Dongyan Niu

My research is aimed at advancing food safety from farm to folk by precisely understand human health risk potentially posed by foodborne pathogens of animal origin (Theme 1) as well as to develop innovative strategies to minimize food safety risk (Theme 2).

To achieve Theme 1, the research activities are centered on defining mechanisms that promote persistence and transmission of zoonotic pathogens in the entire food production system using cutting-edge technologies (e.g. single cell RNA-seq and live-cell imaging microscopy). Our current focuses are 1) towards an understanding of the molecular and cellular basis for biofilm formation of zoonotic pathogens in gastrointestinal and respiratory tract of animal and food processing environment; 2) study physiological growth parameters, population dynamics and alternations of virulence traits of microbial pathogens under real food production environments; 3) Investigate footprint and persistence of antimicrobial resistance genes in livestock production system using metagenomics approaches.

To achieve Theme 2, the #1 research effort focuses on explore effective and environmental friendly measures (e.g. bacteriophage-derived biocontrol, nanotechnology) to intervene antimicrobial resistance transfer and for prevention and control of zoonotic pathogens. We will initially focus our efforts on improved strategies for biocontrol of pathogenic E. coli, Salmonella and Campylobacter spp., the top three most burdensome bacterial foodborne pathogens in terms of costs of foodborne illness and deaths in Canada. To develop better bacteriophage biocontrol products, we are interested in deep understanding interaction and dynamics between phage and their bacterial host at both population and single-cell resolution. We are also interested in gaining knowledge of phage-phage interaction as well as how phageome interact with microbiome and their role in regulation of microbiome structure and metabolism and host immunity in animal and human health. The #2 research direction centers on developing robust, rapid and sensitive innovative technologies for real-time detection of foodborne pathogens and diagnosis of infectious disease. Our current dedication is development of isothermal nucleic acid amplification based platform for diagnosis of animal infectious disease (e.g. BRD).

Trainees will receiving comprehensive training on Molecular and Cellular Microbiology, Virology, Genomics, Transcriptomics, Proteomics, Biochemistry

Publications

1. Peng K., Jin L., Niu Y.D., Huang Q., McAllister T.A., Yang H.E., Denise H., Xu Z., Acharya S., Wang Sh. and Wang Y. 2018. Condensed tannins affect bacterial and fungal microbiomes and mycotoxin production during ensiling and upon aerobic exposure. Applied and Environmental Microbiology. 84: e02274-17.

2. Holman D.B., Klima C.L., Ralston B.J., Niu Y.D., Stanford Kim, Alexander T.W. and McAllister T.A. 2017. Metagenomic sequencing of bronchoalveolar lavage samples from feedlot cattle mortalities associated with bovine respiratory disease. Genome Announc. 5: e01045-17.

3. Wang J., Stanford K., McAllister T.A., Johnson R.P., Chen J., Hou H., Zhang G. and Niu Y.D. 2016. Biofilm formation, virulence gene profiles and antimicrobial resistance of nine serogroups of non-O157 Shiga toxin-producing Escherichia coli. Foodborne Pathogen and Disease, 13. (As corresponding author)

4. Niu Y.D., Cook S., Wang J., Klima C.L., Hsu Y-H., Kropinski A.M. and McAllister T.A. 2015. Comparative analysis of multiple inducible bacteriophages from Mannheimia haemolytica. BMC Microbiology.15:175. (As co-corresponding author).

5. Wang J., Niu Y.D., Chen J., McAllister T.A. and Stanford K. 2015. Complete genome sequence of Escherichia coli O145:NM bacteriophage vB_EcoM_AYO145A, a new member of O1-like phages. Genome Announcement 3:e00539-15. (As corresponding author).

6. Wang J., Niu Y.D., Chen J., Ateba C.N., Johnson R.P. and McAllister T.A. 2015. Feces of feedlot cattle contain a diversity of bacteriophages that lyse non-O157 Shiga toxin-producing Escherichia coli. Canadian Journal of Microbiology, 10.1139/cjm-2015-0163. (As corresponding author).

7. Liu H., Meng R., Wang J., Niu Y.D., Li J., Stanford K. and McAllister T. 2015. Inactivation of Escherichia coli O157 bacteriophages by using a mixture of ferrous sulfate and tea extract. Journal of Food Protection. 78, 2108-2307 (As corresponding author).

