Metabolomic and gut-microbial responses of earthworms exposed to microcystins and nano zero-valent iron in soil.

The earthworm-based vermiremediation facilitated with benign chemicals such as nano zero-valent iron (nZVI) is a promising approach for the remediation of a variety of soil contaminants including cyanotoxins. As the most toxic cyanotoxin, microcystin-LR (MC-LR) enter soil via runoff, irrigated surface water and sewage, and the application of cyanobacterial biofertilizers as part of the sustainable agricultural practice. Earthworms in such remediation systems must sustain the potential risk from both nZVI and MC-LR. In the present study, earthworms (Eisenia fetida) were exposed up to 14 days to MC-LR and nZVI (individually and in mixture), and the toxicity was investigated at both the organismal and metabolic levels, including growth, tissue damage, oxidative stress, metabolic response and gut microbiota. Results showed that co-exposure of MC-LR and nZVI is less potent to earthworms than that of separate exposure. Histological observations in the co-exposure group revealed only minor epidermal brokenness, and KEGG enrichment analysis showed that co-exposure induced earthworms to regulate glutathione biosynthesis for detoxification and reduced adverse effects from MC-LR. The combined use of nZVI promoted the growth and reproduction of soil and earthworm gut bacteria (e.g., Sphingobacterium and Acinetobacter) responsible for the degradation of MC-LR, which might explain the observed antagonism between nZVI and MC-LR in earthworm microcosm. Our study suggests the beneficial use of nZVI to detoxify pollutants in earthworm-based vermiremediation systems where freshwater containing cyanobacterial blooms is frequently used to irrigate soil and supply water for the growth and metabolism of earthworms.

Omics analysis of key pathway in flavour formation and B vitamins synthesis during chickpea milk fermentation by Lactiplantibacillus plantarum.

Chickpea milk is a nutrient-rich plant-based milk, but its pronounced beany flavour limits consumer acceptance. To address this issue, chickpea milk was fermented using two strains of Lactiplantibacillus plantarum, FMBL L23251 and L23252, which efficiently utilize chickpea milk. L. plantarum FMBL L23251 demonstrated superior fermentation characteristics. Fermentation with L. plantarum FMBL L23251 resulted in a 1.90-fold increase in vitamin B3 (271.66 ng/ml to 516.15 ng/ml) and a 1.58-fold increase in vitamin B6 (91.24 ng/ml to 144.16 ng/ml) through the L-aspartic acid pathway and the 1-deoxy-D-xylulose-5-phosphate (DXP)-independent pathway, respectively. Furthermore, L. plantarum FMBL L23251 effectively removed beany flavours due to its enhanced pathway for pyruvate metabolism. The main aldehydes are converted into corresponding alcohols or acids, resulting in 87.74 % and 96.99 % reductions in hexanal and 2-pentyl-furan, respectively. In summary, the fermentation of L. plantarum FMBL L23251 generated fermented chickpea milk that is rich in B vitamins and provides a better flavour.

Elevated levels of butyric acid in the jejunum of an animal model of broiler chickens: from early onset of Clostridium perfringens infection to clinical disease of necrotic enteritis.

