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  • PROJ Diversity of aquatic plant associated microbial communities in field samples

    Jin Zeng, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences,2021.09.16


    Aquatic plant associated samples collected from natural field sites.


  • PROJ Spatiotemporal transcriptome atlas of developing mouse lung

    Guangdun Peng, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,2024.06.03


    The functional development of the mammalian lung is a complex process that relies on the spatial and temporal organization of multiple cell types and their states. However, a comprehensive spatiotemporal transcriptome atlas of the developing lung has yet to be reported. Here we apply high-throughput spatial transcriptomics to allow for a comprehensive assessment of mouse lung development comprised of two important developmental events: branching morphogenesis and alveolar formation. We firstly generate a spatial molecular atlas of mouse lung development spanning from E12.5 to P0 based on integration of published single-cell RNA-sequencing data and identify 10 spatial domains critical for functional lung organization. We observe the establishment of pulmonary airways within the developing lung, accompanied by the proximal-distal patterning by distinct characteristics of gene expression, signaling restriction and transcription factors enrichment. We introduce the alveolar niche heterogeneity with maturation state differences during the later developmental stage around birth and demonstrate differentially expressed genes, such as Angpt2 and Epha3, which may perform a critical role during alveologenesis. In addition, multiple signaling pathways, including ANGPT, VEGF and EPHA, exhibit increased enrichment in more maturing alveolar niche. Furthermore, we create a lineages map connecting spatial domains from adjacent time points in E12.5-P0 lungs and explore TF regulatory networks specific for each lineage.


  • PROJ Organic Carbon Transformation by Marine Heterotrophic Bacteria Adapting to Hypoxia

    Quanrui Chen, ,2024.05.29


    The global increase in hypoxic zones necessitates a comprehensive understanding of marine organic carbon cycling dynamics under hypoxic conditions to evaluate their impact on global carbon cycles and ecosystem health. This study, conducted in the seasonal hypoxia zone of the Yangtze River Estuary, investigates the effects of deoxygenation on the microbial utilization of algal-derived organic carbon. Through culture experiments and molecular analyses, the research explores the adaptability of heterotrophic bacterial communities in response to hypoxia, focusing on changes in composition and metabolic pathways. High-throughput 16S rDNA sequencing is used to analyze shifts in microbial community dynamics and their role in organic carbon transformation. The study aims to provide new insights into the complex interactions between microbial communities and organic matter cycling under hypoxic conditions, informing strategies for managing marine ecosystems amidst global change.


  • PROJ Multi-kingdom microbiota analyses identify bacterial-fungal interactions and biomarkers of colorectal cancer across cohorts

    Ningning Liu, Shanghai Jiao Tong University,2020.12.02


    Despite recent progress in our understanding of the association between the gut microbiome and colorectal cancer (CRC), multi-kingdom gut microbiome dysbiosis in CRC across cohorts is unexplored. We investigated four-kingdom microbiota alterations using CRC metagenomic datasets of 1,368 samples from 8 distinct geographical cohorts. Integrated analysis identified 20 archaeal, 27 bacterial, 20 fungal and 21 viral species for each single-kingdom diagnostic model. However, our data revealed superior diagnostic accuracy for models constructed with multi-kingdom markers, in particular the addition of fungal species. Specifically, 16 multi-kingdom markers including 11 bacterial, 4 fungal and 1 archaeal feature, achieved good performance in diagnosing patients with CRC (area under the receiver operating characteristic curve (AUROC) = 0.83) and maintained accuracy across 3 independent cohorts. Coabundance analysis of the ecological network revealed associations between bacterial and fungal species, such as Talaromyces islandicus and Clostridium saccharobutylicum. Using metagenome shotgun sequencing data, the predictive power of the microbial functional potential was explored and elevated D-amino acid metabolism and butanoate metabolism were observed in CRC. Interestingly, the diagnostic model based on functional EggNOG genes achieved high accuracy (AUROC = 0.86). Collectively, our findings uncovered CRC-associated microbiota common across cohorts and demonstrate the applicability of multi-kingdom and functional markers as CRC diagnostic tools and, potentially, as therapeutic targets for the treatment of CRC.


  • PROJ AMI project

    Chenfen Zhou, PICB,2021.01.22



  • PROJ metagenome data of sponge

    Lu Fan, South University of Science and Technology of China,2023.06.15


    metagenome data of sponge C. concentrica


  • PROJ Human Testicular Aging

    Xin Li, Shanghai Institute of Nutrition and Health,CAS,2024.04.30



  • PROJ Prokaryotic community of urban park

    Jun Yang, Institute of Urban Environment, Chinese Academy of Sciences,2021.03.31


    Here we uesed amplicon sequencing in order to explore the habitat preference of prokaryotic community from Xiamen urban parks


  • PROJ Microeukaryotic community (18SV4) of urban park

    Jun Yang, Institute of Urban Environment, Chinese Academy of Sciences,2021.05.26


    Here we uesed amplicon sequencing in order to explore the habitat preference of microeukaryotic community from Xiamen urban parks


  • PROJ Human_islet_org_10x_scRNAseq_SWQ

    Wenqian Song, Shanghai Institutes for Biological Sciences,2024.05.15