2026-04-02
Mengjian Liu, Zixuan Ye, Xucheng Mo, Yakun Wang, Siyu Li, Yaoli Fu, Yujie Niu
IntroductionNeonatal calves exhibit immature digestive and immune systems, rendering them susceptible to environmental stressors such as cold temperatures, which exacerbate gastrointestinal dysfunction and diarrhea incidence. Antibiotic use for mitigation poses risks, including microbiota disruption and resistance development, necessitating safe probiotic alternatives.MethodsThis study evaluated the effects of Bacillus megaterium supplementation on growth performance, diarrhea occurrence, serum biochemical, immune, and antioxidant parameters, and rectal microbiota composition in neonatal calves under Xinjiang’s cold climate. Fifty crossbred calves were randomly assigned to five groups (n = 10): basal diet (Group I), basal plus 50 mg/day gentamicin (Group II), or basal plus 250, 500, or 1,000 mg/day B. megaterium (Groups III–V). Supplementation occurred via milk over 28 days, with assessments of growth performance, fecal scores, serum indices, and rectal microbiota.Results and discussionThe 500 mg/day B. megaterium treatment (Group IV) significantly increased average daily gain (ADG) and reduced feed-to-gain ratio (F/G) and diarrhea frequency compared to control (p < 0.05). Serum IgG increased, whereas pro-inflammatory cytokines (IL-1β, TNF-α, IFN-γ) decreased in the probiotic group compared with controls (p < 0.05). Antioxidant capacity improved significantly, with GSH-Px and CAT elevated and MDA reduced (p < 0.05). Rectal microbiota Shannon index was significantly higher in Group IV compared to the Group II (median: 2.7 vs. 3.8; p < 0.05). The relative abundance of Firmicutes increased, and beneficial genera (Lactobacillus, Faecalibacterium, Ruminococcaceae_UCG-014) were enriched, whereas Escherichia–Shigella decreased in Group IV (p < 0.05). Beneficial taxa were positively associated with immune and antioxidant markers and negatively associated with pro-inflammatory cytokines. Overall, these findings suggest that B. megaterium is a promising antibiotic alternative for promoting calf health, productivity, and beneficial gut microbiota under cold stress, with implications for more sustainable ruminant production systems.
DOI: 10.3389/fmicb.2026.17489692026-04-02
Emily L. Olsen, Monica E. Embers
Bartonella are gram-negative, facultative intracellular bacteria. Infection by Bartonella manifests as different clinical syndromes collectively known as bartonellosis. The well-known diseases caused by these bacteria are cat scratch disease (Bartonella henselae), trench fever (Bartonella quintana) and Carrion’s disease (Bartonella bacilliformis). Excluding B. bacilliformis, which is evolutionarily more distinct than the other species, Bartonella infections result in self-limiting disease that is often undiagnosed and untreated. However, individuals with compromised immune systems or other undefined conditions may experience clinical manifestations, which can become life-threatening and need to be treated with effective antibiotics. To date, there is no standard treatment course for these infections, and many doctors prescribe antibiotics based on limited case studies. Within the host, Bartonella can grow extracellularly, intracellularly, and in biofilms. To determine an effective antibiotic strategy, it is important to understand Bartonella susceptibility in each of these growth conditions. We hypothesized that combination antibiotic treatments are required to effectively eliminate Bartonella henselae growth, particularly in biofilm and intracellular environments. Our previous work has shown that B. henselae treatment with single antibiotics in different media, as well as in DH82 canine macrophages, was ineffective in eliminating bacteria. We expanded this work with different antibiotics supported by case reports, as well as double and triple combinations. The following antibiotics were tested: doxycycline, gentamicin, azithromycin, azlocillin, rifampin, and clarithromycin. We found that while monotherapy may inhibit growth extracellularly, it is ineffective when used against intracellular bacteria or pre-existing biofilms. Gentamicin in combination with either rifampin or azlocillin significantly reduced bacterial growth in multiple microenvironments. The effectiveness of combination therapy supports the notion that Bartonella species utilize host cells and biofilms as antibiotic evasion strategies.