BACKGROUND: Necrotic enteritis (NE) is an economically important disease of broiler chickens caused by Clostridium perfringens (CP). The pathogenesis, or disease process, of NE is still not clear. This study aimed to identify the alterations of metabolites and metabolic pathways associated with subclinical or clinical NE in CP infected birds and to investigate the possible variations in the metabolic profile of birds infected with different isolates of CP. METHODOLOGY: Using a well-established NE model, the protein content of feed was changed abruptly before exposing birds to CP isolates with different toxin genes combinations (cpa, cpb2, netB, tpeL; cpa, cpb2, netB; or cpa, cpb2). Metabolomics analysis of jejunal contents was performed by a targeted, fully quantitative LC-MS/MS based assay. RESULTS: This study detected statistically significant differential expression of 34 metabolites including organic acids, amino acids, fatty acids, and biogenic amines, including elevation of butyric acid at onset of NE in broiler chickens. Subsequent analysis of broilers infected with CP isolates with different toxin gene combinations confirmed an elevation of butyric acid consistently among 21 differentially expressed metabolites including organic acids, amino acids, and biogenic amines, underscoring its potential role during the development of NE. Furthermore, protein-metabolite network analysis revealed significant alterations in butyric acid and arginine-proline metabolisms. CONCLUSION: This study indicates a significant metabolic difference between CP-infected and non-infected broiler chickens. Among all the metabolites, butyric acid increased significantly in CP-infected birds compared to non-infected healthy broilers. Logistic regression analysis revealed a positive association between butyric acid (coefficient: 1.23, P < 0.01) and CP infection, while showing a negative association with amino acid metabolism. These findings suggest that butyric acid could be a crucial metabolite linked to the occurrence of NE in broiler chickens and may serve as an early indicator of the disease at the farm level. Further metabolomic experiments using different NE animal models and field studies are needed to determine the specificity and to validate metabolites associated with NE, regardless of predisposing factors.

Trade-off strategies for driving the toxicity and metabolic remodeling of copper oxide nanoparticles and copper ions in Ipomoea aquatica.

The ecological safety of copper oxide nanoparticles (CuO NPs) in the environment determines the advancement of nano-agriculture owing to breakthroughs in nanotechnology; however, the release of Cu2+ is an uncontrollable factor. Currently, the trade-off mechanisms of CuO NPs and Cu2+ dominating the potential hazards of plant-nano systems remain unclear. This study proposed the trade-off strategy for reconstructing physiological responses and metabolic profiles and deciphered the differential regulation of dominant CuO NPs and Cu2+ in plants. The results showed that 100 and 500 mg/kg CuO NPs promoted root fresh weight but reduced shoot fresh weight, while 1000 mg/kg Cu2+ demonstrated the strongest inhibition on both roots and shoots. The net photosynthetic perturbation in photosynthetic disorders is accompanied by superoxide anion and hydrogen peroxide accumulation, which are severe under 1000 mg/kg CuO NPs and Cu2+ stress. Metabolomics revealed that CuO NPs significantly altered coumaric acid and derivatives, for example, down-regulating coumaroyl hexoside (isomers of 690 and 691) by 40.79 %. Additionally, Cu2+ treatment severely interfered with the dominant metabolic response, activating plant hormone signal transduction and α-linolenic acid metabolism. The trade-off strategies of galactose metabolism, amino sugar and nucleotide sugar metabolism, pantothenate and coenzyme A (CoA) biosynthesis, and ß-alanine metabolism as differential metabolism were confirmed by comparing the CuO NPs and Cu2+ exposure. Protein secondary structure analysis revealed specific regulation of protein conformation upon exposure to CuO NPs and Cu2+. These findings provide new insights into differential metabolism and environmental effects in plant-nano systems.

Coal-straw co-digestion-induced biogenic methane production: perspectives on microbial communities and associated metabolic pathways.

This study assessed the impacts of wheat straw as a cosubstrate on coal biocoverion into methane and the associated mechanism within methane metabolic pathways. Co-digestion of coal with varying wheat straw concentrations resulted in a remarkable (1246.05%) increase in methane yield compared to that of the control (CK). Moreover, microbial analysis revealed a uniform distribution of Methanosarcinaceae (51.14%) and Methanobacteriaceae (39.90%) in the co-digestion of coal and wheat straw (CWS1) at a ratio of 3:1 (w/w) compared to other treatments such as coal and wheat straw (CWS2) at a ratio of 3:0.5. In addition, Hungatieclostridiaceae and Rhodobacteriaceae were abundant in both co-digesters, whereas the bacterial communities in the CK group were significantly different and more abundant than those in the Peptostreptococcaceae and Enterobacteriaceae groups. The key enzymes related to methanogenic metabolic pathways, including EC: 1.2.99.5 and EC: 2.1.1.86 (facilitating the conversion of CO2 into methane), and EC:1.12.98.1 exhibited significant abundance within CWS1. Aromatic compounds such as 4-(2-chloroanilino)-4-oxobutanoic acid and phthalic acid were substantially more abundant in CWS1 and CWS2 than in CK, indicating the increased bioavailability of coal to microbial activities. This novel approach demonstrates that wheat straw co-digestion with coal during anaerobic digestion modulates microbial communities and their metabolic pathways to enhance methane production from complex substrates such as coal.

