Biomineralized ZIF-8 Encapsulating SOD from Hydrogenobacter Thermophilus: Maintaining Activity in the Intestine and Alleviating Intestinal Oxidative Stress.

Oxidative stress is a major factor leading to inflammation and disease occurrence, and superoxide dismutase (SOD) is a crucial antioxidative metalloenzyme capable of alleviating oxidative stress. In this study, a novel thermostable SOD gene is obtained from the Hydrogenobacter thermophilus strain (HtSOD), transformed and efficiently expressed in Escherichia coli with an activity of 3438 U mg-1, exhibiting excellent thermal stability suitable for scalable production. However, the activity of HtSOD is reduced to less than 10% under the acidic environment. To address the acid resistance and gastrointestinal stability issues, a biomimetic mineralization approach is employed to encapsulate HtSOD within the ZIF-8 (HtSOD@ZIF-8). Gastrointestinal simulation results show that HtSOD@ZIF-8 maintained 70% activity in simulated gastric fluid for 2 h, subsequently recovering to 97% activity in simulated intestinal fluid. Cell and in vivo experiments indicated that HtSOD@ZIF-8 exhibited no cytotoxicity and do not impair growth performance. Furthermore, HtSOD@ZIF-8 increased the relative abundance of beneficial microbiota such as Dubosiella and Alistipes, mitigated oxonic stress and intestinal injury by reducing mitochondrial and total reactive oxygen species (ROS) levels in diquat-induced. Together, HtSOD@ZIF-8 maintains and elucidates activity in the intestine and biocompatibility, providing insights into alleviating oxidative stress in hosts and paving the way for scalable production.

The simultaneous addition of chitosan and peat enhanced the removals of antibiotics resistance genes during biogas residues composting.

Direct reuse of biogas residue (BR) has the potential to contribute to the dissemination of antibiotic resistance genes (ARGs). Although high-temperature composting has been demonstrated as an effective method for the harmless treatment of organic waste, there is few researches on the fate of ARGs in high-temperature composting of BR. This research examined the impact of adding 5% chitosan and 15% peat on physicochemical characteristics, microbial communities, and removal of ARGs during BR-straw composting in 12 Biolan 220L composters for 48 days. Our results showed that the simultaneous addition of chitosan and peat extended the high-temperature period, and increased the highest temperature to 74 °C and germination index. These effects could be attributed to the presence of thermophilic cellulose-decomposing genera (Thermomyces and Thermobifida). Although the microbial communities differed compositionally among temperature stages, their dissimilarity drastically reduced at final stage, indicating that the impact of different treatments on microbial community composition decreases at the end of composting. Peat had a greater impact on aerobic genera capable of cellulose degradation at thermophilic stage than chitosan. Surprisingly, despite the total copy number of ARGs significantly decreased during composting, especially in the treatment with both chitosan and peat, intI1 gene abundance significantly increased 2 logs at thermophilic stage and maintained high level in the final compost, suggesting there is still a potential risk of transmission and proliferation of ARGs. Our work shed some lights on the development of waste resource utilization and emerging contaminants removal technology.

Synthesis of a novel carbon-based nano-emulsifier and its application in viscosity reduction of emulsified Jurassic oil in the Sichuan Basin.

A study was undertaken into the emulsification and viscosity reduction processes of crude oil originating from the Jurassic formation of the Sichuan Basin. Central to this investigation was the successful synthesis of a carbon-based nano emulsifier named GOPH, utilizing graphene oxide as substrate and hydrophilic alkyl glycidyl ether and polyoxyethylene ether as modifiers. The structural integrity of this nano-emulsifier was comprehensively characterized via Fourier transform infrared spectroscopy, scanning electron microscopy, and thermogravimetric analysis. Notably, GOPH nanofluids exhibited a remarkable merit in decreasing the oil/water interfacial tension from 31.96 mN m-1 to a low value of 9.76 mN m-1 with a critical concentration of 45 ppm. Moreover, interfacial film folding experiments revealed that GOPH nanoparticles "jammed" at the oil-water interface, forming a robust film. When Jurassic crude oil was the oil phase, and GOPH nanofluids were introduced into the water phase, the crude oil was successfully induced to form a low-viscosity oil-in-water (O/W) emulsion. Emulsion droplet size and viscosity measurements demonstrated that this emulsion possessed small size distributions with remarkable stability, achieving a viscosity reduction of up to 91.6% at a water content of 80%. The underlying mechanism for this phenomenon mainly lies in the interaction between the carbon-based nano-emulsifier and asphaltene, which form a composite unit, enabling the construction of a flexible interfacial film that significantly stabilizes the O/W emulsion.

Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.

BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties. RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect. CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.

Sinomenine Hydrochloride Regulates the Apoptosis of Endothelial Cells through PPAR-γ to Alleviate PAH.

Pulmonary arterial hypertension is a progressive heart and lung disease that is caused by irreversible pulmonary vascular remodeling. Sinomenine hydrochloride is an alkaloid that is extracted from sinomenium acutum, which has strong anti-inflammatory effects. In this study, male rats were injected with monocrotaline, and endothelial cells were exposed to hypoxia for 24 hours to induce pulmonary arterial hypertension. Apoptosis, inflammation, and oxidative stress pathways were observed the in lungs and cells. Sinomenine hydrochloride repressed the increased right ventricular systolic pressure and attenuated the right ventricular hypertrophy and pulmonary artery remodeling in model rats. It reversed the expression of BCL2 and BAX and prevented the apoptosis of endothelial cells. Additionally, it increased the contents of IKBα and NRF2. P65, P-P65, TNFα, IL1ß, and IL6 levels in the lungs decreased by it. Malondialdehyde contents decreased, and the superoxide dismutase and glutathione peroxidase activity and HO-1 level increased in the treatment group. In vivo, it promoted apoptosis of pulmonary artery endothelial cells. Moreover, by activating PPAR-γ, sinomenine hydrochloride attains the above effects. These data suggested that sinomenine hydrochloride could protect endothelial cells, restrain inflammation and oxidative stress, and enhance pulmonary vascular remodeling.

Zero-waste multistage utilization of dandelion root.

Introduction: In the fragrance and perfume industry, the controlled release of fragrances are crucial factors that contribute to consumer appeal and product quality enhancement. In this study, various aromatic active substances were extracted from dandelion root (DR), which was subsequently calcined to produce high-performance porous biochar material. Methods: The dandelion root biochar (DRB) material was identified as promising adsorbents for the controlled release of fragrances. Furfuryl alcohol was chosen as the model fragrance for inclusion and controlled release studies. Results and discussion: The DRB exhibited a substantial specific surface area of 991.89 m2/g, facilitating efficient storage and controlled release capabilities. Additionally, the DRB's high stability and porous nature facilitated rapid collection and efficient recyclability. This research significantly contributes to the development of a sustainable, zero-waste multistage utilization strategy for dandelion roots, indicating a potential applications in the food flavoring industry and environmental conservations.

A universal oral microbiome-based signature for periodontitis.

We analyzed eight oral microbiota shotgun metagenomic sequencing cohorts from five countries and three continents, identifying 54 species biomarkers and 26 metabolic biomarkers consistently altered in health and disease states across three or more cohorts. Additionally, machine learning models based on taxonomic profiles achieved high accuracy in distinguishing periodontitis patients from controls (internal and external areas under the receiver operating characteristic curves of 0.86 and 0.85, respectively). These results support metagenome-based diagnosis of periodontitis and provide a foundation for further research and effective treatment strategies.

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.

Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.

Activity-based metaproteomics driven discovery and enzymological characterization of potential α-galactosidases in the mouse gut microbiome.

