with a particular focus on the mechanisms by which exercise regulates the gut microbiota to ameliorate T2DM via the gut-organ axis. This review aims to provide a reference for elucidating the relationship between exercise, gut microbiota, and T2DM.

Abstract:Galactose is a ubiquitous monosaccharide in nature, serving not only as a primary carbon source for bioenergy metabolism but also as a precursor for various biological synthesis reactions. In eukaryotic cells, galactose or its derivatives can act as signaling molecules to participate in intercellular communication. Recent studies have revealed that galactose can modulate bacterial virulence by regulating intracellular signal transduction. Accordingly, galactose is considered an underappreciated environmental regulator in bacterial infection. However, the specific regulatory mechanisms remain incompletely elucidated. This review integrates the latest research findings to summarize the bacterial galactose metabolic pathway, the biological implications of galactose metabolism in bacterial virulence and interactions with hosts, and the key proteins (enzymes) in the galactose metabolism pathway as potential targets for developing novel vaccines. It offers new insights and reference for comprehending bacterial infection mechanisms and exploring innovative antibacterial strategies.

Abstract:Acinetobacter spp. are the common opportunistic pathogens worldwide and pose a threat to the health of humans and animals. As the resistance rate to carbapenems aggravates, tigecycline has become one of the last lines for the treatment of multidrug-resistant Acinetobacter spp. infection. The rapid dissemination of tigecycline resistance genes tet(X3), tet(X4), tet(X5), tet(X6), and other variants in recent years has seriously affected the clinical application of new tetracycline antibiotics such as tigecycline, eravacycline, and omadacycline, whereas there is a lack of review on the tet(X) genes in Acinetobacter spp. This article comprehensively expounds the mechanisms of action, epidemiological characteristics, transmission risks, and inhibitors of tet(X) genes in Acinetobacter spp. and evaluates the diversity of their variants, bacterial hosts, geographical distribution, and sampling sources, aiming to provide a theoretical basis for the prevention and control of tet(X)-positive Acinetobacter spp.

Abstract:Adenosine diphosphate-ribosylation (ADPr) is a reversible post-translational modification that is catalyzed by adenosine diphosphate-ribosyltransferases (ARTs) and adenosine diphosphate- ribosylhydrolases (ARHs), and it widely occurs in eukaryotes and prokaryotes. ARHs are a class of key enzymes that can reverse ADPr modification of specific amino acid residues or specific sites/sequences of DNA and RNA. They can regulate the physiological metabolism, signal transduction, gene expression, and other key life processes in bacteria or hosts, playing an important role in the inter/intraspecific competition, stress responses, and pathogenicity of bacteria. This article reviews the classification, structural characteristics, and catalytic mechanisms of bacterial ARHs, aiming to enrich our understanding about the catalytic mechanisms and biological functions of ARHs in bacterial life.

Abstract:Ferroptosis is a novel form of programmed cell death that is iron-dependent and primarily characterized by lipid peroxidation. Studies have indicated that ferroptosis is closely related to the occurrence and development of various diseases. A variety of pathogens have been confirmed to induce ferroptosis of host cells, which facilitates pathogen proliferation and counteracting host immunity. Therefore, ferroptosis extensively participates in the pathophysiological processes caused by pathogen infection. In addition, ferroptosis is involved in the pathological process of many metabolic and poisoning diseases. This paper reviews the research progress in the occurrence and mechanism of ferroptosis in livestock and poultry diseases, aiming to provide reference for further exploring the effect and mechanism of ferroptosis in livestock and poultry diseases.

Abstract:The first human Pegivirus (HPgV-1) and the second human Pegivirus (HPgV-2) are the only two human Pegiviruses that have been identified until now. They share some common features including similar viral genome structure and low pathogenicity, while they also represent unique biological characteristics. HPgV-1 is called “good virus” because of its ability to slow down disease progression and reduce disease severity when co-infecting with HIV and Ebola virus. In addition, HPgV-1 was recently found to be related with lymphoma and neurological diseases. Therefore, HPgV-1 might be a possible breakthrough point in the treatment of refractory diseases caused by HIV and other viruses. HPgV-2 was firstly discovered from the plasma of a hepatitis C virus (HCV)-infected patient in 2015 and was found to always co-infect with HCV but hardly infect healthy people. However, the underlying mechanism of HPgV-2 and HCV co-infection remains to be elucidated. Distinct from most of RNA viruses, HPgV-2 exhibits low genomic diversity with high sequence identity and low intra-host variation, which give the implication of HPgV-2 as an excellent model for studying the mechanisms of viral genome variations. In conclusion, the human Pegiviruses are worthy of sustaining attention and study.

Abstract:Microbially enhanced coalbed methane production has become a research hotspot of coalbed methane production in recent years. Methanogens, the essential microorganisms in coalbed methane production, are usually strictly anaerobic and sensitive to oxygen. [Objective] To understand the changes in the methane production and composition of the anaerobic microbiome after exposure to oxygen, we conducted the enrichment culture of coalbed formation water collected from different regions along the east edge of Ordos Basin in China for air exposure experiments. Our findings are expected to provide scientific support for the future in-situ utilization of large-scale anaerobic fermentation products in coalbed methane production. [Methods] We used the enrichment cultures of coalbed formation water collected from Hancheng (HC), Baode (BD), and Linfen (LF) for air exposure for a series of time schedules within 24 h. The air-exposed enrichment cultures were re-inoculated and cultured. The methane production and community succession were analyzed to evaluate the microbiome tolerance to the aerobic condition. [Results] The microorganisms in all the three regions were still active after 24 hours of air exposure and showed the methane production comparable to that before air exposure. The dominant groups involved in the hydrolysis, acidification, and acetoxylation mainly included Firmicutes, Synergistetes, Proteobacteria, and Bacteroidetes. Methanogenic archaea were mainly Methanosarcina, Methanofollis, and Methanobacterium, belonging to Euryarchaeota. [Conclusion] After 24 hours of air exposure, the methane-producing capacity of the microbiome from the coalbed formation water was not affected and was comparable to that before air exposure. The microbiome did not showcase obvious succession, while the relative abundance of different groups changed accordingly. Our study can give scientific support for the in-situ industrial application of anaerobic enrichment culture from deep coalbed seams during coal degrading in methane production.

