Ginseng-derived nanoparticles potentiate immune checkpoint antibody efficacy by reprogramming the cold tumor microenvironment.

Cold tumor microenvironment (TME) marked with low effector T cell infiltration leads to weak response to immune checkpoint inhibitor (ICI) treatment. Thus, switching cold to hot TME is critical to improve potent ICI therapy. Previously, we reported extracellular vesicle (EV)-like ginseng-derived nanoparticles (GDNPs) that were isolated from Panax ginseng C.A. Mey and can alter M2 polarization to delay the hot tumor B16F10 progression. However, the cold tumor is more common and challenging in the real world. Here, we explored a combinatorial strategy with both GDNPs and PD-1 (programmed cell death protein-1) monoclonal antibody (mAb), which exhibited the ability to alter cold TME and subsequently induce a durable systemic anti-tumor immunity in multiple murine tumor models. GDNPs enhanced PD-1 mAb anti-tumor efficacy in activating tumor-infiltrated T lymphocytes. Our results demonstrated that GDNPs could reprogram tumor-associated macrophages (TAMs) to increase CCL5 and CXCL9 secretion for recruiting CD8+ T cells into the tumor bed, which have the synergism to PD-1 mAb therapy with no detected systemic toxicity. In situ activation of TAMs by GDNPs may broadly serve as a facile platform to modulate the suppressive cold TME and optimize the PD-1 mAb immunotherapy in future clinical application.

Edible and cation-free kiwi fruit derived vesicles mediated EGFR-targeted siRNA delivery to inhibit multidrug resistant lung cancer.

Clinically, activated EGFR mutation associated chemo-drugs resistance has severely threaten NSCLC patients. Nanoparticle based small interfering RNA (siRNA) therapy representing another promising alternative by silencing specific gene while still suffered from charge associated toxicity, strong immunogenicity and poor targetability. Herein, we reported a novel EGFR-mutant NSCLC therapy relying on edible and cation-free kiwi-derived extracellular vesicles (KEVs), which showed sevenfold enhancement of safe dosage compared with widely used cationic liposomes and could be further loaded with Signal Transducer and Activator of Transcription 3 interfering RNA (siSTAT3). siSTAT3 loaded KEVs (STAT3/KEVs) could be easily endowed with EGFR targeting ability (STAT3/EKEVs) and fluorescence by surface modification with tailor-making aptamer through hydrophobic interaction. STAT3/EKEVs with a controlled size of 186 nm displayed excellent stability, high specificity and good cytotoxicity towards EGFR over-expressing and mutant PC9-GR4-AZD1 cells. Intriguingly, the systemic administration of STAT3/EKEVs significantly suppressed subcutaneous PC9-GR4-AZD1 tumor xenografts in nude mice by STAT3 mediated apoptosis. This safe and robust KEVs has emerged as the next generation of gene delivery platform for NSCLC therapy after multiple drug-resistance.

Inhomogeneous antibiotic distribution in sediment profiles in anthropogenically impacted lakes: Source apportionment, fate drivers, and risk assessment.

Antibiotic residues in lake ecosystems have been widely reported; however, the vertical distribution of antibiotics in lake sediment profiles have rarely been examined. This study systematically revealed the vertical distribution pattern, sources, and risks of antibiotics in sediments of four typical agricultural lakes in central China. Nine of 33 target antibiotics were detected with a total concentration range of 39.3-18,250.6 ng/g (dry weight), and the order of average concentration was erythromycin (1447.4 ng/g) > sulfamethoxazole (443.7 ng/g) > oxytetracycline (62.6 ng/g) > enrofloxacin (40.7 ng/g) > others (0.1-2.1 ng/g). The middle-layer sediments (9-27 cm) had significantly higher antibiotic detected number and concentration than those in the top layer (0-9 cm) and bottom layer (27-45 cm) (p < 0.05). Correlation analysis showed that significant relationships existed between antibiotic concentrations and the octanol-water partition coefficients (Kow) of antibiotics (p < 0.05). Redundancy analysis indicated that Pb, Co, Ni, water content, and organic matter (p < 0.05) jointly affected the distribution of antibiotics in sediment profiles. Risk assessment showed that the highest potential ecological and resistance selection risks of antibiotics occurred in the middle-layer sediments, and oxytetracycline, tetracycline, and enrofloxacin had the most extensive potential risks in the sediment profiles. Additionally, the positive matrix factorization model revealed that human medical wastewater (54.5%) contributed more antibiotic pollution than animal excreta (45.5%) in sediment. This work highlights the inhomogeneous distribution of antibiotics in sediment profiles and provides valuable information for the prevention and control of antibiotic contamination in lakes.

