The Metaramanomics Platform

References:

1. Zhidian Diao#, Qiqun Peng#, Sijun Luo, Lingyan Kan, Anle Ge, Wei Gao, Runxia Li, Weiwei Bao, Xixian Wang, Yuetong Ji, Jian Xu*, Shihui Yang*, Bo Ma*. AI-powered high-throughput digital colony picker platform for sorting microbial strains by multi-modal phenotypes. Nature Communications, 2025, 16:8769
2. Xiaoyan Jing, Yanhai Gong, Yishang Ren, Liyan Wang, Runzhi Mu, Pengcheng Sun, Zhidian Diao, Yu Meng, Liming Huang, Xixian Wang, Jia Zhang, Jiaxuan Luan, Yuetong Ji, Bo Ma, Huihui Pan*, Yushu Jing*, Jian Xu*. Mining robust in situ phosphorus-accumulating organisms via single-cell RACS-Culture for rational ecosystem engineering. Water Research, 2025, 284:124025
3. Jia Zhang#*, Jianmei Wang#, Pengfei Zhu#, Zhidian Diao#, Shuhua Tian, Ziyuan Ding, Yongming Duan, Teng Xu, Xuan Zhou, Xixian Wang, Xia Ma, Ting Sun, Xiaoyan Jing, Weilian Hung, Bo Ma, Shi Huang*, Xiaowei Zheng*, Jian Xu*. Raman flow cytometry based single-cell species classification, viable-cell counting and vitality test for probiotic products. iMetaOmics, 2025, 2(3):e70024
4. Xixian Wang#, Sen Wang#, Zhidian Diao#, Xibao Hou#, Yanhai Gong, Qing Sun, Jiaping Zhang, Lihui Ren, Yuandong Li, Yuetong Ji, Wei Shen, Yifeng Yin, Shi Huang, Xiaojin Song, Qiu Cui, Yingang Feng*, Jian Xu*, Bo Ma*. Label-free high-throughput live-cell sorting of genome-wide random mutagenesis libraries for metabolic traits by Raman flow cytometry. Proceedings of the National Academy of Sciences of the United States of America, 2025, 122(22):e2503641122
5. Xiaoyan Jing#, Yanhai Gong#, Zhidian Diao#, Yan Ma#, Yu Meng, Jie Chen, Yishang Ren, Yuting Liang, Yinchao Li, Weihan Sun, Jia Zhang, Yuetong Ji, Zhiqi Cong, Shengying Li, Bo Ma, Zhisong Cui*, Li Ma*, Jian Xu*. Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-Seq. The Innovation, 2025, 6(3):100759
6. Zhidian Diao#, Xiaoyan Jing#, Xibao Hou#, Yu Meng, Jiaping Zhang, Yongshun Wang, Yuetong Ji, Anle Ge, Xixian Wang, Yuting Liang*, Jian Xu*, Bo Ma*. Artificial intelligence-assisted automatic Raman-activated cell sorting (AI-RACS) system for mining specific functional microorganisms in the microbiome. Analytical Chemistry, 2024, 96(46):18416-18426
7. Zhidian Diao#, Xixian Wang#, Jiaping Zhang, Anle Ge, Teng Xu, Lingyan Kan, Yuandong Li, Yuetong Ji, Xiaoyan Jing, Jian Xu*, Bo Ma*. Optical-based microbubble for on-demand droplet release from static droplet array (SDA) for dispensing one droplet into one tube. Biosensors and Bioelectronics, 2023, 240:115639
8. Jia Zhang#, Xiaolu Su#, Yefei Wang#, Xiaohang Wang, Shiqi Zhou, Hui Jia, Xiaoyan Jing, Yanhai Gong, Jichao Wang*, Jian Xu*. Improved single-cell genome amplification by a high-efficiency phi29 DNA polymerase. Frontiers in Bioengineering and Biotechnology, 2023, 11:1233856