DOI: 10.3389/fmicb.2026.17261802026-04-02
JiaLiang Xin, FangJun Li, LuLu Kang, Jie Yang, HaiTong Wang, Wei Wang, Sheng Feng, XinFei Liao, WenJie Li, He Zhang
Chikungunya virus (CHIKV) infection can induce acute kidney injury (AKI) and may be fatal in severe cases, yet effective therapeutic strategies remain unclear. This study integrated computational analysis (network pharmacology and molecular docking) with in vitro experiments to evaluate the protective potential of oxymatrine against CHIKV-induced AKI and to explore its underlying mechanisms. Network pharmacology analysis identified 605 overlapping targets between CHIKV- and AKI-related genes, with core targets including TNF, AKT1, IL6, IL1B, and TP53, which were primarily enriched in the PI3K/AKT signaling pathway. RT-qPCR analysis and molecular docking further indicated that oxymatrine may interact with 18 targets, such as BAX, BCL2, and TLR4, thereby modulating CHIKV-associated PI3K/AKT signaling. In vitro experiments showed that oxymatrine at concentrations of 250–2,000 μM significantly increased the viability of HEK293T cells infected with CHIKV at a MOI of 0.01 for 24 h, with an average increase of approximately 25.8%. At these concentrations, oxymatrine reduced the expression of the CHIKV entry factor TIM-1 and regulated the PI3K/AKT, NF-κB, and TNF signaling pathways, which may contribute to the inhibition of viral replication. Further analysis revealed that CHIKV-induced AKI involved 75 ferroptosis-related targets and was closely associated with inflammatory responses. Oxymatrine may attenuate these effects through the regulation of targets such as SIRT3, AR, and FURIN. Consistently, ELISA results demonstrated that 1,000 μM oxymatrine significantly decreased the levels of IL-1β, TNF-α, and IL-6 in HEK293T cells infected with CHIKV. In conclusion, these findings suggest that oxymatrine may protect against CHIKV-induced AKI by limiting viral replication, modulating PI3K/AKT and NF-κB/TNF signaling pathways, suppressing inflammation, and regulating ferroptosis-related processes.
DOI: 10.3389/fmicb.2026.17821832026-04-01
Mingyu Dang, Ying Tang, Jinxun Chen, Wenwen Xie, Yunfei Zhong, Bo Yu, Erhao Zhang, Zhongbin Wang
IntroductionCymbidium mastersii, a perennial orchid of high ornamental value, faces severe survival challenges due to extremely low natural seed germination rates ( 0.7). Our findings underscore the critical role of trophic interactions in shaping rhizosphere community assembly in alpine plants, thereby contributing to the broader understanding of microbial biogeography along elevational gradients.DiscussionThis study not only confirms that the altitudinal gradient serves as a key environmental filter shaping the rhizosphere microecology of C. mastersii, but more importantly, by integrating metagenomic and metabolomic approaches, we systematically reveal for the first time that altitude differentially selects for microbial taxa with specific functions, ultimately driving the restructuring of the rhizosphere metabolic environment. Moving beyond mere community description, our work aims to elucidate the underlying pathways responsible for these shifts and their potential functional implications for host plant adaptation.
DOI: 10.3389/fmicb.2026.17201372026-04-01
Xiaoyun Ou, Qiaozhen Wang, Shushi Huang, Youzhi Li, Ling Yang, Yuening Luo, Shaojie Wang, Min Liang, Lixia Pan, Bin Liu, Dengfeng Yang
IntroductionA novel strain with strong antagonistic and anti-aflatoxigenic activity against Aspergillus flavus was isolated from a marine environment, highlighting its potential for biocontrol applications in food and agriculture.MethodsThe strain, designated B143, was identified using a polyphasic taxonomic approach combining morphological observation and phylogenetic analysis. Its petroleum ether extract was tested for inhibitory effects on hyphal growth, spore germination, and aflatoxin B1 production in A. flavus. Transcriptome analysis was conducted to identify differentially expressed genes in aflatoxin and ergosterol biosynthesis pathways. Fluorescence staining was used to assess cell wall and membrane integrity, as well as oxidative stress.ResultsStrain B143 was identified as a new species, Nigrograna chlamydospora sp. nov. Its petroleum ether extract significantly inhibited hyphal growth (70.84 ± 4.29%) and spore germination (98.23 ± 0.10%), and reduced aflatoxin B1 production by 35.88%. Transcriptome analysis showed down-regulation of key genes in aflatoxin B1 (adhA, 1.2-fold) and ergosterol (erg5, 1.6-fold) biosynthesis pathways. Fluorescence staining confirmed disruption of cell wall and membrane integrity and induction of oxidative stress in A. flavus.DiscussionThese findings demonstrate that N. chlamydospora B143 exhibits strong dual inhibitory effects against A. flavus growth and aflatoxin production, underscoring its potential as an effective biocontrol agent for mitigating contamination in food and agricultural products.