Lanthanum and magnesium activated palygorskite for adsorption of phosphate in piggery wastewater.

Removing phosphate from wastewater can help alleviate eutrophication. Therefore, in this study, lanthanum and magnesium were loaded onto the thermally modified palygorskite (PAL) using a coprecipitation method, and a composite material was prepared for phosphate recovery. In the pH range of 2-7, the material can effectively adsorb the phosphate. In the kinetic experiment, the material was able to rapidly adsorb phosphate within 4 h of the beginning of the reaction. The adsorption isotherm result of the material was in accordance with Freundlich isotherm model. When pH was 7, the theoretical maximum adsorption capacity was 20.4 mg P/g. When phosphate coexisted with CO32- and HCO3-, the adsorption was significantly inhibited. In the adsorption-desorption experiment, the material can be reused at least five times after elution with 1 mol/L of sodium hydroxide solution. The equilibrium adsorption capacity of the material for total phosphorus in piggery wastewater was 7.25 mg P/g, achieving a total phosphorus removal rate of 95.3%. The characterization of XRD, FT-IR and XPS suggested that phosphate was mainly exchanged with La-OH in the material, forming an amorphous LaPO4 complex.

[Research progress of Angelicae Sinensis Radix and predictive analysis on its quality markers].

Angelicae Sinensis Radix, as a medicinal and edible Chinese medicinal herb, is widely used in clinical practice. It is mainly cultivated in Minxian, Tanchang, Zhangxian and Weiyuan counties of Gansu province. In recent years, with the comprehensive and in-depth study of Angelicae Sinensis Radix in China and abroad, its chemical composition, pharmacological effects and application and development have attracted much attention. In this study, the chemical composition, traditional efficacy, and modern pharmacological effects of Angelicae Sinensis Radix were summarized. On this basis, combined with the core concept of quality markers(Q-markers), the Q-markers of Angelicae Sinensis Radix were discussed from the aspects of mass transfer and traceability and chemical composition specificity, availability, and measurability, which provided scientific basis for the quality evaluation of Angelicae Sinensis Radix.

Mapping Drug-Induced Neuropathy through In-Situ Motor Protein Tracking and Machine Learning.

Chemotherapy can induce toxicity in the central and peripheral nervous systems and result in chronic adverse reactions that impede continuous treatment and reduce patient quality of life. There is a current lack of research to predict, identify, and offset drug-induced neurotoxicity. Rapid and accurate assessment of potential neuropathy is crucial for cost-effective diagnosis and treatment. Here we report dynamic near-infrared upconversion imaging that allows intraneuronal transport to be traced in real time with millisecond resolution, but without photobleaching or blinking. Drug-induced neurotoxicity can be screened prior to phenotyping, on the basis of subtle abnormalities of kinetic characteristics in intraneuronal transport. Moreover, we demonstrate that combining the upconverting nanoplatform with machine learning offers a powerful tool for mapping chemotherapy-induced peripheral neuropathy and assessing drug-induced neurotoxicity.

Diphenylcyclopropenone plays an effective therapeutic role by up-regulating the TSLP/OX40L/IL-13 pathway in severe alopecia areata.

Topical immunotherapy with diphenylcyclopropenone (DPCP) is considered to be the most effective treatment of severe AA. However, the mechanism is unclear and an early predictor for the efficacy needs to be explored. The TSLP/OX40L/IL-13 pathway is an important pathway to initiate and maintain Th2 immune responses. Our previous work suggests this pathway may play a role in severe AA treated with DPCP. Thus, to further investigate the mechanism of TSLP/OX40L/IL-13 pathway in severe AA treated with DPCP and explore the predictor for the efficacy of DPCP therapy, we conducted a prospective study to compare expression levels of TSLP, OX40L, Th2 cytokines IL-4, IL-5 and IL13, and Th1 cytokine IFN-γ in severe AA patients before and after the treatment. Results showed that 21 AA patients were responsive (responders) to the DPCP therapy and 12 were not responsive (non-responders). Responders had lower levels of TSLP, OX40L and IL-13 than non-responders before the treatment. After the DPCP treatment, TSLP, IL-5 and IL-13 increased and IFN-γ decreased in responders while there were no changes of TSLP, IL-4, IL-13 and IFN-γ in non-responders. Our data suggest that the TSLP/OX40L/IL-13 pathway is down-regulated in some severe AA patients and DPCP might play a therapeutic role by up-regulating the pathway in these severe AA patients. The TSLP/OX40L/IL-13 pathway could be a predictor of response to the DPCP therapy for severe AA patients.