9. Jia Zhang#, Lihui Ren#, Lei Zhang#, Yanhai Gong#, Teng Xu, Xiaohang Wang, Cheng Guo, Lei Zhai, Xuejian Yu, Ying Li, Pengfei Zhu, Rongze Chen, Xiaoyan Jing, Gongchao Jing, Shiqi Zhou, Mingyue Xu, Chen Wang, Changkai Niu, Yuanyuan Ge, Bo Ma, Gaishuang Shang, Yunlong Cui*, Su Yao*, Jian Xu*. Single-cell rapid identification, in situ viability and vitality profiling, and genome-based source tracking for probiotics products. iMeta, 2023, 2(3):e117
10. Jian Xu*, Jianzhong Zhang, Yingchun Xu, Yi-Wei Tang, Bo Ma, Yuzhang Wu*. Single cell metabolic phenome and genome via the ramanome technology platform: Precision medicine of infectious diseases at the ultimate precision? iLABMED, 2023, 1(1):5-14
11. Xixian Wang#, Lihui Ren#, Zhidian Diao#, Yuehui He#, Jiaping Zhang, Min Liu, Yuandong Li, Lijun Sun, Rongze Chen, Yuetong Ji, Jian Xu*, and Bo Ma*. Robust spontaneous Raman flow cytometry for single-cell metabolic phenome profiling via pDEP-DLD-RFC. Advanced Science, 2023, 10(16):2207497
12. Min Liu#, Pengfei Zhu#, Lei Zhang#, Yanhai Gong, Chen Wang, Lu Sun, Lili Wang, Rongze Chen, Yuli Mao, Xiaoting Fu, Lili Zhang, Teng Xu, Yuetong Ji, Quanjiang Dong, Bo Ma, Jianzhong Zhang*, Jian Xu*. Single-cell identification, drug susceptibility test, and whole-genome sequencing of Helicobacter pylori directly from gastric biopsy by clinical antimicrobial susceptibility test Ramanometry. Clinical Chemistry, 2022, 68(8):1064-1074
13. Xiaoyan Jing#, Yanhai Gong#, Teng Xu#, Yu Meng, Xiao Han, Xiaolu Su, Jianmei Wang, Yuetong Ji, Yuandong Li, Zhongjun Jia, Bo Ma*, Jian Xu*. One-cell metabolic phenotyping and sequencing of soil microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE). mSystems, 2021, 6(3):e00181-21
14. Yuehui He, Shi Huang, Peng Zhang, Yuetong Ji, Jian Xu. Intra-Ramanome Correlation Analysis unveils metabolite conversion network from an isogenic population of cells. mBio, 2021, 12(4):e01470-21
15. Xixian Wang#, Yi Xin#, Lihui Ren#, Zheng Sun, Pengfei Zhu, Yuetong Ji, Chunyu Li, Jian Xu*, Bo Ma*. Positive dielectrophoresis based Raman-activated droplet sorting for culture-free and label-free screening of enzyme function in vivo. Science Advances, 2020, 6(32):eabb3521
16. Teng Xu#, Yanhai Gong#, Xiaolu Su#, Pengfei Zhu, Jing Dai, Jian Xu*, Bo Ma*. Phenome-genome profiling of single bacterial cell by Raman-activated Gravity-driven Encapsulation and Sequencing. Small, 2020, 16:2001172
17. Yuehui He#, Xixian Wang#, Bo Ma*, Jian Xu*. Ramanome technology platform for label-free screening and sorting of microbial cell factories at single-cell resolution. Biotechnology Advances, 2019, 37(6):107388
18. Jian Xu*, Bo Ma, Xiaoquan Su, Shi Huang, Xin Xu, Xuedong Zhou, Wei Huang, Rob Knight*. Emerging trends for microbiome analysis: from single-cell functional imaging to microbiome big data. Engineering, 2017, 3(1):66-70


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