Background: The Five-flavor Sophora Flavescens Enteric-coated Capsule (FSEC) is widely used to treat ulcerative colitis (UC), yet its underlying molecular mechanisms remain incompletely understood. This study aimed to systematically elucidate the therapeutic mechanisms and clinical value of FSEC by integrating network pharmacology, experimental validation, and clinical data. Methods: A multi-tiered methodological framework was implemented. First, network pharmacology analysis identified potential molecular targets and signaling pathways associated with FSEC in UC. These predictions, including the core targets and the AGE-RAGE/NF-κB signaling pathway, were subsequently validated in a dextran sulfate sodium-induced mouse colitis model in vivo and a lipopolysaccharide-stimulated RAW264.7 macrophage inflammation model in vitro. Finally, a single-center retrospective cohort study of 90 patients evaluated the efficacy and safety of FSEC as monotherapy and in combination with Mesalazine. Results: Network pharmacology identified 12 core targets and predicted the AGE-RAGE/NF-κB pathway as a key mechanism. Experimental validation demonstrated that FSEC inhibits this pathway. Both in vivo and in vitro studies consistently showed that FSEC downregulates RAGE expression and NF-κB p65 phosphorylation, reducing the production of key inflammatory mediators and thereby alleviating intestinal inflammation. Clinically, FSEC monotherapy achieved efficacy comparable to that of Mesalazine, and combination therapy was associated with higher clinical remission and mucosal healing rates, with a favorable safety profile. Conclusions: This comprehensive multi-omics investigation provides integrated evidence that FSEC exerts anti-inflammatory effects, associated with inhibition of the AGE-RAGE/NF-κB pathway. The observed synergy between FSEC and Mesalazine suggests the potential of an integrated therapeutic approach for UC.

BACKGROUND:Regulatory dendritic cell (DCreg) subset exhibits a unique capacity for inducing immune tolerance among the variety subsets of dendritic cells (DCs) within gut-associated lymphoid tissues (GALTs). Fms-like tyrosine kinase 3 ligand (FLT3L) is involved in the differentiation of DCregs and the subsequent expansion of regulatory T-cells (Tregs) mediated by DCregs, though the precise mechanism remains poorly understood. This study aimed to explore the expansion mechanism of Treg induced by DCreg and the role of FLT3L in this process. METHODS:DCregs were distinguished from other DC subsets isolated from GALTs of BALB/c mice through a mixed lymphocyte reaction assay. The functions and mechanisms by which FLT3L promoted Treg expansion via DCregs were investigated in vitro through co-culture experiments involving DCregs and either CD4 + CD25 - T-cells or CD4 + CD25 + T-cells. Additionally, an in vivo experiment was conducted using a dextran sulfate sodium (DSS)-induced colitis model in mice. RESULTS:CD103 + CD11b + DC exhibited DCreg-like functionality and was identified as DCreg for subsequent investigation. Analysis of Foxp3 + Treg percentages within a co-culture system of CD4 + CD25 - T-cells and DCregs, with or without FLT3L, demonstrated the involvement of the FLT3/FLT3L axis in driving the differentiation of precursor T-cells into Foxp3 + Tregs induced by DCregs. Cell migration and co-culture assays revealed that the FLT3/FLT3L axis enhanced DCreg migration toward Tregs via the Rho pathway. Additionally, it was observed that DCregs could promote Treg proliferation through the Notch pathway, as inhibition of Notch signaling by DAPT (N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester) suppressed Treg expansion within the co-culture system of DCregs and CD4 + T-cells or CD4 + CD25 + T-cells. Furthermore, the FLT3/FLT3L axis influenced JAG1 expression in DCregs, indirectly modulating Treg expansion. In vivo experiments further established that FLT3L promoted DCreg expansion and restored Treg balance in DSS-induced colitis models, thereby ameliorating colitis symptoms in mice. CONCLUSION:The FLT3/FLT3L axis is integral to the maintenance of DCreg function in Treg expansion.

Tetracycline antibiotics (TCs), extensively used in aquaculture and livestock production, pose significant ecological risks due to their accumulation in aquatic sediments. This study investigated the efficacy and ecological implications of bioaugmentation with a synthetic microbial consortium for the remediation of TCs-contaminated aquaculture pond sediment. Sediment microcosms were amended with tetracycline (TC) and doxycycline (DOX) at different dosages, with or without consortium inoculation. Bioaugmentation markedly enhanced antibiotic removal, achieving complete degradation within 5-12 days, depending on the dosage. However, both high antibiotic exposure and exogenous microbial introduction lowered microbial alpha diversity. The inoculated strains, Sphingobacterium and Chryseobacterium, were selectively enriched in bioaugmented treatments, indicating a strong adaptability to elevated antibiotic pressure. Notably, bioaugmentation markedly decreased the relative abundance of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), as well as the number of ARG-hosting taxa. These findings underscored the potential of bioaugmentation as an effective and environmentally compatible strategy for mitigating antibiotic pollution and limiting ARG dissemination in sediment environments.