Integrated Transcriptome Analysis of microRNA and mRNA in Mouse Skin Derived Precursors (SKPs) and SKP Derived Fibroblast (SFBs) by RNA-Seq.

BACKGROUND: Skin-derived precursors (SKPs) display the characteristics of self-renewal and multilineage differentiation. OBJECTIVE: The study aimed to explore the molecular mechanisms of mouse SKPs differentiation into SKP-derived fibroblasts (SFBs). METHODS: We compared the microRNA (miRNA) profile in mouse SKPs and SFBs by RNA sequenc-ing. Real-time quantitative reverse transcription PCR (qRT-PCR) was performed to validate the miRNA expression. The integrated analysis of miRNA and mRNA expression data was performed to explore the potential crosstalk of miRNA-mRNA in SKP differentiation. RESULTS: 207 differentially expressed miRNAs and 835 miRNA target genes in the gene list of integrated mRNA expression profiling were identified. Gene Ontology (GO) enrichment analysis revealed that cell differentiation and cell proliferation process were significantly enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the target genes were significantly most enriched in the cytokine-cytokine receptor interaction, cancer pathways and axon guidance signaling pathway. The most upregulated and downregulated target genes were involved in the Wnt, Notch, cytokine-cytokine receptor interaction, TGF-ß, p53 and apoptotic signaling pathway. The miRNA-mRNA regulatory net-works and 507 miRNA-mRNA pairs were constructed. Seven miRNAs (miR-486-3p, miR-504-5p, miR-149-3p, miR-31-5p, miR-484, miR-328-5p and miR-22-5p) and their target genes Wnt4, Dlx2, Se-ma4f, Kit, Kitl, Inpp5d, Igfbp3, Prdm16, Sfn, Irf6 and Clu were identified as miRNA-mRNA crosstalk pairs. CONCLUSION: These genes and signaling pathways might control SKPs proliferation and SKPs differen-tiation into SFBs during the process of SKPs differentiation, which might promote the application of SKPs in the clinical treatment of skin-related diseases by regulating SKPs proliferation and SKPs differ-entiation.

Comparison of the proteomes of mouse Skin Derived Precursors (SKPs) and SKP-derived fibroblasts (SFBs) by iTRAQ.

Skin-derived precursors (SKPs) can differentiate into fibroblasts. However, little is known about the molecular mechanism of the differentiation process. Our previous study has compared the transcriptomes of mouse SKPs and SKP-derived fibroblasts (SFBs) by RNA-Seq analysis and found some genes and signal pathways that might play important roles in the transition from SKPs to SFBs. Here, to further investigate the process by which SKPs differentiate into fibroblasts, we compared the proteomes between SKPs and SFBs using iTRAQ. Our results showed that 243 differentially expressed proteins (DEPs) were identified. Among the 28 DEPs which were related to the functional group of cell differentiation, Down-regulated DEPs collagen XVIII, keratin 10, keratin 5, keratin 14, and TIFIbeta, up-regulated DEPs Thy-1, ANXA1, alpha-catenin, and calreticulin might play important roles in the transition of SKPs to fibroblasts. Further study is needed to clarify the roles of these proteins in the differentiation process of SKPs into fibroblasts, which could facilitate investigations of the detailed molecular mechanisms in the process and make it possible to take advantage of the potential therapeutic applications of SKPs in skin regeneration in the future.

Urea hydrogen bond donor-mediated synthesis of high-index faceted platinum concave nanocubes grown on multi-walled carbon nanotubes and their enhanced electrocatalytic activity.

