Fan Zhang

CDIB DivisionFan Zhang
Assistant Professor

2015-2022 Post doc - Molecular Virology and Microbiology, Baylor College of Medicine 
2015 - Ph.D., Molecular Microbiology, University of Maryland College Park
2009 - M.S., Microbial Ecology, Xiamen University, China
2005 - B.S., Biology, Xiamen University, China

Phone: 225-578-1901
Lab Phone:  225-578-5269

Office: 224 LSB

Research summary: 

Systems biology of host-microbiome interactions


Animals have partnered with microbes throughout evolution to extend their genetic repertoire and metabolic capacity. Evident examples are direct nutrient acquisition by symbiotic nitrogen fixation, or metabolite transformation like microbiome-derived short chain fatty acids and vitamins in human guts. The partnership is driven by both intrinsic and extrinsic demands for nutrients. In this way, nutrients can disrupt the strength of these symbioses, and is especially true for rarer but essential nutrients like phosphorus. Thus, dissection of the molecular pathways that mediate nutrient sharing is broadly relevant for understanding of host-microbe relationships in both health and disease. 

Motivation and Approaches

I have a longstanding interest in the nutritional drivers of host-microbiome interactions. My Ph.D. work identified a microbial pathway that stores poly-phosphate in marine sponge hosts, potentially benefiting their hosts living in phosphate limited coral reefs (Zhang et al, PNAS, 2015). In postdoc training, I leverage free-living nematode Caenorhabditis elegans, a low cost, high throughput, and genetic tractable model to study underlying molecular circuits mediate the partnership. I defined the natural microbiome for soil nematode C. elegans (Zhang et al, Front. Microbiol., 2017), established a high throughput pipeline to characterize microbiome impact on host fitness (Zhang et al, MiMB, 2020), and identified insulin signaling, a host nutrient sensing pathway, as a key regulator in the recruitment of beneficial microbes (Zhang et al, Current Biology, 2021). With these established resources, my lab will apply multi-omics approaches (microbiome, transcriptome, and metabolome), high content microscope imaging, and C. elegans genetic/genomic toolbox to further unravel the molecular underpinning of nutritional programming of host-microbiome interactions. 

Undergraduate, PhD and Research Associate II positions are available. Candidates with relevant experience or research interests in Microbiology, C. elegans biology, and/or Bioinformatics are encouraged to email with their CV.

Selected publications:

complete list of publications

 (* co-authors): 

  1. Zhang, F. *, Weckhorst, J. *, Assié, A., Hosea, C., Ayoub, C.A., Khodakova, A.S., Loeza-Cabrera, M., Vidal, D., Samuel, B.S. 2021. Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut. Current Biology. 31(12):2603-2618.
  2. Han Y, Jiao N, Zhang Y, Zhang F, He C, Liang X, Cai R, Shi Q, Tang K. 2021. Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms. Microbiome. 9(71):1-9.
  3. Dirksen, P., Assié, A., Zimmermann, J., Zhang, F., Tietje, A.M., Marsh, S.A., Félix, M.A., Shapira, M., Kaleta, C., Schulenburg, H. and Samuel, B.S., 2020. CeMbio-The C. elegans microbiome resource. G3: Genes|Genomes|Genetics.10(9):3025-3039.
  4. Zhang, F. *, Jonas, L. *, Lin, H., Hill, R.T. 2019. Microbially mediated nutrient cycles in marine sponges. FEMS Microbiology Ecology. doi: 10.1093/femsec/fiz155
  5. Zhang, F. *, Weckhorst, J. *, Assié, A. *, Khodakova, A.S., Loeza-Cabrera, M., Vidal, D., Samuel, B.S. 2019. High-throughput assessment of changes in the Caenorhabditis elegans gut microbiome. Methods in Molecular Biology. Springer Nature. doi: 10.1007/978-1-0716-0592-9_12
  6. Zhang, F. *, Berg, M. *, Dierking, K., Félix, M.A., Shapira, M., Samuel, B.S., Schulenburg, H. 2017. Caenorhabditis elegans as a model for microbiome research. Frontier in Microbiology. doi:10.3389/fmicb.2017.00485.
  7. Zhang, F., Blasiak, L.C., Karolin, J.O., Powell, R.J., Geddes, C.D., Hill, R.T. 2015. Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges. Proceedings of the National Academy of Sciences U.S.A. 112(14), 4381-4386.
  8. McDonald, R., Zhang, F., Watts, J.E.M., Schreier, H.J. 2015. Diversity of nitrogen fixation genes and associated activity in the gastrointestinal tract of the wood-eating loricariid catfish Panaque nigrolineatus. ISME Journal. 9: 2712–2724.
  9. Zhang, F., Vicente, J., Hill, R.T. 2014. Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima. Frontiers in Microbiology. doi: 10.3389/fmicb.2014.00561
  10. Zhang, F.,* Pita, L.,* Erwin P., Abaid S., López-Legentil S., Hill, R.T.  2014.  Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality. FEMS Microbiology Ecology. 90(3), 699-707.