Abstract:[Objective] To screen and identify cadmium (Cd)-tolerant bacteria with plant growth-promoting effect from contaminated soil of a mining area in Guangxi, characterize the strain screened out in terms of the Cd tolerance, Cd²⁺ removal efficiency, plant growth-promoting effect, and influence on rice growth under Cd stress, and demonstrate the potential of the strain in plant growth and soil remediation. [Methods] Cd-tolerant bacteria were isolated by the dilution coating method and Cd²⁺ concentration gradient acclimation and further identified based on the morphological, physiological, biochemical characteristics and the 16S rRNA gene phylogenetic tree. The Cd tolerance, Cd²⁺ removal efficiency, and plant growth-promoting effect of the target strain were measured by microdilution, inductively coupled plasma mass spectrometry, and colorimetry. Finally, the effect of the strain on the growth of rice plants under Cd stress was investigated by a pot experiment. [Results] Twelve strains of bacteria with good tolerance to Cd²⁺ were isolated from heavy metal-contaminated soil, and one strain with the best tolerance to Cd was identified as Achromobacter sp. A81, which could grow in the presence of 800 mg/L Cd²⁺. Strain A81 cultured with 10 mg/L Cd²⁺ for 7 days showed the maximum Cd²⁺ removal rate of 44.66%. Both the supernatant and cells of strain A81 demonstrated the ability to adsorb Cd²⁺. Under Cd stress, the strain secreted a large amount of extracellular polymeric substances (EPS) primarily composed of insoluble and soluble proteins. Furthermore, this strain was capable of fixing nitrogen, solubilizing phosphorus, and secreting siderophores, indole-3-acetic acid (IAA), and 1-aminocyclopropane-l-carboxylate (ACC) deaminase, demonstrating remarkable plant growth-promoting effect. Pot experiment results revealed that compared with the group subjected to Cd stress, the rice plants inoculated with strain A81 showed increases of 9.08%, 39.59%, 41.94%, and 73.58% in plant height, root length, stem diameter, and fresh weight, respectively. [Conclusion] This study investigated the Cd tolerance, Cd removal efficiency, and plant growth-promoting effect of Achromobacter sp. A81 and assessed the application potential of this strain in Cd-contaminated soil remediation, providing a scientific basis and high-quality strain resources for the microbial remediation of heavy metal pollution and green agricultural development.

Abstract:[Objective] To explore the formation process of multi-species biofilms in paddy soils developed from different parent materials mediated by soil minerals, thus providing a scientific basis for revealing the interaction mechanisms between soil components and multi-species biofilms. [Methods] The multi-species biofilms were extracted from reddish clayey soil and acidic purple soil, and kaolinite and goethite were used as the mineral media. Modern biological microscopy, high-throughput sequencing, and infrared spectroscopy were employed to study the mineral-mediated formation process, structural changes, and bacterial community structure of the biofilm. [Results] Based on the high-throughput sequencing technology of 16S rRNA gene, the flora in the multi-species biofilms in the paddy soils developed from the two parent materials was dominated by Chloroflexi, Acidobacteria, Proteobacteria, Nitrospirae, and Desulfobacterota. Compared with the control without mineral addition, goethite and kaolinite significantly inhibited the formation of the multi-species biofilm dominated by Chloroflexi in the acidic purple soil, decreasing the biofilm biomass by 18.38% and 17.30%, respectively. In the reddish clayey soil dominated by Acidobacteria, goethite and kaolinite promoted the multi-species biofilm formation to varying degrees. Kaolinite demonstrated more significant promotion effect, increasing the biofilm thickness, the secretion of polysaccharides in the biofilm by 7.69%, and the biofilm biomass by 18.99%. [Conclusion] Kaolinite stimulated bacterial production of extracellular substances, promoted the multi-species biofilm formation in reddish clayey soil, and inhibited the multi-species biofilm formation in acidic purple soil. Goethite inhibited the multi-species biofilm formation in acidic purple soil. Compared with kaolinite, goethite is likely to cause cell inactivation. This study further revealed the interaction mechanism between soil components and multi-species biofilms, and the results provided a scientific theoretical basis for promoting the sustainable development of soil health.

Abstract:[Objective] This study isolated the dominant indole-3-acetic acid (IAA)-producing bacteria from the rhizosphere soil of Prunus sachalinensis, determined their plant growth-promoting properties, and clarified the growth-promoting effect by inoculation to the seedlings of the common rootstock Gisela 6, aiming to provide theoretical reference and practical approaches for exploring the biological potential of cherry, establish a benign root-microbial interaction relationship, and solve weak root development. [Methods] We used the beef extract peptone medium to isolate bacteria from the rhizosphere soil and selected various specific media to screen the bacteria and determine the IAA-producing, nitrogen-fixing, phosphorus-solubilizing, potassium-solubilizing, and chemotactic abilities of the bacteria. Then, we constructed a phylogenetic tree based on 16S rRNA gene sequences to identify the bacteria. Finally, potted cherry plants were used to explore the plant growth-promoting effects of the strains. [Results] Five IAA-producing strains were screened from the rhizosphere soil of P. sachalinensis, among which strain D46 had the highest IAA yield (53.10 mg/L). D5 was identified as Priestia sp. D27 and D46 were identified as Enterobacter sp. D43 and D79 were identified as Bacillus sp. All the five strains had the ability to fix nitrogen. D27, D46, and D79 had the ability to solubilize phosphorus, and D5 and D43 had the ability to solubilize potassium. Strains D27, D46, and D79 showed strong integrative chemotaxis to sugars, organic acids, and amino acids. Pot experiments showed that the inoculation of strains D27, D43, D46, and D79 significantly increased the root activity. After the inoculation of strain D27, the total root respiration rate increased by 51.40% compared with that in the control group (CK), and the root respiration rates of glycolysis (EMP), tricarboxylic acid cycle (TCA), and pentose phosphate pathway (PPP) also significantly increased. Strain D27 significantly improved the root architecture of cherry seedlings. After inoculation of strain D5, the net photosynthetic rate of leaves significantly increased by 58.82% compared with that in CK, and the inoculation of strain D27 demonstrated the best performance in improving the water use efficiency of leaves. Strains D27, D46, and D79 significantly increased the plant biomass. [Conclusion] There were IAA-producing bacteria in the rhizosphere of cherry, and the five IAA-producing strains isolated had other plant growth-promoting properties. Strains D27, D46, and D79 demonstrated comprehensive plant growth-promoting effects on cherry seedlings. In the future, we can explore the spectra of plants with growth promoted by the strains and the environmental tolerance of the strains, providing a theoretical basis for mining and enriching the strain resources of plant growth-promoting rhizobacteria.