We have reported, for the first time, in situ growth of high-index {hk0} faceted concave Pt nanocubes on multi-walled carbon nanotubes (CNTs) via an electrochemical method in choline chloride-urea (ChCl-U) based deep eutectic solvents (DESs). Mechanistic studies indicate that a urea hydrogen bond donor (HBD) plays a key role in the formation of concave Pt nanocubes, in which the urea HBD preferentially adsorbs onto the {100} faces and blocks the growth of nanocrystals along the 〈100〉 axis. The as-prepared concave Pt nanocubes are characterized to be enclosed mainly with high-index {710}, {610} and {510} facets. It has been determined that the concave cubic Pt/CNT exhibits higher catalytic activity and stability than the flower-like Pt/CNT and commercial Pt/C catalysts, and this is ascribed to its high density of surface atomic steps and the synergistic effect between the CNT and Pt nanocubes.

Influence of ripening stage on the microwave-assisted pectin extraction from banana peels: A feasibility study targeting both the Homogalacturonan and Rhamnogalacturonan-I region.

This work investigated a sustainable and efficient approach of pectin extraction for banana peel waste valorisation and studied the influence of banana ripening stages (RS at 2,5 and 7). Although pectin content in banana peel raw material decreased during ripening, pectin extraction was favoured. The highest alcohol-insoluble solids (AIS) yield (12.5%) was achieved at 70 °C, 15 mins from RS 7 peel. All extracts were homogalacturan-rich with some rhamnogalacturonan-I content (showing HGA/RG-I ratio > 2) with varied degree of methylation (DM). The highest HGA content (837.2 mg/g AIS) and HGA/RG-I ratio (9.9) were achieved at 110 °C, 0 mins from RS 7, suggesting its promising application as gelling agent. The highest RG-I content (111.1 mg/g AIS) were obtained at 110 °C, 5 mins from RS 7, which was comparable with the pectin with reported prebiotic ability isolated from the literature, suggesting its potential application in novel products.

Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics.

The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R2 = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.

Association of MBL2 gene polymorphisms and MBL levels with dilated cardiomyopathy in a Chinese Han population.

BACKGROUND: It has been reported that Mannose-binding lectin 2 (MBL2) gene polymorphisms and expression levels are related to dilated cardiomyopathy (DCM). This study aimed to investigate the potential association between MBL2 gene polymorphisms and the pathogenesis of DCM. METHODS: Five single nucleotide polymorphisms (SNPs) of the MBL2 gene were genotyped in 440 DCM patients and 532 controls in Southwest China. A luciferase reporter assay was used to detect the transcriptional activity the different genotypes. MBL serum levels, left ventricle ejection fraction (LVEF) and lower left ventricular end-diastolic diameter (LVEDD) were measured. RESULTS: The rs11003125 C allele increased the transcriptional activity of the MBL2 promoter compared with the rs11003125 G allele. The rs11003125 CC carriers had higher MBL serum levels, LVEF and LVEDD than the rs11003125 CG and GG carriers. CONCLUSIONS: Our study first revealed that MBL2 polymorphisms and serum MBL levels were associated with DCM. Allele C in rs11003125 of MBL2 may upregulate the expression levels of MBL. High serum MBL levels may be a protective factor in DCM pathogenesis.

Exploring the efficacy of laser speckle contrast imaging in the stratified diagnosis of rosacea: a quantitative analysis of facial blood flow dynamics across varied regions.

Background: Rosacea has a high incidence, significantly impacts quality of life, and lacks sufficient diagnostic techniques. This study aimed to investigate the feasibility of laser speckle contrast imaging (LSCI) for measuring facial blood perfusion in patients with rosacea and to identify differences in blood flow among various facial regions associated with different rosacea subtypes. Methods: From June to December 2023, 45 patients were recruited, with 9 excluded, leaving 36 subjects: 12 with erythematotelangiectatic rosacea (ETR), 12 with papulopustular rosacea (PPR), and 12 healthy controls. The Think View multispectral imaging analyzer assessed inflammation via gray reading values across the full face and five facial areas: forehead, nose, cheeks, and chin. LSCI measured and analyzed blood perfusion in the same areas. Plasma biomarkers interleukin-6 (IL-6), IL-1ß, and tumor necrosis factor-α (TNF-α) were tested in different groups. Results: Both ETR and PPR groups showed increased average blood perfusion and facial inflammation intensity by gray values compared to controls, with statistically significant differences. Average blood perfusion of ETR and PPR groups showed increased values in the forehead, cheeks, and nose, compared to controls, and the values in the cheeks were statistically different between ETR and PPR. The facial inflammation intensity of the ETR group showed increased values in the forehead and cheeks, and the PPR group showed increased gray values in the forehead, cheeks, nose, and chin compared to controls, and the values for the cheeks, nose, and chin were statistically significantly different between ETR and PPR. Plasma biomarkers IL-6, IL-1ß, and TNF-α were significantly elevated in both ETR and PPR groups compared to controls. Conclusion: LSCI is a valuable, non-invasive tool for assessing blood flow dynamics in rosacea, providing a data foundation for clinical research. Different rosacea subtypes exhibit distinct lesion distribution and blood flow patterns, and both ETR and PPR could affect all facial areas, particularly the cheeks in ETR and the forehead, nose, and chin in PPR.

NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes.

Antibiotic resistance genes (ARGs) are emerging pollutants present in various environments. Identifying ARGs has become a growing concern in recent years. Several databases, including the Antibiotic Resistance Genes Database (ARDB), Comprehensive Antibiotic Resistance Database (CARD), and Structured Antibiotic Resistance Genes (SARG), have been applied to detect ARGs. However, these databases have limitations, which hinder the comprehensive profiling of ARGs in environmental samples. To address these issues, we constructed a non-redundant antibiotic resistance genes database (NRD) by consolidating sequences from ARDB, CARD, and SARG. We identified the homologous proteins of NRD from Non-redundant Protein Database (NR) and the Protein DataBank Database (PDB) and clustered them to establish a non-redundant comprehensive antibiotic resistance genes database (NCRD) with similarities of 100% (NCRD100) and 95% (NCRD95). To demonstrate the advantages of NCRD, we compared it with other databases by using metagenome datasets. Results revealed its strong ability in detecting potential ARGs.

Lignin recovery from cocoa bean shell using microwave-assisted extraction and deep eutectic solvents.

Lignin is the second most abundant natural polymer after cellulose, and valorisation of lignin-rich streams has attracted increasing attention recently. This paper presents a novel and sustainable method to recover lignin from Cocoa Bean Shells (CBS) using Deep Eutectic Solvents (DES) and microwaves. A DES containing p-toluenesulfonic acid, choline chloride and glycerol (2:1:1 M ratio) was selected based on its dielectric properties. Under 200 W microwave power, the optimum yield of 95.5 % lignin was achieved at 130 °C and 30 min. DES-extracted lignin exhibited unique structural characteristics including larger particle sizes (242.5 µm D50 size), structural diversity (410.4 µm D90-D10 size) and H/G sub-unit ratio (71.9 %) compared with commercial Kraft lignin (77.2 µm, 157.9 µm and 0.1 % respectively), indicating the potential of DES in the modification and upgrading of lignin for novel value-added products.

Ginseng-derived nanoparticles reprogram macrophages to regulate arginase-1 release for ameliorating T cell exhaustion in tumor microenvironment.

BACKGROUND: Lines of evidence indicated that, immune checkpoints (ICs) inhibitors enhanced T cell immune response to exert anti-tumor effects. However, T cell exhaustion has been so far a major obstacle to antitumor immunotherapy in colorectal cancer patients. Our previous studies showed that ginseng-derived nanoparticles (GDNPs) inhibited the growth of various tumors by reprograming tumor-associated macrophages (TAMs) and downregulated the ICs expression on T cells in tumor microenvironment (TME), but the underlying effector mechanisms remained unclear. METHODS: The correlation between arginase-1 (ARG1) and T cells was computed based on the colorectal cancer patients in TCGA database. In vitro, we observed that GDNPs reprogrammed TAMs inhibited ARG1 release and ultimately ameliorated T cell exhaustion according to several techniques including WB, PCR, ELISA and flow cytometry. We also used an in vivo MC38 tumor-bearing model and administered GDNPs to assess their anti-tumor effects through multiple indices. The mechanism that GDNPs improved T cell exhaustion was further clarified using the bioinformatics tools and flow cytometry. RESULTS: GDNPs reprogramed TAMs via reducing ARG1 production. Moreover, normalized arginine metabolism ameliorated T cell exhaustion through mTOR-T-bet axis, resulting in reduced ICs expression and enhanced CD8+ T cells expansion. CONCLUSIONS: By regulating the mTOR-T-bet axis, GDNPs reprogramed macrophages to regulate ARG1 release, which further ameliorated T cell exhaustion in TME. These findings provided new insights into comprehending the mechanisms underlying the mitigation of T cell exhaustion, which may facilitate the development of innovative therapeutic strategies in the field of cancer treatment.