DOI: 10.3389/fmicb.2026.18011992026-04-01
Xinyu Liu, Xiaojian He, Mi Li, Quanbing Pan, Bin Huang, Leye Huang, Jie Wang
IntroductionThe emission of carbon dioxide (CO₂) and methane (CH₄) during composting not only contributes to the greenhouse effect but also leads to carbon loss, thereby reducing humus production and compromising the quality of the final compost product. This study investigated the efficacy and underlying mechanisms of biochar and cellulase addition, individually and in combination, in mitigating emissions and enhancing compost quality within a cattle manure-sugarcane bagasse co-composting system.MethodsBy monitoring key composting parameters and combining with high-throughput sequencing analysis of bacterial and fungal communities, the changes of microbial structure and function were evaluated, focusing on organic carbon transformation, humification pathway and greenhouse gas mitigation mechanism.Results and discussionThe results demonstrated that compared with the control, the combined application of biochar and cellulase (particularly the treatment with 5% biochar, denoted as MC5) significantly reduced the cumulative emissions of CO2 and CH4 by 18.6 and 31.2%, respectively. In addition, the combined treatment promoted the synthesis of humic substances, markedly increased humic acid content by 41.0% (from 28.56 to 40.27 mg/g) and the humification index (HI) by 75.6% (from 2.35 to 4.13). Microbial community analysis revealed that the combined amendment shaped the microbial succession by enriching lignocellulose-degrading fungi (such as Mycothermus) and humification-promoting bacteria (e.g., Chryseolinea), while suppressing taxa associated with greenhouse gas emissions (e.g., Clostridium), thereby directing a greater carbon flux toward humification pathways. This study confirms that the synergy between biochar and cellulase effectively mitigates greenhouse gas emissions and improves the quality of compost, providing a theoretical basis for developing low-carbon, high-value composting technologies.
DOI: 10.3389/fmicb.2026.18039202026-04-01
Changpeng Sang, Wenyue Chen, Enrui Li, Meihua Lian, Zhiheng Li, Xiaojun Li
Sediment is the sink of antibiotic resistance genes (ARGs) in aquatic systems. The pollution of ARGs in sediments is becoming severe and complicated. However, the relationships between heavy metals/antibiotics with ARGs in sediments are unclear. Thus, we collected river sediment samples to investigate the effects of 18 antibiotics/8 heavy metal (loid)s on ARGs' contamination. Results showed that tetracycline, lipopeptide and sulfonamide were 100% detection, where tetracyclines were the most abundant, ranging from 44 ng/g to 408 ng/g dw. Meanwhile, arsenic, zinc, and cadmium were the most seriously contaminated with the concentrations of 4–812 mg/kg, 155–6158 mg/kg, 0.1–23 mg/kg, respectively. The abundance of ARGs (tetA, sul1, sul2, and qnrA) were not only closely with antibiotics, but also significantly positively correlated with heavy metals. What's more, the heavy metals had significant positive correlations with MGEs such as plasmids, integrons, and efflux pumps, suggesting that heavy metals could potentially drive the propagation of ARGs in sediments. The rand-forest model showed the heavy metal (loid)s contributed up to 70% to the ARGs pollution in sediments. This study extends our understanding of the correlation between ARGs and heavy metals/antibiotics and emphasizes the importance of considering co-existing heavy metals in the ARG pollution in coastal watersheds.