Abstract:[Objective] We investigated the occurrence of ginger bacterial wilt, identified the pathogens, and screened the antagonistic bacteria, aiming to provide a scientific basis for the control of the disease. [Methods] We systematically investigated the occurrence of bacterial wilt in the main ginger production areas in Chenzhou City, Hunan Province. The ginger tubers with typical symptoms of bacterial wilt and the rhizosphere soil were collected. Major pathogens were isolated and identified based on morphological characteristics and molecular evidence. The pathogenicity of the isolates was determined by inoculation of the isolates to ginger seedlings. Moreover, the sequevars of Ralstonia solanacearum isolates were identified based on the endogenous glucanase gene egl. Finally, the Bacillus strains for biocontrol of the pathogens were screened, and their biocontrol effects were measured. [Results] The average incidence of ginger bacterial wilt in the field was 8.52%. Two bacterial strains FJAT-15492 and FJAT-15494 were isolated from diseased ginger tubers, and three bacterial strains FJAT-15495, FJAT-15496, and FJAT-15497 were isolated from the rhizosphere soil of diseased ginger. The strain FJAT-15492 was identified as Enterobacter mori and the other four isolates were R. solanacearum. Both the isolates of E. mori and R. solanacearum could infect ginger seedlings and cause bacterial wilt. R. solanacearum strains existed in both diseased ginger tubers and rhizosphere soil, while E. mori only existed in diseased ginger tubers, with the count (1.33×10³CFU/g) lower than that (5.67×10³ CFU/g) of R. solanacearum.Furthermore, the R. Solanacearum isolates were identified as phylotype Ⅰ and sequevar 14. Brevibacillus brevis FJAT-JK-2 demonstrated inhibitory effect on R. solanacearum, and Bacillus velezensis FJAT-54560 on E. mori, with inhibition zone diameters of 19.41 mm and 16.11 mm and indoor control effects of 69.45% and 61.11%, respectively. Moreover, the fermentation mixture of the two biocontrol strains had the field control effect of 52.57%. [Conclusion] This work identified the pathogens of ginger bacterial wilt and provided two new biocontrol strains against the disease.

Abstract:[Objective] To study the mechanism of plant growth-promoting rhizobacterium (PGPR) in the rhizosphere of sea rice and the effects of PGPR on the growth of terrestrial crops under salt stress. [Methods] The salt tolerance, alkali-reducing ability, and plant growth-promoting effect were determined for 15 bacterial strains isolated from the rhizosphere soil of sea rice. Highly active strains were selected for species identification and construction of a consortium. The effect of the consortium on the seed germination of mung bean was verified. [Results] The 15 strains of PGPR were moderately halophilic and strain SL-1 was an extreme halophile among them. Four halophilic strains had alkali tolerance and alkali-degrading effect, among which strain SH-3 had the highest alkali-degrading effect (16.83%). These four strains demonstrated different plant growth-promoting effects. All the strains could produce extracellular polymers (EPS), and strain SH-3 had the highest EPS production (0.47 g/g). The strains were capable of producing indole-3-acetic acid (IAA), with the yields between 0.70 mg/L and 1.48 mg/L. Three highly active strains SL-1, SM-1 and SH-3 belonging to Bacillus and Enterobacter were used to construct a consortium. Seed germination experiments showed that PGPR and the consortium promoted the seed germination of mung bean under salt stress. Moreover, the consortium showcased stronger promoting effect on seed germination than single PGPR. Compared with the control group, the consortium was more effective at the salt concentration of 15 g/L. Specifically, it improved the root length, germination rate, and simplified vitality index, while decreasing the relative salt injure rate from 80.53% to 18.95% and increasing the salt tolerance threshold of mung bean seeds from 10 g/L to 15 g/L. The data indicated that strains of the consortium coordinated to promote the seed germination of mung bean. The correlation analysis showed a strong positive correlation between EPS and IAA, both of which promoted the seed germination, growth, and development of mung bean under salt stress. [Conclusion] Strains SL-1, SM-1 and SH-3 had strong halophilicity, alkali tolerance, and abilities of degrading alkali, producing EPS and IAA, and promoting plant growth. The findings provide a scientific basis for the rational development and utilization of soil microbial resources and the improvement of saline-alkali soil environment.

Abstract:[Objective] To explore the differences and potential associations of endophytic microbial communities in different niches of chili pepper and provide a theoretical basis for the exploration and application of endophytic microbial resources in chili pepper. [Methods] The 16S rRNA and internal transcribed spacer (ITS) genes sequencing were employed to study the community structure characteristics of endophytic bacteria and fungi in different ecological niches (roots, stems, leaves, and fruits) of 91 pepper germplasm accessions, along with functional annotations. Additionally, co-occurrence network analysis and traceability analysis were performed on the endophytic bacterial communities. [Results] The operational taxonomic unit (OTU) of endophytic microbial communities were highly common among the four ecological niches, including 46.36% common bacterial OTUs and 29.66% common fungal OTUs. The diversity of endophytic bacterial and fungal communities in chili pepper exhibited variations across different ecological niches, with the endophytic communities in roots being distinctly separated from those in the other three niches (P<0.05). The Shannon index of endophytic bacteria varied significantly among niches, whereas that of endophytic fungi remained relatively stable. The dominant endophytic bacteria in chili pepper were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being enriched in the roots and Firmicutes and Bacteroidetes being predominant in the fruits. Ascomycota and Basidiomycota, the dominant endophytic fungal phyla, exhibited minimal differences in relative abundance across the four ecological niches. Functional annotation results indicated that chili pepper harbored various endophytic bacteria capable of synthesizing secondary metabolites and antibiotics. Within the fungal community, pathogenic fungi were found to have the highest relative abundance. Additionally, more than 80.0% of the endophytic bacteria in chili pepper originated from their directly associated morphologically lower niches, exhibiting complex interaction networks, strong community stability, and a modular structure. [Conclusion] Compared with the endophytic fungal community, the endophytic bacterial community in chili pepper is sensitive to changes in ecological niches, while the niche specificity of the fungi is comparatively weak. The endophytic bacteria associated with each niche of chili pepper primarily originate from the niche located beneath, exhibiting significant niche enrichment, where the roots serving as a crucial source in shaping the endophytic bacterial community.