Vitamin B6 Pathway Maintains Glioblastoma Cell Survival in 3D Spheroid Cultures.

Glioblastoma (GBM) is a deadly brain cancer. The prognosis of GBM patients has marginally improved over the last three decades. The response of GBMs to initial treatment is inevitably followed by relapse. Thus, there is an urgent need to identify and develop new therapeutics to target this cancer and improve both patient outcomes and long-term survival. Metabolic reprogramming is considered one of the hallmarks of cancers. However, cell-based studies fail to accurately recapitulate the in vivo tumour microenvironment that influences metabolic signalling and rewiring. Against this backdrop, we conducted global, untargeted metabolomics analysis of the G7 and R24 GBM 2D monolayers and 3D spheroid cultures under identical cell culture conditions. Our studies revealed that the levels of multiple metabolites associated with the vitamin B6 pathway were significantly altered in 3D spheroids compared to the 2D monolayer cultures. Importantly, we show that pharmacological intervention with hydralazine, a small molecule that reduces vitamin B6 levels, resulted in the cell death of 3D GBM spheroid cultures. Thus, our study shows that inhibition of the vitamin B6 pathway is a novel therapeutic strategy for the development of targeted therapies in GBMs.

Continuous self-circulating up-flow granular sludge fluidized bed process treating low-strength real municipal wastewater at high hydraulic loads.

Conditions conducive to aerobic granular sludge (AGS) growth and maintenance are very difficult to realize in continuous-flow biological treatment processes. This study conducted a continuous-flow self-circulating up-flow granular sludge fluidized bed (Zier process) treating real urban wastewater approximately one year. The substantial self-circulating multiple times (RSCMT, 8-15 times) and up-flow velocity (8-15 m/h) generated by aeration, the only power equipment in Zier process, facilitated pollutant removal, particle granulation and stabilization. With hydraulic retention time of 5 h, RSCMT of 9.3-14.4 times and chemical oxygen demand (COD)/total nitrogen (TN) ratio of 5.9 ± 1.0, the effluent COD, ammonia nitrogen and TN were 28.6 ± 7.7, 1.1 ± 1.2, and 13.3 ± 1.7 mg/L, respectively. The median particle size was 150-250 µm and effluent suspended solids concentration was 33.4 ± 14.5 mg/L. It is unnecessary to set up sludge reflux which simplifies the subsequent mud-water separation facilities. The Zier process provides a new process structure for implementation of continuous-flow AGS process.

Effects of manure and nitrogen fertilization on soil microbial carbon fixation genes and associated communities in the Loess Plateau of China.