The gut microbiota offers an extensive resource of enzymes, but many remain uncharacterized. To distinguish the activities of similar annotated proteins and mine the potentially applicable ones in the microbiome, we applied an effective Activity-Based Metaproteomics (ABMP) strategy using a specific activity-based probe (ABP) to screen the entire gut microbiome for directly discovering active enzymes and their potential applications, not for exploring host-microbiome interactions. By using an activity-based cyclophellitol aziridine probe specific to α-galactosidases (AGAL), we successfully identified and characterized several gut microbiota enzymes possessing AGAL activities. Cryo-electron microscopy analysis of a newly characterized enzyme (AGLA5) revealed the covalent binding conformations between the AGAL5 active site and the cyclophellitol aziridine ABP, which could provide insights into the enzyme's catalytic mechanism. The four newly characterized AGALs have diverse potential activities, including raffinose family oligosaccharides (RFOs) hydrolysis and enzymatic blood group transformation. Collectively, we present a ABMP platform that facilitates gut microbiota AGALs discovery, biochemical activity annotations and potential industrial or biopharmaceutical applications.

Manganese-catalyzed oxidation of furfuryl alcohols and furfurals to efficient synthesis of furoic acids.

Herein, the direct oxidation of furfuryl alcohols and furfurals to the corresponding furoic acids is performed highly efficiently with potassium hydroxide as the base in the presence of a catalytic amount of PNP pincer manganese catalyst in dioxane. The manganese catalytic system can not only achieve the dehydrogenation conversion of furfuryl alcohols to prepare furoic acids but can also achieve the synthesis of furoic acids from furfurals under more moderate conditions and with less reaction time. In addition, the bifunctional furfuryl alcohols or furfurals can also be efficiently converted into dicarboxylic acid products under optimal reaction conditions.

Intratumoral microbiome promotes liver metastasis and dampens adjuvant imatinib treatment in gastrointestinal stromal tumor.

Understanding the determinants of long-term liver metastasis (LM) outcomes in gastrointestinal stromal tumor (GIST) patients is crucial. We established the feature selection model of intratumoral microbiome at the surgery, achieving robust predictive accuracies of 0.953 and 0.897 AUCs in discovery (n = 74) and validation (n = 34) cohorts, respectively. Notably, despite the significant reduction in LM occurrence with adjuvant imatinib (AI) treatment, intratumoral microbiome exerted independently stronger effects on post-operative LM. Employing both 16S and full-length rRNA sequencing, we pinpoint intracellular Shewanella algae as a foremost LM risk factor in both AI- and non-AI-treated patients. Experimental validation confirmed S. algae's intratumoral presence in GIST, along with migration/invasion-promoting effects on GIST cells. Furthermore, S. algae promoted LM and impeded AI treatment in metastatic mouse models. Our findings advocate for incorporating intratumoral microbiome evaluation at surgery, and propose S. algae as a therapeutic target for LM suppression in GIST.

Simultaneous ST-elevation in lead augmented vector right (aVR) and III in non-ST-elevation acute coronary syndromes.