Abstract:[Objective] To explore the effects of strain CDWB36 and its metabolite pyrroloquinoline quinone (PQQ) on the drought resistance and growth of pepper, so as to provide efficient strain resources for the development and utilization of multifunctional microbial agents. [Methods] A strain CDWB36 was identified based on the morphological characteristics and the 16S rRNA gene-based phylogenetic tree. HPLC and spectroscopy were employed to detect PQQ. The fermentation conditions were optimized by single factor tests with PQQ production as the indicator. The effects of the PQQ-containing microbial agent on the growth, physio-biochemical characteristics, soil nutrients, and rhizosphere microbial community structure of pepper under drought stress were determined by pot experiments. [Results] Strain CDWB36 was identified as Acinetobacter calcoaceticus and it had the ability to produce PQQ. The optimum conditions of strain CDWB36 for producing PQQ were 10 g/L yeast powder, 4 g/L mixed nitrogen sources (ammonium sulfate:glutamic acid:tyrosine=2:1:1), 1.0 g/L MgSO₄, 0.40 g/L CaCl₂, 0.5% inoculum amount, 28 ℃, and pH 6.5. The PQQ production of the strain in shake flasks after 7 days of fermentation at the optimized conditions reached 61.48 mg/L, which increased by 3.3 times compared with that before optimization. Compared with CK, the PQQ-containing microbial agent increased the plant height, stem diameter, aboveground fresh weight, and belowground fresh weight of pepper by 35.05%, 8.22%, 14.41%, and 51.70%, respectively, demonstrating better plant growth-promoting effect than the PQQ solution. Moreover, the PQQ-containing microbial agent significantly improved the activities of antioxidant enzymes and the content of osmoregulatory substances (soluble sugar, soluble protein, and proline) in leaves, while increasing the soil nutrient content. The PQQ-containing microbial agent significantly changed the relative abundance of bacteria and fungi in the rhizosphere soil of pepper, increasing the relative abundance of Bacillus, Aspergillus, and Streptococcus by 1.99 times, 1.38 times, and 8.75 times, respectively, compared with CK. [Conclusion] A. calcoaceticus CDWB36 has the ability to produce PQQ. Optimizing the fermentation conditions can effectively enhance the PQQ production. The fermentation broth of CDWB36 significantly promotes pepper growth under drought stress, and PQQ is a key substance in the broth for promoting pepper growth. Therefore, the strain has broad application prospects in enhancing the stress resistance and promoting the growth of plants.

Abstract:[Objective] To observe the effects of supplementing compound probiotics on the structure of gut microbiota, content of short-chain fatty acids (SCFAs), and levels of inflammatory cytokines in Chinese wrestlers. [Methods] Eighteen non-sports undergraduates from Shandong Sport University were recruited as a control group, while 30 Chinese wrestlers served as the experimental group. Both groups received oral compound probiotics for 8 weeks. Venous blood and stool samples were collected before and after the intervention. Enzyme-linked immunosorbent assay (ELISA) was used to measure inflammatory cytokines levels in plasma. The structural characteristics of gut microbiota were analyzed using 16S rRNA gene sequencing of the V3−V4 region, and gas chromatography-mass spectrometry (GC-MS) was employed to determine SCFAs content in stool samples. [Results] Prior to the intervention, the experimental group exhibited lower levels of interleukin-1 (IL-1), interleukin-6 (IL-6), and C reactive protein (CRP) (P<0.001, P<0.01, P<0.01), and higher levels of interleukin-10 (IL-10) compared to the control group (P<0.001). After 8 weeks of probiotic supplementation, plasma levels of IL-6 and CRP in the Chinese wrestlers further declined (P<0.01, P<0.05). Before the intervention, the abundance of Bifidobacterium adolescentis was higher in Chinese wrestlers than that in the control group (P<0.01). Following 8 weeks of supplementation, Chinese wrestlers showed an increased abundance of Collinsella (P<0.01), a decreased abundance of Faecalibacterium (P<0.01), and reduced α-diversity in gut microbiota (P<0.01). Prior to the intervention, there was no significant difference in SCFAs content between the two groups. After 8 weeks of intervention with compound probiotics, the content of acetic acid and butyric acid in the stool samples increased in both the control group (P<0.01, P<0.05) and the experimental group (P<0.05). The correlation analysis results indicated a positive correlation between B. adolescentis abundance and plasma IL-10 level (r=0.233, P=0.037) and negative correlations of B. adolescentis and C. aerofaciens abundance with plasma IL-6 level (r=−0.499, P=0.000; r=−0.366, P=0.001) in Chinese wrestlers. Additionally, there was a positive correlation between C. aerofaciens abundance and the butyric acid content in stool samples of Chinese wrestlers (r=0.243, P=0.032). [Conclusion] The 8 weeks intervention with compound probiotics effectively reduced pro-inflammatory cytokine levels and increased anti-inflammatory cytokine levels in plasma. Furthermore, it enhanced the abundance of butyric acid-producing bacteria in the gut microbiota, promoting the production of SCFAs, and improving anti-inflammatory capacity.