The effects of long-term fertilization on soil carbon (C) cycling have been a key focus of agricultural sustainable development research. However, the influences of different fertilization treatments on soil microbial C fixation profiles are still unclear. Metagenomics technology and multivariate analysis were employed to inquire changes in soil properties, soil microbial C fixation genes and associated bacterial communities, and the influence of dominant soil properties on C fixation genes. The contents of soil C and nitrogen fractions were signicficantly higher in manure or combined with nitrogen fertilization (NM) than other treatments. The composition of soil microbial C fixation genes and associated bacterial communities varied among different fertilization treatments. Compared with other treatments, the total abundance of microbial C fixation genes and the abundance of Proteobacteria were significantly higher in NM than in other treatments, as well as the abundances of C fixation genes involved in dicarboxylate/4-hydroxybutyrate cycle and reductive citrate cycle. Key functional genes and main bacterial communities presented in the middle of the co-occurrence network. Soil organic carbon, total nitrogen, and microbial biomass nitrogen were the dominant soil properties influencing microbial C fixation genes and associated bacterial communitis. Fertilization increased the abundance of C fixation genes by affecting the changes in bacterial communities abundance mediated by soil properties. Overall, elucidating the responses of soil microbial C fixation genes and associated communities to different fertilization will enhance our understanding of the processes of soil C fixation in farmland.

Identification of serum biomarkers for chronic kidney disease using serum metabolomics.

This study aimed to identify biomarkers for chronic kidney disease (CKD) by studying serum metabolomics. Serum samples were collected from 194 non-dialysis CKD patients and 317 healthy controls (HC). Using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS), untargeted metabolomics analysis was conducted. A random forest model was developed and validated in separate sets of HC and CKD patients. The serum metabolomic profiles of patients with chronic kidney disease (CKD) exhibited significant differences compared to healthy controls (HC). A total of 314 metabolites were identified as significantly different, with 179 being upregulated and 135 being downregulated in CKD patients. KEGG enrichment analysis revealed several key pathways, including arginine biosynthesis, phenylalanine metabolism, linoleic acid metabolism, and purine metabolism. The diagnostic efficacy of the classifier was high, with an area under the curve of 1 in the training and validation sets and 0.9435 in the cross-validation set. This study provides comprehensive insights into serum metabolism in non-dialysis CKD patients, highlighting the potential involvement of abnormal biological metabolism in CKD pathogenesis. Exploring metabolites may offer new possibilities for the management of CKD.

Intestinal microflora and metabolites affect the progression of acute pancreatitis (AP).

Specific intestinal metabolites are closely associated with the classification, severity, and necrosis of acute pancreatitis (AP) and provide novel insights for in-depth clinical investigations. In this study, the gut microbiota and metabolites of 49 AP patients at different treatment stages and severities were analysed via 16S rDNA sequencing and untargeted metabolomics to investigate the trends in gut microbiota composition and metabolome profiles observed in patients with severe AP. These findings revealed an imbalance in intestinal flora homeostasis among AP patients characterized by a decrease in probiotics and an increase in opportunistic pathogens, which leads to damage to the intestinal mucosal barrier through reduced short-chain fatty acid (SCFA) secretion and disruption of the intestinal epithelium. This dysbiosis influences energy metabolism, anti-inflammatory responses, and immune regulation, and these results highlight significant differences in energy metabolism pathways. These findings suggest that the differential composition of intestinal flora, along with alterations in intestinal metabolites and metabolic pathways, contribute to the compromised integrity of the intestinal mucosal barrier and disturbances in energy metabolism in patients with severe AP.

Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.

Metabolite profiling is a powerful approach for the clinical diagnosis of complex diseases, ranging from cardiometabolic diseases, cancer, and cognitive disorders to respiratory pathologies and conditions that involve dysregulated metabolism. Because of the importance of systems-level interpretation, many methods have been developed to identify biologically significant pathways using metabolomics data. In this review, we first describe a complete metabolomics workflow (sample preparation, data acquisition, pre-processing, downstream analysis, etc.). We then comprehensively review 24 approaches capable of performing functional analysis, including those that combine metabolomics data with other types of data to investigate the disease-relevant changes at multiple omics layers. We discuss their availability, implementation, capability for pre-processing and quality control, supported omics types, embedded databases, pathway analysis methodologies, and integration techniques. We also provide a rating and evaluation of each software, focusing on their key technique, software accessibility, documentation, and user-friendliness. Following our guideline, life scientists can easily choose a suitable method depending on method rating, available data, input format, and method category. More importantly, we highlight outstanding challenges and potential solutions that need to be addressed by future research. To further assist users in executing the reviewed methods, we provide wrappers of the software packages at https://github.com/tinnlab/metabolite-pathway-review-docker.

