Xu Zhang – NorthOmics

Last Updated on June 29, 2021

Research Associate

xzhan7[AT]uottawa.ca

Xu Zhang completed a B.Sc. degree in Biotechnology (2006) and M.Sc. degree in Microbiology (2009) in Lanzhou University, China. He obtained his Ph.D. degree in Microbiology from the Shanghai Jiao Tong University in 2013. He is currently a postdoctoral fellow at the OISB, University of Ottawa, under the supervision of Professors Daniel Figeys and Alain Stintzi. His research focuses on the host–gut microbe interactions with multiomic strategies including proteomics/metaproteomics, metagenomics, and metatranscriptomics, in the context of human disease including metabolic syndrome and inflammatory bowel disease.

Publications in NorthOmics lab:

Dong L, Lu D, Chen R, Lin Y, Zhu H, Zhang Z, Cai S, Cui P, Song G, Rao D, Yi X, Wu Y, Song N, Liu F, Zou Y, Zhang S, Zhang X, Wang X, Qiu S, Zhou J, Wang S, Zhang X, Shi Y, Figeys D, Ding L, Wang P, Zhang B, Rodriguez H, Gao Q, Gao D, Zhou H and Fan J. Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma. (2022) Cancer Cell. 40, 70-87.e15 Pubmed Cancer Cell

Li H, Zhang X, Chen R, Cheng K, Ning Z, Li J, Twine S, Stintzi A, Mack D and Figeys D. Elevated colonic microbiota-associated paucimannosidic and truncated N-glycans in pediatric ulcerative colitis. (2021) J Proteomics. 249, 104369 Pubmed J Proteomics

Mayne J, Zhang X, Butcher J, Walker K, Ning Z, Wójcik E, Dastych J, Stintzi A and Figeys D. Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach. (2021) Viruses. 13, Pubmed Viruses PMC Article

D'Aoust PM, Graber TE, Mercier E, Montpetit D, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Servos MR, Srikanthan N, MacKenzie M, Figeys D, Manuel D, Jüni P, MacKenzie AE and Delatolla R. Catching a resurgence: Increase in SARS-CoV-2 viral RNA identified in wastewater 48 h before COVID-19 clinical tests and 96 h before hospitalizations. (2021) Sci Total Environ. 770, 145319 Pubmed Sci Total Environ PMC Article

Zhang X, Cheng K, Ning Z, Mayne J, Walker K, Chi H, Farnsworth CL, Lee K and Figeys D. Exploring the Microbiome-Wide Lysine Acetylation, Succinylation, and Propionylation in Human Gut Microbiota. (2021) Anal Chem. 93, 6594-6598 Pubmed Anal Chem

D'Aoust PM, Mercier E, Montpetit D, Jia JJ, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Langlois MA, Servos MR, MacKenzie M, Figeys D, MacKenzie AE, Graber TE and Delatolla R. Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence. (2021) Water Res. 188, 116560 Pubmed Water Res PMC Article

Smyth P, Zhang X, Ning Z, Mayne J, Moore JI, Walker K, Lavallée-Adam M and Figeys D. Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics. (2020) Anal Chem. 92, 15711-15718 Pubmed Anal Chem

Li L, Chang L, Zhang X, Ning Z, Mayne J, Ye Y, Stintzi A, Liu J and Figeys D. Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes. (2020) Gut Microbes. 11, 1348-1361 Pubmed Gut Microbes PMC Article

Simopoulos CMA, Ning Z, Zhang X, Li L, Walker K, Lavallée-Adam M and Figeys D. pepFunk: a tool for peptide-centric functional analysis of metaproteomic human gut microbiome studies. (2020) Bioinformatics. 36, 4171-4179 Pubmed Bioinformatics

Zhang X, Ning Z, Mayne J, Yang Y, Deeke SA, Walker K, Farnsworth CL, Stokes MP, Couture JF, Mack D, Stintzi A and Figeys D. Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease. (2020) Nat Commun. 11, 4120 Pubmed Nat Commun PMC Article

Hao Z, Li L, Ning Z, Zhang X, Mayne J, Cheng K, Walker K, Liu H and Figeys D. Metaproteomics Reveals Growth Phase-Dependent Responses of an Gut Microbiota to Metformin. (2020) J Am Soc Mass Spectrom. 31, 1448-1458 Pubmed J Am Soc Mass Spectrom

Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J and Figeys D. MetaLab 2.0 Enables Accurate Post-Translational Modifications Profiling in Metaproteomics. (2020) J Am Soc Mass Spectrom. 31, 1473-1482 Pubmed J Am Soc Mass Spectrom

Comerlato CB, Zhang X, Walker K, Brandelli A and Figeys D. Comparative proteomic analysis reveals metabolic variability of probiotic Enterococcus durans during aerobic and anaerobic cultivation. (2020) J Proteomics. 220, 103764 Pubmed J Proteomics

Wang J, Zhang X, Li L, Ning Z, Mayne J, Schmitt-Ulms C, Walker K, Cheng K and Figeys D. Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics. (2020) Anal Chem. 92, 5379-5386 Pubmed Anal Chem

Li L, Ning Z, Zhang X, Mayne J, Cheng K, Stintzi A and Figeys D. RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs. (2020) Microbiome. 8, 33 Pubmed Microbiome PMC Article

Li H, Li L, Cheng K, Ning Z, Mayne J, Zhang X, Walker K, Chen R, Twine S, Li J and Figeys D. Chemoenzymatic Method for Glycoproteomic N-Glycan Type Quantitation. (2020) Anal Chem. 92, 1618-1627 Pubmed Anal Chem

Zhang X, Li L, Butcher J, Stintzi A and Figeys D. Advancing functional and translational microbiome research using meta-omics approaches. (2019) Microbiome. 7, 154 Pubmed Microbiome PMC Article

Li L, Abou-Samra E, Ning Z, Zhang X, Mayne J, Wang J, Cheng K, Walker K, Stintzi A and Figeys D. An in vitro model maintaining taxon-specific functional activities of the gut microbiome. (2019) Nat Commun. 10, 4146 Pubmed Nat Commun PMC Article

Peters DL, Wang W, Zhang X, Ning Z, Mayne J and Figeys D. Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome. (2019) Proteomics. 19, e1800363 Pubmed Proteomics

Wang Y, Niu Q, Zhang X, Liu L, Wang Y, Chen Y, Negi M, Figeys D, Li YY and Zhang T. Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics. (2019) Microbiome. 7, 122 Pubmed Microbiome PMC Article

Zhang X and Figeys D. Perspective and Guidelines for Metaproteomics in Microbiome Studies. (2019) J Proteome Res. 18, 2370-2380 Pubmed J Proteome Res

Liao B, Ning Z, Cheng K, Zhang X, Li L, Mayne J and Figeys D. iMetaLab 1.0: a web platform for metaproteomics data analysis. (2018) Bioinformatics. 34, 3954-3956 Pubmed Bioinformatics

Zhang X, Deeke SA, Ning Z, Starr AE, Butcher J, Li J, Mayne J, Cheng K, Liao B, Li L, Singleton R, Mack D, Stintzi A and Figeys D. Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. (2018) Nat Commun. 9, 2873 Pubmed Nat Commun PMC Article

Zhang X, Li L, Mayne J, Ning Z, Stintzi A and Figeys D. Assessing the impact of protein extraction methods for human gut metaproteomics. (2018) J Proteomics. 180, 120-127 Pubmed J Proteomics

Deeke SA, Starr AE, Ning Z, Ahmadi S, Zhang X, Mayne J, Chiang CK, Singleton R, Benchimol EI, Mack DR, Stintzi A and Figeys D. