Fangchao Song

Portrait of Fangchao Song
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  • Title
    Staff Scientist
  • Email
    song22@llnl.gov
  • Phone
    (925) 422-0300
  • Organization
    PLS-BBTD-BIOSCIENCES, BIOTECHNOLOGY

My research sits at the intersection of microbiology, biomaterials, and engineering, focusing on understanding and engineering complex biosystems across multiple scales—from gene functions and metabolic pathways to biofilms and microbiomes. I leverage systems and synthetic biology approaches to explore microbial systems, applying droplet-based ultra-high-throughput experimentation, functional genomics, mathematical modeling, and molecular biology tools. My work aims to unravel complex microbial systems from the cellular to the ecosystem level, ultimately guiding the engineering of functional microbial systems for diverse applications.

I was trained as a chemical engineer but have expanded my expertise to include mathematical modeling, polymers, microbial biofilms, microbiomes, and synthetic and systems biology throughout my master's, Ph.D., and postdoctoral research. Before joining Lawrence Livermore National Laboratory as a staff scientist on December 2022, I was a postdoctoral researcher at Lawrence Berkeley National Laboratory.

Selected previous projects:

  1. Development of high throughput methods for understanding complex microbial communities. Lawrence Berkeley National Laboratory. Advisor: Adam P. Arkin.
  2. Effects of substrate stiffness on bacterial biofilm formation. Syracuse University. Advisor: Dacheng Ren.
  3. Kinetics and modelling of melt/solid polycondensation of poly(L-lactic acid). Zhejiang University. Advisor: Linbo Wu.
  4. Synthesis and characterization of carbosilane dendrimers used as silica-based stationary phases in high performance liquid chromatography. Shandong University. Advisor: Shengyu Feng.

Ph.D., Chemical Engineering, Syracuse University, Syracuse, New York

M.S., Chemical Engineering, Zhejiang University, Hangzhou, China

B.S., Chemical Engineering, Shandong University, Jinan, China

Fangchao's google scholar

Peer reviewed publications:

  1.  “A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening”. Noel Ha, Jenny R. Onley, Kai Deng, Peter Andeer, Benjamin P. Bowen, Kshitiz Gupta, Peter W. Kim, Nathaniel Kuch, Mark Kutschke, Alex Parker, Fangchao Song, Brian Fox, Paul Adams, Markus de Raad, Trent R. Northen. Lab on a Chip (2023).
  2. “Towards environmental control of microbiomes”. William A. Sharpless, Kyle B. Sander, Fangchao Song, Jennifer V. Kuehl, Adam P. Arkin†. bioRxiv (2022).
  3. “A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis”. Fangchao Song†, Jennifer V. Kuehl, Arjun Chandran, Adam P. Arkin†. mSystems (2021).
  4. “Cyclic-di-GMP and oprF are involved in the response of Pseudomonas aeruginosa to substrate material stiffness during attachment on polydimethylsiloxane (PDMS)”. Fangchao Song*, Hao Wang*, Karin Sauer, Dacheng Ren†, (*equally contributed). Frontiers in Microbiology (2018).
  5. “How bacteria respond to material stiffness during attachment: a role of Escherichia coli flagellar motility”. Fangchao Song, Megan Brasch, Hao Wang, James H. Henderson, Karin Sauer, Dacheng Ren†. ACS Applied Materials & Interfaces (2017).
  6. “Phagocytosis of Escherichia coli biofilm cells with different aspect ratios: a role of substratum material stiffness”. Yanrui Zhao*, Fangchao Song*, Hao Wang, Junlin Zhou†, Dacheng Ren†, (*equally contributed). Applied Microbiology and Biotechnology (2017).
  7. “Actual measurement, hygrothermal response experiment and growth prediction analysis of microbial contamination of central air conditioning system in Dalian, China”.  Yang Lv†, Guangyao Hu, Chunyang Wang, Wenjie Yuan, Shanshan Wei, Jiaoqi Gao, Boyuan Wang, Fangchao Song. Scientific Report 7 44109 (2017).
  8. “Effects of surface properties on bacterial adhesion and biofilm formation”. Fangchao Song, Hyun Koo, Dacheng Ren†. Journal of Dental Research 94 1027-1034 (2015).
  9. “Stiffness of cross-linked poly(dimethylsiloxane) affects bacterial adhesion and antibiotic susceptibility of attached cells”. Fangchao Song, Dacheng Ren†. Langmuir 30 10354-10362 (2014).
  10. “Controlling persister cells of Pseudomonas aeruginosa PDO300 by (Z)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one”. Jiachuan Pan, Fangchao Song, Dacheng Ren†. Bioorganic & Medicinal Chemistry Letters 23 4648-4651 (2013).
  11. “(Z)-4-bromo-5-(bromomethylene)-3-methylfuran-2(5H)-one sensitizes Escherichia coli persister cells to antibiotics”. Jiachuan Pan, Xin Xie, Wang Tian, Ali Adem Bahar, Nan Lin, Fangchao Song, Jing An, Dacheng Ren†. Applied Microbiology and Biotechnology 97 9145-9154 (2013).
  12. “Synthesis of high molecular weight poly(L-lactic acid) via melt/solid state polycondensation: II: Effect of pre-crystallization on solid state polycondensation of poly(L-lactic acid)”. Bo Peng, Hongbing Hou, Fangchao Song, Linbo Wu†. Industrial & Engineering Chemistry Research 51 5190-5196 (2012).
  13. “Synthesis of high molecular weight poly(L-lactic acid) via melt/solid polycondensation. I: Intensification of dehydration and oligomerization during melt polycondensation”. Fangchao Song, Linbo Wu†. Journal of Applied Polymer Science 120 2780-2785 (2011).
  14. “Kinetics and modeling of melt polycondensation reaction for synthesis of poly(butylene succinate-co-butylene terephthalate) I- Esterification”. Lixia Hu, Linbo Wu†, Fangchao Song, Bo-Geng Li. Macromolecular Reaction Engineering 4 621-632 (2010). 

Conference talks and posters:

  1. Soil microbial spatial interactome by Single Micro Particle sequencing (SiMPle-seq). Xiangpeng Li, Fangchao Song, Cyrille Delly, Vee Xu, Fatlum Hajredini, Adam P. Arkin, Adam Abate. The Joint Berkeley Initiative for Microbiome Sciences (JBIMS) Workshop, Berkeley, CA, 2023.
  2. From fast to furious phenotyping of microbes: advancing the understanding of microbial diversities and gene functions using droplet microfluidics and high throughput sequencing. Fangchao Song, X. Lyu, M. Moore, A. Hung, J. V. Kuehl, H. Carlson, M. Price, V. Mutalik, A. M. Deutschbauer, A. P. Arkin, P. D. Adams. Department of Energy Genomic Sciences Program Annual Principal Investigator Meeting, Washington D.C., 2022.
  3. Metabolic network modeling and metabolomics integration for comparative analysis of biogeochemical reactions in multiple river systems.Aimee Kessell†, Fangchao Song, Janaka Edirisinghe, Christopher Henry, Hyun-Seob Song, PNNL summer school consortium. AGU Fall Meeting,San Francisco, CA, 2020. (†Presenter) Link: https://drive.google.com/file/d/1OA-pP-dyfWQ-VNhSHjRUDoDk0IO7HRr7/view
  4. Revealing genetic functions during bacterial adhesion and biofilm formation using barcode transposon mutant library. Fangchao Song†, Syliva Illouz, Adam M. Deutschbauer, Adam P. Arkin. AIChE Annual Meeting, San Francisco, CA, 2020. Link to the presentation: https://youtu.be/AruGQWWofHc
  5. Massive screening of metabolites using picolitre droplet array with nanostructure initiator mass spectrometry. Noel S. Ha†, Markus de Raad, Fangchao Song, Kai Deng, Nicole Ing, Anup K. Singh, Trent R. Northen. MicroTAS 2019: The 23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, Basel, Switzerland, 2019.
  6. Revealing cell interactions in complex microbial community by high throughput droplet barcode sequencing. Fangchao Song†, Leqian Liu, Jiahao Shi, Adam R. Abate, Adam P. Arkin. The American Society for Microbiology Annual Meeting, San Francisco, CA, 2019. Related short talk: https://www.youtube.com/watch?v=BuOjoXFv9D0
  7. A droplet based high throughput method to reveal microbial interactions in complex microbial community. Fangchao Song†, Leqian Liu, Jiahao Shi, Adam R. Abate, Adam P. Arkin. Keystone Microbiome: Chemical Mechanisms and Biological Consequences, Montreal, Canada, 2019.
  8. New technologies for the large-scale screening of microbial interaction. Markus de Raad*, Fangchao Song*,†, Tim Veth, Leqian Liu, Estelle Couradeau, Jiahao Shi, Adam R. Abate, Adam M. Deutschbauer, Trent R. Northen, Adam P. Arkin. Department of Energy Genomic Sciences Program Annual Principal Investigator Meeting, Washington D.C., 2019 (*equally contributed)
  9. Core Values: large-scale analysis of environmental constraints on microbial community assembly activity, and dispersal in groundwater and sediment from a contaminated subsurface aquifer. L Lui†, HJ Smith, F von Netzer, KB De Leon, E Majumder, J Kuehl, F Song, A Sczesnak, MP Thorgersen, G Xiaoxuan, F Poole, B Bowen, SM Kosina, JW Moon, JD Van Nostrand, N Daliang, CJ Paradis, KF Walker, KA Lowe, G Zane, AB Aaring, D Joyner, X Wu, A Kazakov, JM Chandonia, P Novichkov, R Chakraborty, MWW Adams, T Hazen, JD Wall, MW Fields, AP Arkin, PD Adams. AGU Fall Meeting, Washington, D.C., 2018
  10. How material stiffness affects E. coli attachment: A role of MotB. Fangchao Song, Megan Brasch, Hao Wang, James Henderson, Karin Sauer, Dacheng Ren†. EUROBIOFILMS 2017, Amsterdam, The Netherlands, 2017.
  11. motB is involved in the response of Escherichia coli to material stiffness during biofilm formation. Fangchao Song†, Megan Brasch, James Henderson, Dacheng Ren. AIChE Annual Meeting, San Francisco, CA, 2016.
  12. A role of material stiffness in bacterial adhesion and biofilm formation. Fangchao Song, Dacheng Ren†. The 7th American Society for Microbiology Conference on Biofilm, Chicago, IL, 2016.
  13. Material stiffness affects bacterial adhesion and the physiology of attached cells. Fangchao Song†, Dacheng Ren. The 3rd Stevens Conference on Bacteria-Material Interactions, Hoboken, NJ, 2015.
  14. Surface stiffness affects bacterial adhesion, growth and antibiotic susceptibility of attached cells. Fangchao Song†, Dacheng Ren. AIChE Annual Meeting, Atlanta, GA, 2014.
  15. Stiffness of cross-linked poly(dimethylsiloxane) affects bacterial adhesion and antibiotic susceptibility of attached cells. Fangchao Song†, Dacheng Ren. The American Society for Microbiology Annual Meeting, Boston, MA, 2014.
  16. Polycondensation technologies for synthesis of poly(L-lactic acid) materials. Linbo Wu†, Weichao Wang, Dan Cao, Hongbing Hou, Fangchao Song, Zhaoqin Ma, Xiangying Sun, Bo Peng. The 4th International Conference of Technology and Application of Biodegradable Plastics, Shanghai, China, 2010.
  17. Kinetics of melt polycondensation of L-lactic acid. Fangchao Song, Linbo Wu†. The 6th Chinese National Chemical and Biochemical Engineering Annual Meeting, Changsha, China, 2010.

Patents:

  1. Melt/solid state polycondensation preparation method for polylactic acid. CN102040730.
  2. Melt/solid phase polycondensation preparation method of polylactic acid material with high molecular weight and high crystallinity.CN102002147.
  • Berkeley Lab Research SLAM Finalist, Lawrence Berkeley National Laboratory (2019)
  • Outstanding Graduate Student in Chemical Engineering, Syracuse University (2016).
  • Syracuse University Outstanding Teaching Assistant Award, Syracuse University (2015).

Certifications and Trainings:

  • Certification of successfully completing UC Davis Genome Center - Genome Wide Association Study Workshop, 2021
  • Certificate of completion, Multi-Scale Microbial Modeling Dynamics Summer School, 2020.
  • Certification of successfully completing UC Davis Genome Center - Genome Assembly Workshop, 2020.
  • UCSF Scientific Leadership and Management Skills Course, Gladstone Institute at UCSF, San Francisco, CA, 2019.
  • Certificate of training in Microbial Genomics & Metagenomics for a certified IMG user, Joint Genome Institute, 2018
  • Certification of successfully completing UC Davis Genome Center - Microbial Community Analysis Workshop, 2017.
  • Certification of successfully completing CSHL Synthetic Biology, 2017.
  • Certification of successfully completing KIx Explore Statistics with R, 2014.
  • Certification of successfully completing MITx 6.002x Circuits and Electronics, 2012.
  • National Computer Rank Examination Certificate - Database, 2005.