Comparative study of polysaccharide metabolites in purple, orange, and white Ipomoea batatas tubers.

We employed LC-MS/MS to investigate the metabolic profiles of polysaccharide compounds in white, orange, and purple sweet potato flesh. Comparisons between Orange vs White, Purple vs Orange, and Purple vs White identified 69 polysaccharide metabolites, including 23, 36, and 44 differential metabolites, respectively, with distinct differentiation. Among the three sample groups, 14 polysaccharide compounds and 2 anthocyanins exhibited significant differences. Our further analysis indicated that anthocyanins occupy a central position in the related network diagram and are interconnected with polysaccharides. In metabolic pathways, sucrose and the anthocyanin precursor UDP-glucose were upregulated in purple sweet potatoes, along with elevated levels of pelargonidin 3-O-ß-D-sambubioside and delphinidin 3,5-diglucoside. Conversely, sucrose was downregulated in purple sweet potatoes while increasing in white and orange varieties. Therefore, we hypothesize that the competition between sugars and anthocyanins for shared biosynthesis precursors is attributed to differential polysaccharide metabolites among sweet potato tubers of three colors.

Targeted metabolomic profiling of acute ST-segment elevation myocardial infarction.

Myocardial infarction is a major cause of morbidity and mortality worldwide. Metabolomic investigations may be useful for understanding the pathogenesis of ST-segment elevation myocardial infarction (STEMI). STEMI patients were comprehensively examined via targeted metabolomic profiling, machine learning and weighted correlation network analysis. A total of 195 subjects, including 68 STEMI patients, 84 patients with stable angina pectoris (SAP) and 43 non-CVD patients, were enrolled in the study. Metabolomic profiling involving the quantitative analysis of 87 endogenous metabolites in plasma was conducted. This study is the first to perform targeted metabolomic profiling in patients with STEMI. We identified 36 significantly altered metabolites in STEMI patients. Increased levels of four amino acids, eight acylcarnitines, six metabolites of the NO-urea cycle and neurotransmitters, and three intermediates of tryptophan metabolism were detected. The following metabolites exhibited decreased levels: six amino acids, three acylcarnitines, three components of the NO-urea cycle and neurotransmitters, and three intermediates of tryptophan metabolism. We found that the significant changes in tryptophan metabolism observed in STEMI patients-the increase in anthranilic acid and tryptophol and decrease in xanthurenic acid and 3-OH-kynurenine-may play important roles in STEMI pathogenesis. On the basis of the differences in the constructed weighted correlation networks, new significant metabolite ratios were identified. Among the 22 significantly altered metabolite ratios identified, 13 were between STEMI patients and non-CVD patients, and 17 were between STEMI patients and SAP patients. Seven of these ratios were common to both comparisons (STEMI patients vs. non-CVD patients and STEMI patients vs. SAP patients). Additionally, two ratios were consistently observed among the STEMI, SAP and non-CVD groups (anthranilic acid: aspartic acid and GSG (glutamine: serine + glycine)). These findings provide new insight into the diagnosis and pathogenesis of STEMI.

Deciphering the impact of stickwater hydrolysate on growth performance, immune response, and IGF-1/PI3K/AKT/mTOR signaling pathway in Siberian sturgeon (Acipenser baerii) fingerlings.