Abstract:[Objective] Streptococcus suis is a prevalent pathogen attacking pigs and a zoonotic agent. In 1998, an outbreak of S. suis infection in Jiangsu caused numerous pig deaths and 14 human deaths. Therefore, investigating S. suis infections in healthy pigs from slaughterhouses in Jiangsu is crucial for public health. [Methods] Tonsils were collected from healthy pigs in slaughterhouses of Jiangsu in 2023, and S. suis was isolated, identified, and serotyped. The pathogenicity of S. suis isolates to zebrafish and mouse models was examined. Furthermore, the antibiotic resistance characteristics and genes and the antimicrobial susceptibility of the isolates were identified and evaluated. [Results] The positive rate of S. suis in the samples collected from Kunshan in July 2023 was 50.85% (30/59). A total of 62 strains were isolated from the samples collected from Kunshan, and serotype 31 (12.90%, 8/62) had the highest isolation rate, followed by serotype 19 (11.29%, 7/62) and serotype NCL2 (8.06%, 5/62). In the samples collected from Danyang in July and November 2023, the positive rate of S. suis was 60.71% (34/56), and 77 strains were isolated. Serotype 16 had the highest isolation rate of 11.69% (9/77), followed by serotype 9 (10.39%, 8/77), serotype 21 (10.39%, 8/77), and serotype 31 (10.39%, 8/77). The isolates from both regions exhibited high resistance to lincosamides (98.56%, 137/139), macrolides (95.68%, 133/139), and tetracyclines (96.40%, 134/139). Furthermore, 97.84% (136/139) of strains were multi-drug resistant. All the strains were sensitive to cefotaxime and vancomycin. According to the sources and serotypes, we selected 42 representative strains (18 from Kunshan and 24 from Danyang) to perform zebrafish infection experiments. At a dose of 3×10⁶ CFU/fish, seven strains exhibited high pathogenicity to zebrafish, causing the mortality rates ≥80.00%. Three strains (serotypes 1, 3, and 23) causing mortality rates ≥80.00% in zebrafish and comparable to the virulent strain SC070731 were selected for mouse infection experiments. All the three strains led to the mortality rates ≥80.00% in mice. [Conclusion] The healthy pigs in Jiangsu have a high carrying rate of S. suis (55.65%, 64/115), and 97.84% (136/139) of the isolates are multi-drug resistant. Strains of serotypes 1, 3, and 23 exhibited strong pathogenicity.

Abstract:[Objective] To elucidate the structural and functional characteristics of the gut microbiota of Trypoxylus dichotomus larvae and isolate cellulose-degrading bacteria. [Methods] Metagenomic sequencing was employed to analyze the structure and functions of the gut microbiota. Cellulose-degrading bacteria were isolated and screened from the larval gut with carboxymethyl cellulose (CMC) as the sole carbon source. The strains were identified based on morphological characteristics and molecular evidence. [Results] The gut microbiota was dominated by bacteria, which accounted for 81.3%. At the phylum level, Firmicutes (45.8%) and Bacteroidota (20.3%) were the dominant phyla. The top three abundant genera were Clostridium (3.90%), Bacteroidia (3.52%), and Dysgonomonas (2.41%). The functional analysis of metagenome data revealed that the genes of the gut microbiota were mainly associated with carbohydrate, amino acid, and energy metabolism. The annotation in the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the genes related to carbohydrate metabolism were predominant. The annotation in the carbohydrate-active enzyme database (CAZy) indicated that 48 856 (7.43%) genes were successfully annotated to 344 carbohydrate metabolism enzyme families, with glycoside hydrolase (GH, 48.67%) being the most dominant enzyme family in the gut bacteria. Among the top ten functionally abundant enzymes, six belonged to the GH family. Additionally, three strains of cellulose-degrading bacteria, TRC-3 (Bacillus subtilis), TRC-5 (B. subtilis), and TRC-6 (B. safensis), were isolated from the gut. TRC-3 exhibited stronger activities of filter paper enzyme, endoglucanase, exoglucanase, and β-glucosidase. [Conclusion] The gut microbiota of Trypoxylus dichotomus larvae exhibits high diversity and complexity, carrying a large number of genes encoding carbohydrate-active enzymes and harboring rich cellulose-degrading bacteria.

Abstract:[Objective] To studyhydroxyl radical the differentially expressed genes (DEGs) in Halomonas campaniensis XH26 after co-culture with Fe₃O₄ nanoparticles (NPs), and clarify the molecular mechanism of Fe₃O₄ NPs in increasing the ectoine accumulation in strain XH26. [Methods] Strain XH26 was co-cultured with low-, medium-, and high-concentration (0.01, 0.10, and 0.50 g/L respectively in L, M, and H groups) Fe₃O₄ NPs, and the strain cultured without Fe₃O₄ NPs (0 g/L) was taken as the control group (C). Transcriptome sequencing was performed by Illumina HiSeq 300PE. The DEGs between different groups were mined, and key genes were screened for RT-qPCR verification. [Results] Compared with group C, group M showed an increase of 55.67% (708.87 mg/L) in ectoine accumulation, and groups M and H showed increased ferrous ions and antioxidant capacity. The hydroxyl radical content in group H was higher than that in group M. The transcriptomics analysis showed that the DEGs between groups M and C were enriched in arginine/proline metabolism (13), nitrogen metabolism (11), and sulfur metabolism (10) pathways. They were mainly related to the ectoine synthesis pathways (11), electron transport pathways (7), and antioxidant enzyme systems (5). RT-qPCR was employed to verify the expression of lysC, asd, and ectABC involved in ectoine synthesis, astA/B/D/E in arginine metabolic pathway, and argE/H in urea cycle, which showed the results consistent with the results of RNA-seq. [Conclusion] Ectoine is an important stable protective agent for bacterial cells and biomacromolecules. Strain XH26 exposed to the stress of Fe₃O₄ NPs showed increased intracellular reactive oxygen species and altered amino acid/nitrogen metabolism processes. Strain XH26 increased the accumulation of ectoine to cope with the stress of Fe₃O₄ NPs by improving the antioxidant capacity.

Abstract:[Objective] Based on the critical role of type I signal peptidase in the secretion system, this study explores the interaction between signal peptidase and signal peptides to guide the optimization of aminopeptidase secretion expression in Bacillus amyloliquefaciens. [Methods] The endogenous signal peptidase and signal peptide of Bacillus amyloliquefaciens TCCC 19030 were examined using relative fluorescence intensity and enzyme activity for analysis, and molecular docking to study their interaction. [Results] The signal peptide YolC fused with aminopeptidase exhibited the highest extracellular enzyme activity, reaching 11 847.67 U/mL. Overexpression of the signal peptidase SipW increased aminopeptidase activity to 16 261 U/mL. Molecular docking results also showed that YolC had the lowest binding free energy with SipW, at −4.4 kcal/mol. [Conclusion] Optimization of signal peptides and overexpression of signal peptidase can effectively enhance the secretion of aminopeptidase. The binding energy between signal peptidase and signal peptide is a key factor influencing the secretion levels of the target protein.

Abstract:[Objective] Preliminary studies have identified four protein elicitors from the whole genome of Saccharothrix yanglingensis Hhs.015 that can induce a hypersensitive response (HR) in Nicotiana benthamiana. This study investigated the two elicitors capable of triggering a strong HR and their associated immune mechanisms, aiming to provide a basis for probing into the molecular mechanisms by which Hhs.015 enhances the disease resistance of plants. [Methods] The protein elicitors capable of inducing the immune responses of plants were screened based on the HR and reactive oxygen species (ROS) levels. A prokaryotic expression system was used to purify the proteins. Furthermore, we verified the roles of the protein elicitors in inducing plant disease resistance by observing the disease spots, measuring the activities of defense-related enzymes, and analyzing the expression of defense genes. Additionally, we treated Arabidopsis thaliana seedlings with the protein elicitors to evaluate the plant growth-promoting effects of the elicitors. [Results] The protein elicitors HSyp1 and HSyp2 from Hhs.015 that could induce a HR, callose and ROS deposition, and upregulation of defense genes in N.benthamiana, were screened and found to be soluble. HSyp1 and HSyp2 enhanced the resistance of different plants to Sclerotinia sclerotiorum, Phytophthora capsica, and Valsa mali. Furthermore, HSyp1 and HSyp2 promoted the cotyledon and root development of A. thaliana seedlings, and HSyp2 exhibited stronger plant growth-promoting effect than HSyp1. [Conclusion] This study identified two protein elicitors HSyp1 and HSyp2 capable of triggering immune responses, enhance disease resistance, and promoting growth of plants. The findings provide a theoretical basis for the development of new biocontrol agents and offer experimental evidence for their future field application.

Abstract:[Objective] The basic leucine zipper (bZIP) factors are a group of large and conserved transcription factors in eukaryotes, and they are involved in the growth, development, and infection of pathogenic fungi in plants. This study aims to identify the bZIP transcription factors in the whole genome of Setosphaeria turcica and explore their functions during HT-toxin induction. [Methods] The members of the bZIP family were screened and identified from the genome database of Setosphaeria turcica, and their physicochemical properties, conserved domains, subcellular localization, cis-acting elements, phylogenetic relationship, and protein-protein interaction network were analyzed. The RNA-seq database was used to analyze the expression of bZIP family members during pathogen infection and HT-toxin induction. [Results]Fourteen bZIP family members (StbZIP1–14) were screened from the genome of Setosphaeria turcica, with significant differences in physical and chemical properties. These factors had the lengths of 226–613 aa, relative molecular weights of 25.24–66.30 kDa, isoelectric points of 4.66–10.36, and the subcellular localization in the nucleus. These factors carried 660 cis-acting elements involved in abiotic stress, hormone induction, cell cycle regulation, enhancers, and core promoters. The phylogenetic analysis with 11 other major pathogenic fungi in plants indicated that StbZIPs were clustered into 10 groups and had a clear co-linear relationship with AabZIPs of Alternaria alternata. The expression levels of StbZIP1, StbZIP5, StbZIP7, StbZIP10, and StbZIP11were significantly correlated with HT-toxin induction, among which StbZIP5 had the highest expression level and demonstrated upregulated expression after 21 days and 28 days of HT-toxin induction. The protein-protein interaction network of StbZIPs predicted three StbZIPs interaction pathways centered on StbZIP5. [Conclusion] The members of the bZIP family of Setosphaeria turcica have significant physicochemical and structural differences, extensive genetic diversity, and significant functional differentiation, playing an important role in transcriptional regulation during HT-toxin induction.

Abstract:Campanumoea lancifolia (Roxb.) Merr. is a new plant species with both medicinal and edible values, demonstrating broad prospects for development and utilization. However, as its cultivation area expands, root rot has become increasingly severe. In the fields with severe root rot, the losses can reach up to 40%, accounting for 75% to 90% of the losses caused by all diseases affecting C. lancifolia. Root rot directly leads to declines in fruit yield and quality, affecting the commercial value of the fruits and reducing farmers’ incomes. Thus, it is urgent to address the root rot in C. lancifolia. [Objective] To isolate and identify the pathogens causing root rot in C. lancifolia and investigate the inhibitory effects of essential oils extracted from four aromatic medicinal plants on the growth of these pathogens. [Methods] Pathogens were isolated from C. lancifolia plants displaying typical root rot symptoms by the tissue culture method. The pathogens were identified based on morphological and molecular evidence and verified according to Koch’s postulates. Essential oils were extracted from four aromatic medicinal plants by steam distillation. The Oxford cup method was employed to examine the inhibitory effects of the essential oils on the pathogens, and the 96-well plate method was used to determine the minimum inhibitory concentrations (MICs) of the essential oils. [Results] Four pathogenic strains were isolated and identified from the roots of diseased C. lancifolia plants. Re-inoculation of these pathogens induced root rot symptoms consistent with those observed in the field. The pathogens were identified as Fusarium oxysporum, Fusarium solani, Colletotrichum liriopes, and Stagonosporopsis pogostemonis. The essential oils exhibited strong inhibitory effects on these pathogens, with inhibition rates ranging from 32.94% to 95.29%. Additionally, the MICs of the four essential oils against the pathogens ranged from 0.031 mg/mL to 4.000 mg/mL. [Conclusion] This study demonstrates that F. oxysporum, F. solani, C. liriopes, and S. pogostemonis are pathogenic to C. lancifolia. This is the first report of F. solani, C. liriopes, and S. pogostemonis causing root rot in C. lancifolia. Furthermore, the essential oils extracted from the selected four aromatic plants exhibited strong inhibitory effects on the pathogens causing root rot in C. lancifolia, which coincides with the theory of aromatic plants dispelling pathogens in traditional Chinese medicine. The findings lay a scientific foundation for the development of botanical pesticides against root rot in C. lancifolia and the eco-friendly cultivation of this plant.