Background Ustekinumab (UST) was approved in China for moderate-to-severe Crohn’s disease (CD) in 2020. The prevalence rates of tuberculosis and hepatitis B virus (HBV) infection are high in China, and no guideline clearly states that tuberculosis chemoprophylaxis or prophylactic anti-HBV therapy should be prescribed before UST administration. This study aimed to assess the risk of tuberculosis and HBV reactivation in CD patients with latent tuberculosis infection (LTBI) and previous HBV infection receiving UST. Methods A multicenter retrospective cohort study was carried out at 68 hospitals in China to assess 721 adult CD cases administered UST between May 1, 2020, and December 31, 2021. CD and concurrent LTBI or HBV carrier were included. Hepatitis B serology, T-SPOT.TB, and tuberculin skin tests were performed at baseline. The primary outcome was tuberculosis or HBV reactivation. Results Patients with CD-concomitant LTBI or who were HBV carriers receiving UST therapy were retrospectively enrolled from 15 hospitals in China. A total of 53 CD with LTBI patients and 17 CD with HBV carrier patients receiving UST were included. Treatment and follow-up durations were 50 ± 20 weeks and 50 ± 15 weeks in the LTBI and HBV carrier groups, respectively. A total of 25 CD patients with LTBI underwent chemoprophylaxis and 28 did not. A total of 11 HBV carriers had antiviral prophylaxis and 6 did not. No patient experienced tuberculosis or HBV reactivation or liver dysfunction during follow-up. Conclusions UST was safe for treatment of CD because no patient developed tuberculosis, persistent hepatitis, or acute liver failure during therapy, whether with a prophylactic regimen or not, based on our sample size and limited follow-up time.

o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.

Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.

Mangrove wetlands, as one of the natural ecosystems with the most ecological services, have garnered widespread attention about their microbial driven biogeochemical cycling. Urbanization have led to different spatial patterns of environmental conditions and microbial communities in mangroves. However, viruses, as the pivotal drivers of biogeochemical cycling in mangroves, remain inadequately explored in terms of how their ecological potential and complex interactions with host respond to functional zonings. To address this knowledge gap, we conducted a comprehensive investigation on the structural and functional properties of temperate and lytic viruses in mangrove wetlands from different functional zonings by jointly using high-throughput sequencing, prokaryotic and viral metagenomics. Multiple environmental factors were found to significantly influence the taxonomic and functional composition, as well as lysogen-lysis decision-making of mangrove viruses. Furthermore, enriched auxiliary metabolic genes (AMGs) involved in methane, nitrogen and sulfur metabolism, and heavy metal resistance were unveiled in mangrove viruses, whose community composition was closely related to lifestyle and host. The virus-host pairs with different lifestyles were also discovered to react to environmental changes in different ways, which provided an empirical evidence for how virus and bacteria dynamics were specific to viral lifestyles in nature. This study expands our comprehension of the intricate interactions among virus, prokaryotic host and the environment in mangrove wetlands from multiple perspectives, including viral lifestyles, virus-host interactions, and habitat dependence. Importantly, it provides a new ecological perspective on how mangrove viruses are adapted to the stress posed by urbanization.

Tetracyclines antibiotics (TCs) pose notable environmental challenges due to their persistence in the effluent of wastewater treatment systems. Bioaugmentation offers a promising strategy for their removal, yet information is still very limited. This study aimed to assess the efficacy of bioaugmentation using wild-type (Sphingobacterium sp. WM1) and engineered tetX-carrying (PUC-tetX) strains for enhancing tetracycline (TC) removal in sequencing batch reactors (SBRs). Bioaugmentation mitigated TC's inhibitory effects on denitrification and phosphorus removal processes within SBR systems. Specifically, strain WM1 outperformed strain PUC-tetX in removing TC from sludge and maintained a longer viability. TC addition (500 μg/L, at an environmentally relevant concentration) and bioaugmentation did not significantly impact overall microbial community diversity. Notably, the introduction of these exogenous bacteria markedly increased the abundance of the tetX gene, correlating with the increase in TC degradation. Interestingly, MAGs associated with the Chloroflexi phylum in bioaugmented reactors showed the transfer of the tetX gene to autochthonous bacterial species, promoting TC removal capability. These findings underscored the potential of bioaugmentation to enhance antibiotic removal and provided insights into the dynamics of ARGs and tetX gene within activated sludge systems.

Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.

Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1). The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community. Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted.

Drinking water distribution systems (DWDSs) are important for supplying high-quality water to consumers and disinfectant is widely used to control microbial regrowth in DWDSs. However, the disinfectant's influences on microbial community and antibiotic resistome in DWDS biofilms and the underlying mechanisms driving their dynamics remain elusive. The study investigated the effects of chlorine and chloramine disinfection on the microbiome and antibiotic resistome of biofilms in bench-scale DWDSs using metagenomics assembly. Additionally, the biofilm activity and viability were monitored based on adenosine triphosphate (ATP) and flow cytometer (FCM) staining. The results showed that both chlorine and chloramine disinfectants decreased biofilm ATP, although chloramine at a lower dosage (1 mg/L) could increase it. Chloramine caused a greater decrease in living cells than chlorine. Furthermore, the disinfectants significantly lowered the microbial community diversity and altered microbial community structure. Certain bacterial taxa were enriched, such as Mycobacterium, Sphingomonas, Sphingopyxis, Azospira, and Dechloromonas. Pseudomonas aeruginosa exhibited high resistance towards disinfectants. The disinfectants also decreased the complexity of microbial community networks. Some functional taxa (e.g., Nitrospira, Nitrobacter, Nitrosomonas) were identified as keystones in chloramine-treated DWDS microbial ecological networks. Stochasticity drove biofilm microbial community assembly, and disinfectants increased the contributions of stochastic processes. Chlorine had greater promotion effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and ARG hosts than chloramine. The disinfectants also selected pathogens, such as Acinetobacter baumannii and Klebsiella pneumonia, and these pathogens also harbored ARGs and MGEs. Overall, this study provides new insights into the effects of disinfectants on biofilm microbiome and antibiotic resistome, highlighting the importance of monitoring and managing disinfection practices in DWDSs.

Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms’ activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.

Amino acid metabolism by microorganisms is a new but important pathway for the formation of NDMA precursors in water. We investigated the properties of nitrosamine precursors produced through microbial metabolism of amino acids by polarity rapid assessment method and molecular weight fractionation by ultrafiltration method. The PRAM results showed that the positively charged fraction and the non-polar fraction accounted for most (45 %-79 % and 6 %-82 %, respectively) of the NDMA precursors. The MW fractionation results also indicate the dominant precursors had MWs <1 kDa or over 10 kDa. NDMA precursors produced through amino acid metabolism were identified and quantified. Dimethylamine, N-methyl-alanine and alanine methyl ester were produced during the metabolism of ala-nine and peptone. Together, N-methyl-alanine and dimethylamine averagely contributed 24 % (12 %-44 %) of the NDMA precursors in the alanine medium. The NDMA precursor formation pathway during alanine metabolism in-volves the methylation of alanine to form N-methyl-alanine and the decomposition of alanine anabolism products to form dimethylamine. Nitrosamine precursors are generally formed through anabolism or methylation, but biogenic amines or NH3 can be produced through catabolism before nitrosamine precursor synthesis. Microbial community analysis was performed and Ralstonia was found to be a likely key genus contributing to NDMA precursor formation during alanine metabolism.

Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.

Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.

Figuring out the comprehensive metabolic mechanism of sulfonamide antibiotics (SA) is critical to improve and optimize SA removal in the bioremediation process, but relevant studies are still lacking. Here, an approach integrating metagenomic analysis, degraders’ isolation, reverse transcriptional quantification and targeted metabolite determination was used to decipher microbial interactions and functional genes’ characteristics in SA-degrading microbial consortia enriched from wetland sediments. The SA-degrading consortia could rapidly catalyze ipso-hydroxylation and subsequent reactions of SA to achieve the complete mineralization of sulfadiazine and partial mineralization of the other two typical SA (sulfamethoxazole and sulfamethazine). Paenarthrobacter, Achromobacter, Pseudomonas and Methylobacterium were identified as the primary participants for the initial transformation of SA. Among them, Methylobacterium could metabolize the heterocyclic intermediate of sulfadiazine (2-aminopyrimidine), and the owning of sadABC genes (SA degradation genes) made Paenarthrobacter have relatively higher SA-degrading activity. Besides, the coexistence of sadABC genes and sul1 gene (SA resistance gene) gave Paenarthrobacter a dual resistance mechanism to SA. The results of reverse transcription quantification further demonstrated that the activity of sadA gene was related to the biodegradation of SA. Additionally, sadABC genes were relatively conserved in a few Microbacteriaceae and Micrococcaceae SA-degraders, but the multiple recombination events caused by densely nested transposase encoding genes resulted in the differential sequence of sadAB genes in Paenarthrobacter genome. These new findings provide valuable information for the selection and construction of engineered microbiomes.

Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.

As an emerging pollutant, the antibiotic tetracycline (TC) has been consistently detected in wastewater and activated sludge. Biodegradation represents a potentially crucial pathway to dissipate TC contamination. However, few efficient TC-degrading bacteria have been isolated and a comprehensive understanding of the molecular mechanisms underlying TC degradation is still lacking. In this study, a novel TC-degrading bacterium, designated as Sphingobacterium sp. WM1, was successfully isolated from activated sludge. Strain WM1 exhibited a remarkable performance in degrading 50 mg/L TC within 1 day under co-metabolic conditions. Genomic analysis of the strain WM1 unveiled the presence of three functional tetX genes. Unraveling the complex molecular mechanisms, transcriptome analysis highlighted the role of upregulated transmembrane transport and acceler-ated electron transport in facilitating TC degradation. Proteomics confirmed the up-regulation of proteins involved in cellular biosynthesis/metabolism and ribosomal processes. Crucially, the tetX gene-encoding protein showed a significant upregulation, indicating its role in TC degradation. Heterologous expression of the tetX gene resulted in TC dissipation from an initial 51.9 mg/L to 4.2 mg/L within 24 h. The degradation pathway encompassed TC hydroxylation, transforming into TP461 and subsequent metabolites, which effectively depleted TC's inhibitory activity. Notably, the tetX genes in strain WM1 showed limited potential for horizontal gene transfer. Collectively, strain WM1 & PRIME;s potent TC degradation capacity signals a promise for enhancing TC clean-up strategies.

More and more focus has been placed on the processes by which viruses interact with bacteria to influence the biogeochemical cycles. The intricacy of soil matrix and the incompleteness of databases, however, constrains the investigation on the mechanisms of soil viruses exerting ecological functions. The modification of ICTV classification system in 2021 was also a huge shock to the results of the existing studies on virome. We used viral metagenomes combined with soil properties to investigate the viral community composition and auxiliary metabolic genes (AMGs) profiles of various lifestyles in soils of Mount Everest at different altitudes. Viral lifestyles and soil nutrient levels were found to significantly influence the diversity and composition of viral communities. Temperate virus lifestyle dominated in high-altitude soils with lower level of nutrients because of its stronger survival adaptability, and the structural and functional diversity of viral communities was positively correlated with the contents of nutrients (total carbon and total nitrogen). The primary types of AMGs carried by temperate and virulent viruses differed, while a variety of genes involved in carbon metabolism highlighted the potential importance of viruses in the soil carbon cycle of Mount Everest. Moreover, the abundance of AMGs encoding carbohydrate-active enzymes had a significant and positive correlation with soil C/N ratio. Overall, these findings provide a context for further exploration on the regulatory mechanisms of viruses in carbon cycle via interactions with microorganisms.

BackgroundThe role and underlying mechanism of liver macrophages and their derived miR-155-5p in hepatic lymphangiogenesis in liver fibrosis remain unclear. Here, we investigated the mechanism by which macrophages and miR-155-5p were involved in lymphangiogenesis during liver fibrosis and cirrhosis.MethodsIn vivo, hepatic lymphatic vessel expansion was evaluated; the liver macrophage subsets, proportion of peripherally-derived macrophages and expressions of CCL25, MCP-1, VAP-1 and MAdCAM-1 were documented; and miR-155-5p in the peripheral blood and liver was detected. In vitro, macrophages with miR-155-5p overexpression and inhibition were used to clarify the effect of miR-155-5p on regulation of macrophage polarization and the possible signalling pathway.ResultsHepatic lymphangiogenesis was observed in mice with liver fibrosis and cirrhosis challenged with carbon tetrachloride (CCl4). In the liver, the number of M1 macrophages was associated with lymphangiogenesis and the degree of fibrosis. The liver recruitment of peripherally-derived macrophages occurred during liver fibrosis. The levels of miR-155-5p in the liver and peripheral blood gradually increased with aggravation of liver fibrosis. In vitro, SOCS1, a target of miR-155-5p, regulated macrophage polarization into the M1 phenotype through the JAK1/STAT1 pathway.ConclusionMiR-155-5p-SOCS1/JAK1/STAT1 pathway participates in hepatic lymphangiogenesis in mice with liver fibrosis and cirrhosis induced by CCl4 by regulating the polarization of macrophages into the M1 phenotype.