Project description:Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Here we deconvoluted a highly efficient cellulose-degrading and methanogenic consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. A time-series analysis was performed over the entire lifetime span of the microbial community and comprised of metagenomic, metatranscriptomic, metabolomics, metaproteomic and 16S rRNA gene analysis for 8 time points, in triplicate. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were isolated and sequenced. Both the recovered MAGs and the isolated strains were used as a database for further functional meta-omics. Absolute quantitative metatranscriptomics was performed thanks the spike-in of an in vitro transcribed RNA as an internal standard and label-free quantification was used for the metaproteomic analysis. The present dataset has been used for several publications. The first aim of the project was to characterize the interactions between uncultured populations in a lignocellulose-degrading community. Furthermore, because of the in-depth multi-omics characterization of the community, the dataset was used to develop new approaches for meta-omics integration as well as to assess the protein-to-RNA ratio of multiple microbial populations simultaneously. Modifications of multi-omics toolkits allowed us to assess the linearity between transcriptome and proteome for each population over time and reveal deeper functional-related trends and integrative co-dependent metabolisms that drive the overall phenotype of microbial communities.
Project description:In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg NH3-N/L).
Project description:Highland barley liquor is a distilled spirit made from highland barley on the Tibetan Plateau, but its alcohol yield is limited by the high fiber content of the raw material. In the field of biomass resources, functional microorganisms are commonly used in pretreatment to degrade cellulose and other substances, improving fermentation output. In this study, we isolated the cellulose-degrading probiotic Lactobacillus delbrueckii GR-8 (CMCase 6.21 U/mL) from the traditional vegetable-based fermented food "Jiangshui" and applied biological pretreatment to the fermentation of highland barley liquor. During pretreatment, probiotics enhanced cellulase and amylase activities in the fermented grains, resulting in a 25% reduction in cellulose content and a 112% increase in free reducing sugar content. The pretreatment significantly altered the microbial community structure, enhancing microbial diversity. After distillation, alcohol yield increased by 3.5%, and total acid and ester contents rose by 25% and 23%, respectively. Pyrazine compounds increased by 1290%, while higher alcohols like nonanol, phenylethanol, and hexanol decreased. The treated liquor caused less harm to mice, who showed improved memory, motor skills, and lower oxidative liver damage. This study demonstrates that biological pretreatment enhances both fermentation and the quality of Chinese spirits.
Project description:We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.
Project description:Biocrusts not only are considered ecosystem pioneers, but also have been recognized as a model system for soil ecosystem research. Furthermore, visually distinguishable phenotypic traits and stable physiological characteristics make biocrusts have significant advantages in meta-omics researches. So, we collected four types of biocrusts, applied metaproteome, to explore active microbial metabolism.
2021-08-02 | PXD027685 |
Project description:Metatranscriptome analysis of cellulose degrading microbial communities
| PRJNA1404889 | ENA
Project description:Metagenomic analysis of cellulose degrading microbial communities
Project description:Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert, sampled over two years with different weather conditions, with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed.
Project description:In this study, we created a synthetic mucin-degrading microbial community to specifically study mucin-driven ecological interactions in vitro. The synthetic community consisted of primary mucin degraders and cross-feeders. We tracked community composition and dynamics and the mucin-degrading enzymes that were produced.