Abstract:[Objective] This study investigated the optimal proportion of green manure replacing chemical fertilizer and its effect on soil fungal community in the paddy field of Ultisol, aiming to achieve soil fertilization and sustainable utilization of Ultisol in southern China. [Methods] This study set seven treatments: no fertilizer (Control), application of Chinese milk vetch without chemical fertilizer in early season rice (G), conventional application of chemical fertilizer in early season rice (NPK100), application of Chinese milk vetch and conventional chemical fertilizer in early season rice (NPK100+G), application of Chinese milk vetch and 80% conventional chemical fertilizer in early season rice (NPK80+G), application of Chinese milk vetch and 60% conventional chemical fertilizer in early season rice (NPK60+G), and application of Chinese milk vetch and 40% conventional chemical fertilizer in early season rice (NPK40+G). The conventional chemical fertilizer was applied in late season rice for other treatments except the Control. The root surface soil samples of different treatments were collected at the maturity stage of late rice for the measurement of soil properties. At the same time, high-throughput sequencing (Illumina MiSeq) was employed to analyze the features of soil fungal community. [Results] Compared with NPK100, the treatments of green manure replacing chemical fertilizer increased the yields of rice and straw. Different treatments significantly altered the soil fungal community composition (P=0.001). Replacing medium and low amounts of chemical fertilizer with green manure increased the relative abundance of saprophytic fungi in soil, which increased the conversion rate of soil organic matter and nutrient turnover rate. Compared with NPK100, replacing 0, 20%, and 40% chemical fertilizer with green manure increased the relative abundance of saprophytic fungi in soil by 33.55%, 167.27%, and 55.28%, respectively. In addition, replacing medium and low amounts of chemical fertilizer with green manure decreased the relative abundance and diversity of potential plant pathogens in soil. [Conclusion] Replacing medium and low amounts (20%–40%) of chemical fertilizer with green manure not only increased rice yield but also reduced environmental pollution, improved soil nutrients, and optimized the fungal community in soil. This study systematically evaluated the effect of replacing different proportions of chemical fertilizer with green manure on the Ultisol paddy ecosystems. The results provided a theoretical basis for the sustainable development of agriculture in the Ultisol region of southern China.

Abstract:Truffles must be symbiotic with plants to form ectomycorrhiza (ECM), which facilitates the formation of fruiting bodies by mutually beneficial exchanges of substances. [Objective] To elucidate the flow of substances between Tuber sinense and Pinus yunnanensis in a symbiosis relationship. [Methods] Liquid chromatography-mass spectrometry (LC-MS) was employed to analyze the metabolite profiles of freshly harvested T. sinense (SL) and P. yunnanensis roots (SG). [Results] In SL and SG, 1 304 and 1 516 substances were detected respectively, including 399 SL-specific substances (SLSs) and 611 SG-specific substances (SGSs). There were 294 common differential substances, including 93 up-regulated substances (DEMs-up) and 201 down-regulated substances in SL. The network correlation analysis revealed that 92 of the 100 substances with the relative content ≥2.0 (40 SLSs and SGSs and 60 DEMs-up) displayed significant correlations. Twenty-nine associated substances in SLSs and SGSs and 19 substances in DEMs-up were enriched in 15 important pathways, which mainly involved secondary metabolite biosynthesis, amino acid biosynthesis and metabolism, and vitamin biosynthesis and metabolism. [Conclusion] A network correlation existed between T. sinense and P. yunnanensis pine roots metabolites. Some substances in truffles and pine roots, including adenosine 3',5'-cyclic monophosphate (cAMP), phytosterol, and indole-3-acetic acid, had regulatory effects on the development of fruiting bodies. The findings provided a theoretical basis for further studying the potential signaling molecules associated with fruiting body development and elucidating the symbiotic mechanism between T. sinense and pines. Additionally, this study laid a practical basis for screening the substances promoting the growth of mycorrhizal seedlings and fruiting bodies and for large-scale artificial cultivation of truffles.

Abstract:[Objective] Carbon and nitrogen sources play an important role in providing the energy required for fungal growth and increasing secondary metabolite production. This study aims to investigate the effects of carbon and nitrogen restriction on the growth of Inonotus obliquus and the production of triterpenoid secondary metabolites. [Methods] l-glutamine and d-anhydrous glucose were used as the nitrogen and carbon sources, respectively. A nutrient-sufficient medium (0.877 g/L l-glutamine and 20.000 g/L of d-anhydrous glucose) served as the control group (CK). The experimental groups included a nitrogen-limited medium (N-L) with 0.044 g/L l-glutamine and a carbon-limited medium (C-L) with 2.000 g/L d-anhydrous glucose. In the plate experiment, inoculated plates were incubated at 28 ℃ in a constant temperature incubator, and colony diameters were measured and recorded daily. In the shake flask fermentation experiment, samples were collected on the 5th and 10th days to measure biomass, triterpene content, and the expression levels of triterpene synthesis-related genes. [Results] The plate experiment showed that the C-L group had the fastest mycelium extension, but the mycelium was sparse, and the aging was greatly delayed. The N-L group exhibited faster mycelium extension than the CK group but slower than the C-L group, with the fastest mycelium aging. The shake flask fermentation results showed that the N-L group had the highest biomass. qPCR results demonstrated an upregulation trend in most triterpenoid synthase genes under C-L and N-L conditions. GC-MS analysis revealed that both lanosterol and inotodiol content increased in the C-L and N-L groups compared to the CK group. [Conclusion] Nutritional restriction conditions stimulate the accumulation of triterpenes in I. obliquus.

