Project description:Total RNA from rumen epithelial tissues of cows fed alfalfa hay (AL),Rice straw (RS) or Corn stover (CS)diet were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR.
Project description:Total RNA from duodenum, jejunum, liver and mammary gland tissues of cows fed alfalfa hay (AL),Rice straw (RS) or Corn stover (CS) diet were sequenced using Illumina HiSeq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR and SAS software.
Project description:<p _msttexthash='40138319' _msthash='17867'>Background Ammonia-oxidizing bacteria (AOB) play a crucial role in the microbiome of the global nitrogen cycle. Yet, their regulatory functions in the metabolic pathways involved in organic material stabilization (OMS) are not fully understood. We employed metabolomics, microbiomics, and molecular biology techniques to investigate for the first time the metabolic changes and regulatory mechanisms of OMS in a cow manure and straw biostabilization system inoculated with a novel exogenous consortium-AOB (C-AOB). </p><p _msttexthash='40138319' _msthash='17867'>Results C-AOB engaged in nitrogen metabolism during the thermophilic phase and participated in carbon metabolism during the stabilization phase of OMS. Glutamate was a key metabolite bridging the carbon and nitrogen metabolic networks, which increased during humic formation. C-AOB inoculation stimulated NO2- production, enhanced glycolysis and the tricarboxylic acid cycle, thereby facilitating glutamate conversion and contributing to humic formation. Additionally, NO2- served as a nitrogen source for microbial proliferation, thus enhancing microbial community activity and stability. The observed increase in the abundance of amoA, that encodes ammonia monooxygenase, indicates a close association between C-AOB inoculation and increased glutamate content. </p><p _msttexthash='40138319' _msthash='17867'>Conclusions The key metabolites, enzymes, and genes, particularly those associated with glutamate, played a role in regulating OMS by C-AOB. These findings underscore the regulatory roles of AOB in the metabolic pathways involved in OMS, which is of global concern.</p>
2025-10-23 | MTBLS13207 | MetaboLights
Project description:Effects of phenyl acids on different degradation phases during thermophilic anaerobic digestion
Project description:Comparative transcriptional profiling of N. crassa grown on five major crop straws of China (barley, corn, rice, soybean and wheat straws) revealed a highly overlapping group of 430 genes, the Biomass commonly Induced Core Set (BICS). A large proportion of induced carbohydrate-active-enzyme (CAZy) genes (82 out of 113) were also conserved across the five plant straws. Excluding 178 genes within the BICS that were also up-regulated under no-carbon conditions, the remaining 252 genes were defined as the Biomass Regulon (BR). Interestingly, 88 genes were only induced by plant biomass and not by three individual polysaccharides (Avicel, xylan, and pectin); these were denoted as the Biomass Unique Set (BUS). Deletion of one BUS gene, the transcriptional regulator rca-1, significantly improved lignocellulase production using plant biomass as the sole carbon source, possibly functioning via de-repression of the regulator clr-2. Thus, this result suggests that rca-1 is a potential engineering target for biorefineries, especially for plant biomass direct microbial conversion processes. Conidia of Neurospora crass wild type were inoculated at 10^6 conidia/mL into 100 mL 1×Vogel’s salts with 2% (w/w) ground crop straws, barley straw, corn straw, rice straw, soybean straw and wheat straw respectively for 30 h or 2% sucrose for 16 h. Then, mycelia were harvested through filtration and immediately frozen in liquid nitrogen.Total RNA from frozen sample was isolated with TRIzol reagent (Invitrogen) and further treated with DNase I (RNeasy Mini Kit, QIAGEN). The qualified RNA was prepared with standard protocol from Shenzhen BGI (China) and sequenced on the Illumina HiSeqTM 2000 platform.