8. Cao Zh., Zhang J., Niu Y.D., Jin L., Cui N., Cao F., Ma Y., Li Zh., Li X. and Xu Y. 2015. Isolation and characterization of a “phiKMV-like” bacteriophage and its therapeutic effect on mink hemorrhagic pneumonia. PloS One, 10:e0116571.

9. Liu H., Niu Y.D., Meng R., Wang J., Li J., Johnson R.P., Stanford K and McAllister T.  2015. Control of Escherichia coli O157 on beef at 37, 22 and 4°C by T5-, T1-, T4- and O1-like bacteriophages. Food Microbiology. 51, 69−73.

10. Niu Y.D., McAllister T.A., Nash J.H.E., Kropinski A.M. and Stanford K. 2014. Four Escherichia coli O157:H7 phages: A new bacteriophage genus and taxonomic classification of T1-like phages. PLoS ONE. 9: e100426. (As co-corresponding author).

11. Hallewell J., Niu Y.D., Munns K., McAllister T.A., Johnson R.P., Ackermann H.W., Thomas J.E. and Stanford K. 2014. Differing populations of endemic bacteriophages in cattle shedding high and low numbers of Escherichia coli O157:H7 bacteria in feces. Applied and Environmental Microbiology. 80:3819–3825.

12. Liu H., Niu Y.D., Li, J., Stanford K., and McAllister T.A. Rapid and accurate detection of bacteriophage activity against Escherichia coli O157:H7 by propidium monoazide Real-Time PCR. BioMed Research International. 2014, article # 319351.

13. Hsu Y-H., Cook S., Alexander T., Klima C., Niu, Y.D., Selinger B.L. and McAllister T. 2013. Investigation of Mannheimia haemolytica bacteriophages relative to host diversity. Journal of Applied Microbiology. 114:1592–1603.

14. Niu Y.D, Stanford K., Kropinski A.M., Ackermann H-W, Johnson R.P., She Y-M., Ahmed R., Villegas A. and McAlister T.A. 2012. Genomic, proteomic and physiological characterization of a T5-like bacteriophage for control of Shiga toxin-producing Escherichia coli O157:H7. PLoS ONE. 7: e34585. doi:10.1371/journal.pone.0034585. (As co-corresponding author).

15. Niu Y.D, Stanford K., Ackermann H-W and McAlister T.A. 2012. Characterization of 4 T1-like lytic bacteriophages that lyse Shiga-toxin Escherichia coli O157:H7. Canadian Journal of Microbiology. 58:923–927.

16. Xue H.Y., Niu Y.D., Gao G.Z., Lin Q.Y., Jin L.J., and Xu Y.P. 2011. Aucubin modulated Bcl-2 family proteins expression and inhibits caspases cascade in H2O2-induced PC12 cells. Molecular Biology Reports. 38: 3561–3567.

17. Stanford K., McAllister T.A., Niu Y.D., Stephens T.P., Mazzocco A., Waddell T.E., Johnson R.P. 2010. Oral delivery systems for encapsulated bacteriophages targeted at Escherichia coli O157:H7 in feedlot cattle. Journal of Food Protection. 73: 1304–1312.

18. Niu Y.D., McAllister T.A., Xu Y., Johnson R.P., Stephens T. P., and Stanford K. 2009. Prevalence and impact of bacteriophages on the presence of E. coli O157:H7 in feedlot cattle and their environment. Applied and Environmental Microbiology. 75:1271–1278.

19. Niu Y.D., Johnson R.P., Xu Y., McAllister T.A., Sharma R., Louie M. and Stanford K. 2009. Host range and lytic capability of four bacteriophages against bovine and clinical human isolates of Shiga toxin-producing Escherichia coli O157:H7. Journal of Applied Microbiology. 107: 646–656.

20. Niu Y.D., Xu Y.P., McAllister T.A., Rozema E., Stephens T.P., Bach S.J., Johnson R.P. and Stanford K. 2008. Comparison of fecal vs. rectoanal mucosal swab sampling for detecting Escherichia coli O157:H7 in experimentally inoculated cattle used in assessing bacteriophage as a mitigation strategy. Journal of Food Protection. 71: 691–698.