Abstract:Inhibitors including sugar degradation products (e.g., 5-hydroxymethylfurfural and furfural) and phenols (e.g., 4-hydroxybenzoic acid and vanillin) from lignin degradation are inevitably formed in the pretreatment process of lignocellulose raw materials, exerting a negative impact on the fermentation efficiency. [Objective] To improve the tolerance of yeast to inhibitors in cellulose hydrolysates and ensure the efficient production of industrial biomass ethanol. [Methods] The model strain W303-1A was domesticated with the inhibitor furfural and p-hydroxybenzoic acid alone or in combination. The growth curves and ethanol fermentation performance of the domesticated strain and the original strain were compared under different inhibitor concentrations. We then conducted high-throughput genome resequencing of both the domesticated and original strains to identify the mutations in genes related to the glucose metabolism and drug resistance, thereby analyzing the variation points related to inhibitor tolerance. [Results] In the medium containing 2.0 g/L furfural, the ethanol yield of F-2 was 19.40 g/L, which was 2 times higher than that of the original strain. In the medium containing 1.6 g/L furfural and p-hydroxybenzoic acid, the highest ethanol yield of B-2 was 20.22 g/L, 7.6 times that of the original strain. Then, high-throughput genome resequencing of the original and domesticated strains revealed several mutations in the genes encoding ethanol dehydrogenase, fructose-1,6-diphosphate aldolase, and pyruvate dehydrogenase in the glucose metabolism pathway. The mutations of YAP1 (transcriptional activator involved in oxidative stress response and REDOX homeostasis), PDR5 (pleiotropic ABC transporter tolerant to multiple chemicals), and RPN4 (zinc finger protein) genes played an important role in the inhibitor tolerance of Saccharomyces cerevisiae. [Conclusion] The findings provide more targets for further optimization and construction of model strains.

Abstract:[Objective] Epoxide hydrolases (EHs) play a key role in the synthesis of chiral pharmaceuticals. We explored new EHs by engineering or gene retrieval, aiming to enrich and discover more high-performance EHs. [Methods] A novel epoxide hydrolase (Aspergillus carlsbadensisepoxide hydrolase, AcEH) from Aspergillus carlsbadensis was identified by gene retrieval technology. We then used AutoDock2 to predict the key hydrolysis sites of AcEH and employed computational design to clarify the influences of important sites on the structure and catalytic mechanism of AcEH. [Results] The primary structure of the novel EH had three characteristic α/β EH motifs: HGWP, GYTFS, and GGDIGS. AcEH exhibited high activity and could completely hydrolyze styrene oxide (SO) within 15 min, with a specific activity of 13 951 U/g. The K_m, V_max, and k_cat/K_m of AcEH were (107.07±57.98) mmol/L, (37.22±17.85) μmol/(min·mg), and 1.17 mmol/(L·s), respectively. The key hydrolysis sites of AcEH were Asp192-His372-Glu346, which catalyzed the triad, and two conserved tyrosine residues, Tyr251/314. The mutations R49L and R49Y caused enzyme inactivation, while the mutation Y45L resulted in the formation of inactive inclusion bodies. The interaction network revealed that changes in the 49th amino acid residue disrupted the interactions between key active site residues, leading to enzyme inactivation. On the other hand, the alteration of the 45th amino acid residue destabilized the enzyme structure, leading to the formation of inclusion bodies. [Conclusion] This study discovered a novel EH and analyzed its hydrolysis mechanism. The findings provide valuable insights for further research and engineering on this enzyme.

Abstract:Metagenomics has enriched our understanding about the composition and functions of digestive tract microbiota in animals. Currently, metagenomic sequencing can generally achieve the classification rate of species between 15% and 45% at the read level. Therefore, improving the alignment rate of microbial reads in metagenomics can help to further mine microbial information from metagenome data. [Objective] To enhance the classification ability for digestive tract microbiota in ruminants by extending the Kraken2 standard database, thereby deeply mining the microbial information from metagenome data. [Methods] A total of 14 827 metagenome-assembled genomes (MAGs) of the rumen fluid, feces, and digestive tracts of cattle, sheep, and goats were collected. After quality control and filtering, 3 095 species-level genome bins (SGBs) were retained. These SGBs were integrated into the Kraken2 standard database following taxonomic classification and functional prediction, and the classification effect was evaluated. [Results] In the genome taxonomy database (GTDB), the 3 095 SGBs were identified as bacteria belonging to 782 genera of 28 phyla (3 053 SGBs) and archaea belonging to 8 genera of 2 phyla (42 SGBs). The functional prediction based on eggNOG annotated the SGBs into 26 clusters of orthologous groups of proteins (COGs). The Kyoto encyclopedia of genes and genomes (KEGG) enrichment categorized the top 25 ortholog groups (KO entries) into 14 pathways. The prediction of carbohydrate-active enzymes (CAZy) showed that 593 SGBs were annotated into six classes of CAZymes: auxiliary activities (AA), carbohydrate esterases (CE), glycosyltransferases (GT), carbohydrate-binding modules (CBM), glycoside hydrolases (GH), and polysaccharide lyases (PL). Among them, GH was the most common class. The addition of 3 095 SGBs to the Kraken2 standard database (May 2024) increased the number of species in the database by 5.00%, extending the size from 87.2 Gb to 98.2 Gb. Furthermore, a study about the effect of diet fiber-to-concentrate ratio on the rumen microbiota of Holstein cows by metagenomics was reassessed, which showed that the integration of SGBs into the database raised the species alignment rate of rumen metagenome reads from (19.35±1.81)% to (51.04±2.05)%. The principal component analysis results at the species level indicated that the extended database enhanced the ability to distinguish rumen microbiota structures under two different diet fiber-to-concentrate ratios. The linear discriminant analysis effect size results indicated that the microbial markers for low-fiber and high-fiber diets were Xylanibacter ruminicola and Aristaeella hokkaidonensis, respectively, in the standard database, whereas they were Prevotella sp. 902800365 and Prevotella sp. 900316445, respectively, in the extended database. [Conclusion] In summary, introducing SGBs to extend the Kraken2 standard database can increase species coverage and improve the alignment rate of species at the metagenome read level, thereby enhancing the understanding of microbial information in metagenome data.