A feeding trial lasting 56 days was carried out to assess how the inclusion of stickwater hydrolysate (SWH) in the diet of Siberian sturgeon (Acipenser baerii) fingerlings affected their growth performance, immunity, digestive enzyme activity, and gene expression linked to the IGF-1/PI3K/AKT/mTOR signaling pathway. Siberian sturgeon fingerlings were acclimatized and fed isonitrogenous, isoenergetic diets with varying SWH concentrations (0%, 0.5%, 1.5%, and 2.5%). Growth parameters, serum proteins, immunological and digestive enzyme activities, and gene expression levels were assessed post-trial. Results demonstrated that 0.5%, and 1.5% SWH treatments significantly improved weight gain, specific growth rate, feed conversion ratio, and protein efficiency ratio. Notably, these diets also elevated serum protein and plasma globulin levels, reduced albumin-to-globulin ratios, and enhanced lysozyme, myeloperoxidase (MPO) activities, and immunoglobulin (Ig) M levels, indicating an immunostimulatory effect. Digestive enzyme activities were markedly increased in the SWH groups, particularly at 1.5%. Gene expression analyses revealed upregulation of mtorc1, s6K, akt, pi3k, and igf1, with concurrent downregulation of 4e-bp1 in the muscle of fish, signifying activation of the IGF-1/PI3K/AKT/mTOR pathway, which is central to protein synthesis and muscle growth. In conclusion, SWH at appropriate levels significantly enhances growth, digestive efficiency, and immune function in Siberian sturgeon fingerlings, while also activating key metabolic pathways.

Microbial degradation of contaminants of emerging concern: metabolic, genetic and omics insights for enhanced bioremediation.

The perpetual release of natural/synthetic pollutants into the environment poses major risks to ecological balance and human health. Amongst these, contaminants of emerging concern (CECs) are characterized by their recent introduction/detection in various niches, thereby causing significant hazards and necessitating their removal. Pharmaceuticals, plasticizers, cyanotoxins and emerging pesticides are major groups of CECs that are highly toxic and found to occur in various compartments of the biosphere. The sources of these compounds can be multipartite including industrial discharge, improper disposal, excretion of unmetabolized residues, eutrophication etc., while their fate and persistence are determined by factors such as physico-chemical properties, environmental conditions, biodegradability and hydrological factors. The resultant exposure of these compounds to microbiota has imposed a selection pressure and resulted in evolution of metabolic pathways for their biotransformation and/or utilization as sole source of carbon and energy. Such microbial degradation phenotype can be exploited to clean-up CECs from the environment, offering a cost-effective and eco-friendly alternative to abiotic methods of removal, thereby mitigating their toxicity. However, efficient bioprocess development for bioremediation strategies requires extensive understanding of individual components such as pathway gene clusters, proteins/enzymes, metabolites and associated regulatory mechanisms. "Omics" and "Meta-omics" techniques aid in providing crucial insights into the complex interactions and functions of these components as well as microbial community, enabling more effective and targeted bioremediation. Aside from natural isolates, metabolic engineering approaches employ the application of genetic engineering to enhance metabolic diversity and degradation rates. The integration of omics data will further aid in developing systemic-level bioremediation and metabolic engineering strategies, thereby optimising the clean-up process. This review describes bacterial catabolic pathways, genetics, and application of omics and metabolic engineering for bioremediation of four major groups of CECs: pharmaceuticals, plasticizers, cyanotoxins, and emerging pesticides.

Investigation of bioactive components and metabolic pathways of Zhen-wu-tang in rat plasma and renal tissue by UPLC-Q-TOF/MS.