DOI: 10.3389/fmicb.2026.17778202026-04-01
Sixu Lin, Xue Yang, Junyao Wang, Qinghua Yu, Bing Li, Xuerui Yan
Extracellular Monascus pigments (eMPs), as a crucial component of Monascus pigments (MPs) with functional activities, have been widely utilized. In this study, the effect of L-cysteine on the eMPs production capacity of S109 were investigated, along with the physiological and molecular response of S109 under L-cysteine. The results indicated that increasing the concentration of L-cysteine could promote the growth of S109 and improve the cell membrane permeability and fluidity. However, high concentration of L-cysteine did not constantly promote the yield of eMPs. The optimal condition was achieved with the addition of 2 g/L L-cysteine, under which the production of eMPs increased from 80.42 ± 0.37 to 329.20 ± 2.69 U/mL. Under this condition, all genes involved in the MPs synthesis and secretion pathway were approximately up-regulated. This study proposed a simple and effective method to improve the eMPs, which laid the foundation for the substantial improvement of Monascus fermentation industry.
DOI: 10.3389/fmicb.2026.17778882026-04-01
Dong Fang, Rui Shi
ObjectiveThis study aimed to develop a predictive model based on Automated Machine Learning (AutoML) to achieve early and precise warning of Carbapenem-resistant Organisms (CRO) infections in hospitalized patients, thereby providing technological support for proactive prevention and control.MethodsA retrospective cohort study design was employed. Data from 958 hospitalized patients with CRO and Carbapenem-susceptible Organisms (CSO) infections were collected at CR and WISCO General Hospital between January 2022 and June 2025. An AutoML framework based on an Improved Hannibal Barcid Optimization algorithm (IHBO) was proposed. The model was constructed through dual-stage optimization (feature selection and hyperparameter tuning) and compared against five traditional algorithms, including Logistic Regression (LR) and Support Vector Machine (SVM). Model performance was evaluated using metrics including the Area Under the Receiver Operating Characteristic Curve (AUC), the Area Under the Precision-Recall Curve (AUPRC), and the F1 score. Key feature contributions and interaction mechanisms were analyzed using Shapley Additive exPlanations (SHAP).ResultsRegarding model performance, the IHBO-optimized AutoML model demonstrated superior discriminative ability and robustness in the independent test set compared to others. Its ROC-AUC reached 0.8941 and PR-AUC reached 0.0.8844, significantly higher than those of the other models. Simultaneously, it achieved an F1 score of 0.8114, with sensitivity and specificity of 0.7917 and 0.8392, respectively. Calibration analysis indicated this model had the highest accuracy in predicted probabilities (Brier Score = 0.134). Decision curve analysis confirmed its significant clinical net benefit across the 1–71% risk threshold range. Feature analysis identified five core predictors ranked by importance: Antifungal Medication Usage, ICU Length of Stay Stratification, APACHE II Score > 15, Aminoglycoside Antibiotic Exposure, and Indwelling Urinary Catheter Use. SHAP interaction analysis further revealed: (1) Antifungal use significantly increases CRO risk, especially in patients with APACHE II > 15; (2) ICU stay duration shows dose-response relationship with CRO risk, amplified when APACHE II > 15; and (3) Combined use of aminoglycoside and urinary catheter creates synergistic risk, indicating additive effect of multiple risk factors; (4) Triple high-risk combination (antifungal + ICU > 7 days + APACHE II > 15) shows highest SHAP values, requiring intensive infection control measures. Based on these findings, a clinical decision support tool integrating the key features was developed, enabling the visual output of individualized infection risk.ConclusionThe IHBO-AutoML model developed in this study overcomes the limitations of traditional static methods. It employs explainable machine learning to elucidate the core driver mechanism involving the synergy between antifungal use and critical illness, the biological feedback loop linking prolonged ICU stay and organ failure, and the spatially specific resistance evolution induced by the interaction of drugs and medical devices. The model provides a precise tool for proactive prevention and control, facilitating the transition in carbapenem-resistant organism management modes.