How has airport service quality changed in the context of COVID-19: A data-driven crowdsourcing approach based on sentiment analysis.

Airport service quality (ASQ) is a competitive advantage for airport management in today's airport market. Since the COVID-19 health crisis has unprecedentedly influenced airport regulations and operations, effective measurement of ASQ has become crucial for airport administrations. Surveying travelers' attitudes is useful for ASQ assessment but collecting responses could be time-consuming and costly. Therefore, this paper adopts a data-driven crowdsourcing approach to study ASQ during the COVID-19 pandemic by investigating Google Maps reviews from the 98 busiest U.S. airports. To do so, this study develops a topical ontology of keywords regarding ASQ attributes and uses a sentiment tool to derive passengers' attitudes. Through sentiment analysis, Google Maps reviews show more positive sentiment toward environment and personnel but remain constant about facilities during COVID-19. The lexical salience-valence analysis (LSVA) is then applied to explain such changes by tracking the sentiment of frequent words in reviews. Through correlation and regression analysis, this study demonstrates that rating is significantly related to check-in, environment, and personnel in pre-and post-COVID periods. Additionally, the effect of access, wayfinding, facilities, and environment on rating significantly differs between the two periods. The findings illustrate the effectiveness of leveraging online reviews and offer practical implications for what matters to air travelers, especially in the COVID-19 context.

Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment.

The increasing pollution of urban drinking water sources by antibiotic resistance genes (ARGs) threatens human health worldwide. However, the distribution and influencing factors of ARGs, especially how to reveal the risks of ARGs in this environment remains unclear. Hence, Chaohu Lake was selected as an example to investigate the characteristics of ARGs and explore the interactions among physicochemical factors, microorganisms, and ARGs by metagenomic approach. In this work, 75 ARG subtypes with an average of 30.4 × /Gb (ranging from 15.2 ×/Gb to 57.9 ×/Gb) were identified, and multidrug and bacA were most frequent in Chaohu Lake. Non-random co-occurrence patterns and potential host bacteria of ARGs were revealed through co-occurrence networks. Microbial community and mobile genetic elements (MGEs) were the major direct factors in ARG profiles. The dissemination of ARGs was mainly driven by plasmids. Considering the interactions among MGEs, human bacterial pathogens, and ARGs, antibiotic resistome risk index (ARRI) was proposed to manifest the risks of ARGs. Overall, our work systemically investigated the composition and associated factors of ARGs and built ARRI to estimate the potential risks of ARGs in a typical urban drinking water source, providing an intuitive indicator for managing similar lakes.

Comprehensive analysis of 84 Faecalibacterium prausnitzii strains uncovers their genetic diversity, functional characteristics, and potential risks.

Faecalibacterium prausnitzii is a beneficial human gut microbe and a candidate for next-generation probiotics. With probiotics now being used in clinical treatments, concerns about their safety and side effects need to be considered. Therefore, it is essential to obtain a comprehensive understanding of the genetic diversity, functional characteristics, and potential risks of different F. prausnitzii strains. In this study, we collected the genetic information of 84 F . prausnitzii strains to conduct a pan-genome analysis with multiple perspectives. Based on single-copy genes and the sequences of 16S rRNA and the compositions of the pan-genome, different phylogenetic analyses of F. prausnitzii strains were performed, which showed the genetic diversity among them. Among the proteins of the pan-genome, we found that the accessory clusters made a greater contribution to the primary genetic functions of F. prausnitzii strains than the core and specific clusters. The functional annotations of F. prausnitzii showed that only a very small number of proteins were related to human diseases and there were no secondary metabolic gene clusters encoding harmful products. At the same time, complete fatty acid metabolism was detected in F. prausnitzii. In addition, we detected harmful elements, including antibiotic resistance genes, virulence factors, and pathogenic genes, and proposed the probiotic potential risk index (PPRI) and probiotic potential risk score (PPRS) to classify these 84 strains into low-, medium-, and high-risk groups. Finally, 15 strains were identified as low-risk strains and prioritized for clinical application. Undoubtedly, our results provide a comprehensive understanding and insight into F. prausnitzii, and PPRI and PPRS can be applied to evaluate the potential risks of probiotics in general and to guide the application of probiotics in clinical application.