INTRODUCTION: Zhen-wu-tang (ZWT) is a traditional Chinese medicine (TCM) formula for the treatment of several kidney diseases. However, due to the complexity of the TCM formula, there is a lack of accurate knowledge of the chemical constituents of ZWT and its bioactive components, as well as in vivo metabolic pathway studies. OBJECTIVES: The chemical composition of ZWT and its bioactive components along with the metabolic pathways were investigated by a combination of chemical profiling and serum pharmacochemistry. METHODS: High-resolution ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry was used to identify the chemical components of ZWT and its bioactive components and metabolites in vivo. RESULTS: As a result, a total of 110 chemical components were identified from ZWT solution, mainly amino acids, alkaloids, gingerols, monoterpene glycosides and terpenoids, and so on. In addition, 24 prototype components and 36 metabolites were detected in rat plasma. Meanwhile, 8 prototype components were detected in rat kidney tissue but no metabolites. Interestingly, 4 of the 28 bioactive components were detected in both plasma and renal tissue, which were atractylenolide III, trimethoxyaconitane, methyl gallate, and paeoniflorin. The metabolic pathways mainly involved Phases I and/or II metabolic reactions such as hydrolysis, oxidation, reduction and hydration, methylation/demethylation, sulphation, glucuronidation, acetylation, and glutathione conjugation. CONCLUSION: Overall, the present study has comprehensively elucidated the chemical composition of ZWT and its potential bioactive components and metabolites, which provides a basis for the basic study of its pharmacodynamic substances and a reference for the study of the bioactive components of TCM formulae.

Organic manure rather than chemical fertilization improved dark CO2 fixation by regulating associated microbial functional traits in upland red soils.

Dark microbial fixation of CO2 is an indispensable process for soil carbon sequestration. However, the whole genetic information involved in dark CO2 fixation and its influence on dark CO2 fixation rates under diversified fertilization regimes were largely unclear. Here, revealed by 13C-CO2 labeling, dark CO2 fixation rates in upland red soils ranged from 0.029 mg kg-1 d-1 to 0.092 mg kg-1 d-1, and it was 75.49 % higher (P < 0.05) in organic manure (OM) soil but 44.2 % decline (P < 0.05) in chemical nitrogen fertilizer (N) soil compared to unfertilized (CK) soil. In addition, the normalized abundance and Chao1 index of dark CO2 fixation genes (KO level) were significantly different between OM and N soils, showing the highest and lowest, respectively. And they were positively (P < 0.05) correlated with dark CO2 fixation rate. Besides, among the identified CO2 fixation pathways in this study, the DC/4-HB cycle (M00374) was enriched in OM soil, yet the 3-HP cycle (M00376) was enriched in N soil, and their relative abundances were positively and negatively correlated (P < 0.05) with dark CO2 fixation rate, respectively. The PLS-SEM analysis revealed that dark CO2 fixation-related functional traits (i.e. normalized abundance, Chao1 index and gene composition) were directly and positively associated with dark CO2 fixation rate, and organic manure could exert a positive effect on soil dark CO2 fixation rate through enhancing soil properties (e.g., pH and soil organic carbon) and further altering associated microbial functional traits. These results have implications for explaining and predicting the soil CO2 fixation process from the perspective of microbial functional potential.

[Metabolite identification of isochlorogenic acid A in rats by HPLC-Q-Exactive Orbitrap-MS].

Isochlorogenic acid A(ICA) is the main active component of several TCMs, such as Artemisiae Scopariae Herba. This study aims to identify the metabolites of orally administered ICA in rat plasma, urine, and feces, and to speculate on its potential metabolic pathways. Rats were administered ICA orally, and samples of plasma, urine, and feces were collected at different time points. High-performance liquid chromatography-quadrupole Exactive Orbitrap-mass spectrometry(HPLC-Q-Exactive Orbitrap-MS) was used in combination with reference standards, retention time comparison, fragmentation pattern analysis, and literature data to identify the metabolites in the biological samples. A total of 39 metabolites(M1-M39) of ICA were preliminarily identified from rat samples, including 31 from plasma(M1-M10, M12-M24, M26-M28, M30, M34-M35, M38-M39), 34 from urine(M1-M11, M13-M15, M19-M25, M27-M39), and 11 from feces(M2-M3, M6, M15, M21-M23, M32, M34, M36-M37). The main metabolic pathways included hydrolysis, glucuronidation, methylation, and sulfonation reactions. This study revealed the metabolic profile of ICA in rat plasma, urine, and feces, providing references for the in-depth elucidation of its pharmacologically active components.