DOI: 10.3389/fmicb.2026.17753442026-04-01
Uma Venkatesan, Rajiniraja Muniyan
Food wrapping plays a critical role in maintaining the superior quality, protection, and preservation of food commodities by preventing contamination and spoilage. The current study investigated the biological potential, chromatographic profiling, molecular docking, and simulation studies of Cardiospermum halicacabum L. leaf fractions. Furthermore, the bioactive fraction of C. halicacabum was incorporated with chitosan and pectin matrices (Chi/Pec/CF) to develop an innovative antioxidative and antibacterial edible film for packaging fresh-cut fruit. Antioxidant and antimicrobial activities were estimated using different solvent extracts (petroleum ether, chloroform, and ethanol). Among these, the ethanol extract exhibited the highest free radical scavenging activity and the strongest antimicrobial activity. Furthermore, bioactivity-guided fractionation with antimicrobial activity was performed using column chromatography. The bioactive fraction was subjected to GC–MS analysis, identifying 27 phytocomponents, which were subsequently evaluated by docking analysis against DNA gyrase B from S. aureus and dihydrofolate reductase from E. coli. The results indicated that three compounds exhibited higher binding affinities than the reference compounds. The docking scores of Hit 1 (4′-pentylbicyclohexyl-4-carboxamide) were −9.57 and −16.33 kcal/mol, Hit 2 (2-formyl-9-[beta-d-ribofuranosyl] hypoxanthine) were −10.95 and −15.00 kcal/mol, and Hit 3 (2-hydroxymethyl-9-[beta-d-ribofuranosyl] hypoxanthine) were −11.18 and −14.80 kcal/mol against the respective target proteins. Moreover, the overall bioactive fraction was used to develop the Chi/Pec/CF film as a packaging material, and it was evaluated for extending the shelf life of fresh apple slices stored for 6 days at 4 °C. Overall, the results highlight the potential of these composite films as promising food packaging materials owing to their antimicrobial, antioxidative, and biodegradable properties.
DOI: 10.3389/fmicb.2026.18121962026-04-01
Quentin Jehanne, Anne Conrad, Raphaële Nove Josserand, Nicolas Benech, Paul Marie Schatz, Lucie Bénéjat, Astrid Ducournau, Johanna Aptel, Moeava Martin, Marine Jauvain, Olivier Dauwalder, Philippe Lehours
Because few studies have focused on recurrent Campylobacter bacteremia, we investigated two clinical cases of patients with common variable immunodeficiency and repeated Campylobacter bacteremia over a period of 6–10 years. We analyzed and compared genomes from isolates obtained from both patients during follow-up. For patient #1, 18 isolates of Campylobacter coli and 17 isolates of Campylobacter jejuni were obtained from 2014 to 2024. For patient #2, 10 isolates of C. coli were obtained from 2019 to 2024. Next-generation sequencing was used to identify species, characterize antimicrobial resistance, perform multilocus sequence typing, and analyze core-genome single-nucleotide polymorphisms, as well as to uncover potential sources of contamination. For patient #1, all 18 C. coli isolates obtained from 2022 to 2024 were from the same clonal complex and source of contamination (chicken) and exhibited high levels of genomic resemblance based on core-genome single-nucleotide polymorphism analysis. Each C. coli isolate probably originated from the same initial strain. However, two clusters of C. jejuni were identified: one consisting of isolates from 2014 and the other consisting of the remaining isolates from 2022 to 2024. A 16S rRNA mutation in position A1387G was present in four C. coli isolates from 2022 and 2023, and this was associated with gentamicin resistance. One C. coli isolate was also resistant to ertapenem and exhibited an amino acid duplication within the PorA protein sequence. For patient #2, each C. coli isolate was from the same clonal complex, which was of porcine origin. Similar to patient #1, three of the isolates from 2023 had an A1464G 16S rRNA mutation and were gentamicin resistant. Retrospective analyses of antimicrobial use for both patients highlighted an association between antimicrobial selection pressure and the emergence of resistance markers, suggesting in vivo selection.
DOI: 10.3389/fmicb.2026.1750824