Background: The value of ST-elevation in lead augmented vector right (aVR) remains controversial in clinical practice. This study aimed to investigate the association of simultaneous ST-elevation in lead aVR and III with angiographic findings and clinical outcomes in patients with non-ST-elevation acute coronary syndromes (NSTEACS). Methods: In this observational study, patients who had been diagnosed with NSTEACS and presented with ST-elevation in lead aVR and without ST-elevation in any other two contiguous leads were enrolled from January 2018 to June 2019. Demographic, baseline clinical, angiographic and interventional characteristics as well as clinical outcomes were collected and recorded on standardized case report forms. Results: A total of 157 patients meeting the criteria were finally enrolled in this study and classified into two groups according to the presence of ST-elevation in lead III. Patients in the two groups were similar in average age and previous history of hypertension, diabetes mellitus, hyperlipidemia, chronic kidney disease, stroke, and peripheral vascular diseases (all P>0.05). Patients with ST-elevation in lead III tended to present with myocardial hypertrophy in the echocardiography (P=0.02). The cases with ST-elevation in lead III showed higher high sensitivity troponin T (hs-TnT; P=0.08) and creatinine kinase MB isoenzyme (CK-MB; P<0.01) whereas those without ST-elevation in lead III showed higher N-terminal pro brain natriuretic peptide (NT-proBNP; P=0.02). Of note, patients with ST-elevation in lead III presented with more ST-depression in multiple leads [especially in lead I, augmented vector left (aVL), V3-V6] as well as higher degree of ST-depression (all P<0.05) and were more likely to develop multi-vessel and left main trunk (LM) lesions (P=0.04), with 20% of the cases having a LM lesion and 60% having triple vessel lesions. Patients with ST-elevation in lead III were at increased risk of 3-year major adverse cardiovascular events (MACEs), despite no significant statistical difference between the two groups (hazard ratio =1.29; P=0.26). Conclusions: The NSTEACS cases with simultaneous ST-elevation in lead III and aVR tended to present with more multiple leads with ST-depression, higher degree of ST-depression, and more LM or multi-vessel lesions, suggesting a broader range of severe myocardial ischemia. The concurrent presentation of ST-elevation in lead III and aVR may play a vital role in the diagnosis, risk-stratification, and prediction of poor prognosis during the management of NSTEACS patients.

VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes.

Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.

Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome.

Introduction: The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages. Methods: In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes. Results: The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways. Discussion: This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.

ScRNA-seq revealed the tumor microenvironment heterogeneity related to the occurrence and metastasis in upper urinary tract urothelial carcinoma.

Metastasis is the greatest clinical challenge for UTUCs, which may have distinct molecular and cellular characteristics from earlier cancers. Herein, we provide single-cell transcriptome profiles of UTUC para cancer normal tissue, primary tumor lesions, and lymphatic metastases to explore possible mechanisms associated with UTUC occurrence and metastasis. From 28,315 cells obtained from normal and tumor tissues of 3 high-grade UTUC patients, we revealed the origin of UTUC tumor cells and the homology between metastatic and primary tumor cells. Unlike the immunomicroenvironment suppression of other tumors, we found no immunosuppression in the tumor microenvironment of UTUC. Moreover, it is imperative to note that stromal cells are pivotal in the advancement of UTUC. This comprehensive single-cell exploration enhances our comprehension of the molecular and cellular dynamics of metastatic UTUCs and discloses promising diagnostic and therapeutic targets in cancer-microenvironment interactions.

MXene@c-MWCNT Adhesive Silica Nanofiber Membranes Enhancing Electromagnetic Interference Shielding and Thermal Insulation Performance in Extreme Environments.

A lightweight flexible thermally stable composite is fabricated by combining silica nanofiber membranes (SNM) with MXene@c-MWCNT hybrid film. The flexible SNM with outstanding thermal insulation are prepared from tetraethyl orthosilicate hydrolysis and condensation by electrospinning and high-temperature calcination; the MXene@c-MWCNTx:y films are prepared by vacuum filtration technology. In particular, the SNM and MXene@c-MWCNT6:4 as one unit layer (SMC1) are bonded together with 5 wt% polyvinyl alcohol (PVA) solution, which exhibits low thermal conductivity (0.066 W m-1 K-1) and good electromagnetic interference (EMI) shielding performance (average EMI SET, 37.8 dB). With the increase in functional unit layer, the overall thermal insulation performance of the whole composite film (SMCx) remains stable, and EMI shielding performance is greatly improved, especially for SMC3 with three unit layers, the average EMI SET is as high as 55.4 dB. In addition, the organic combination of rigid SNM and tough MXene@c-MWCNT6:4 makes SMCx exhibit good mechanical tensile strength. Importantly, SMCx exhibit stable EMI shielding and excellent thermal insulation even in extreme heat and cold environment. Therefore, this work provides a novel design idea and important reference value for EMI shielding and thermal insulation components used in extreme environmental protection equipment in the future.