Unveiling microbial dynamics in lung adenocarcinoma and adjacent nontumor tissues: insights from nicotine exposure and diverse clinical stages via nanopore sequencing technology.

Background: Lung is the largest mucosal area of the human body and directly connected to the external environment, facing microbial exposure and environmental stimuli. Therefore, studying the internal microorganisms of the lung is crucial for a deeper understanding of the relationship between microorganisms and the occurrence and progression of lung cancer. Methods: Tumor and adjacent nontumor tissues were collected from 38 lung adenocarcinoma patients and used nanopore sequencing technology to sequence the 16s full-length sequence of bacteria, and combining bioinformatics methods to identify and quantitatively analyze microorganisms in tissues, as well as to enrich the metabolic pathways of microorganisms. Results: the microbial composition in lung adenocarcinoma tissues is highly similar to that in adjacent tissues, but the alpha diversity is significantly lower than that in adjacent tissues. The difference analysis results show that the bacterial communities of Streptococcaceae, Lactobacillaceae, and Neisseriales were significantly enriched in cancer tissues. The results of metabolic pathway analysis indicate that pathways related to cellular communication, transcription, and protein synthesis were significantly enriched in cancer tissue. In addition, clinical staging analysis of nicotine exposure and lung cancer found that Haemophilus, paralinfluenzae, Streptococcus gordonii were significantly enriched in the nicotine exposure group, while the microbiota of Cardiobactereae and Cardiobacterales were significantly enriched in stage II tumors. The microbiota significantly enriched in IA-II stages were Neisseriaeae, Enterobacteriales, and Cardiobacterales, respectively. Conclusion: Nanopore sequencing technology was performed on the full length 16s sequence, which preliminarily depicted the microbial changes and enrichment of microbial metabolic pathways in tumor and adjacent nontumor tissues. The relationship between nicotine exposure, tumor progression, and microorganisms was explored, providing a theoretical basis for the treatment of lung cancer through microbial targets.

Development of oriented microbial consortium-based compound enzyme strengthens food waste hydrolysis and antibiotic resistance genes removal: Deciphering of performance, metabolic pathways and microbial communities.

Enzymatic hydrolysis has been considered as an eco-friendly pretreatment method for enhancing bioconversion process of food waste (FW). However, existing commercial enzymes and microbial monomer-based compound enzymes (MME) have the issues of uneven distribution of enzymatic activity and low matching degree with the components of FW, leading to low efficiency with enzymatic hydrolysis and removal of antibiotic resistance genes (ARGs). This study used FW as the substrate, under the co-culture system, produced a microbial consortium-based compound enzymes (MCE) with oriented and well-matching degree for FW hydrolysis and ARGs removal, of which the performance, metabolic pathways and microbial communities were also investigated in depth. Results showed that the best performance for ARGs was achieved by the MCE prepared by mixing 1:5 of Aspergillus oryzae and Aspergillus niger after 12 days fermentation. The highest soluble chemical oxygen demand (SCOD) concentration and ARGs removal could respectively reach 83.90 ± 1.67 g/L and 45.95% after MCE pretreatment. The analysis of metabolic pathways revealed that 1:5 MCE pretreatment strengthened the catalytic activity of carbohydrate-active enzymes, increased the abundances of genes involved in cellulose and starch degradation, polysaccharide synthesis, ATP binding cassette (ABC) transporters and global regulation, while decreased the abundances of genes involved in mating pair formation system, two-component regulatory systems and quorum sensing, thereby enhanced FW hydrolysis and restrained ARGs dissemination. Microbial community analysis further indicated that the 1:5 MCE pretreatment promoted growth, metabolism and richness of functional microbes, while inhibited the host microbes of ARGs. It is expected that this study can provide useful insights into understanding the fate of ARGs in food waste during MCE pretreatment process.