UBE2N promotes cell viability and glycolysis by promoting Axin1 ubiquitination in prostate cancer cells.

BACKGROUND: Ubiquitin-conjugating enzyme E2 N (UBE2N) is recognized in the progression of some cancers; however, little research has been conducted to describe its role in prostate cancer. The purpose of this paper is to explore the function and mechanism of UBE2N in prostate cancer cells. METHODS: UBE2N expression was detected in Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) data, prostate cancer tissue microarrays, and prostate cancer cell lines, respectively. UBE2N knockdown or overexpression was used to analyze its role in cell viability and glycolysis of prostate cancer cells and tumor growth. XAV939 or Axin1 overexpression was co-treated with UBE2N overexpression to detect the involvement of the Wnt/ß-catenin signaling and Axin1 in the UBE2N function. UBE2N interacting with Axin1 was analyzed by co-immunoprecipitation assay. RESULTS: UBE2N was upregulated in prostate cancer and the UBE2N-high expression correlated with the poor prognosis of prostate cancer. UBE2N knockdown inhibited cell viability and glycolysis in prostate cancer cells and restricted tumor formation in tumor-bearing mice. Wnt/ß-catenin inhibition and Axin1 overexpression reversed the promoting viability and glycolysis function of UBE2N. UBE2N promoted Axin1 ubiquitination and decreased Axin1 protein level.

Quantifying the contributions of meteorology, emissions, and transport to ground-level ozone in the Pearl River Delta, China.

Ozone pollution presents a growing air quality threat in urban agglomerations in China. It remains challenge to distinguish the roles of emissions of precursors, chemical production and transportations in shaping the ground-level ozone trends, largely due to complicated interactions among these 3 major processes. This study elucidates the formation factors of ozone pollution and categorizes them into local emissions (anthropogenic and biogenic emissions), transport (precursor transport and direct transport from various regions), and meteorology. Particularly, we attribute meteorology, which affects biogenic emissions and chemical formation as well as transportation, to a perturbation term with fluctuating ranges. The Community Multiscale Air Quality (CMAQ) model was utilized to implement this framework, using the Pearl River Delta region as a case study, to simulate a severe ozone pollution episode in autumn 2019 that affected the entire country. Our findings demonstrate that the average impact of meteorological conditions changed consistently with the variation of ozone pollution levels, indicating that meteorological conditions can exert significant control over the degree of ozone pollution. As the maximum daily 8-hour average (MDA8) ozone concentrations increased from 20 % below to 30 % above the National Ambient Air Quality Standard II, contributions from emissions and precursor transport were enhanced. Concurrently, direct transport within Guangdong province rose from 13.8 % to 22.7 %, underscoring the importance of regional joint prevention and control measures under adverse weather conditions. Regarding biogenic emissions and precursor transport that cannot be directly controlled, we found that their contributions were generally greater in urban areas with high nitrogen oxides (NOx) levels, primarily due to the stronger atmospheric oxidation capacity facilitating ozone formation. Our results indicate that not only local anthropogenic emissions can be controlled in urban areas, but also the impacts of local biogenic emissions and precursor transport can be potentially regulated through reducing atmospheric oxidation capacity.

A simplified electrochemical model for lithium-ion batteries based on ensemble learning.

The mass transfer in lithium-ion batteries is a low-frequency dynamic that affects their voltage and performance. To find an effective way to describe the mass transfer in lithium-ion batteries, a simplified electrochemical lithium-ion battery model based on ensemble learning is proposed. The proposed model simplifies lithium-ion transfer in electrode particles with ensemble learning which ensembles discrete-time realization algorithm (DRA), fractional-order Padé approximation model (FOM), and three parameters (TPM) parabolic. The lithium-ion transfer in the electrolyte is simplified by the first-order inertial element (FIE). The results show that the proposed model achieves not only accurate lithium-ion concentration prediction in solid and electrolyte phase but also precise voltage prediction with low computational complexity.

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments.

BACKGROUND: Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS: We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS: The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.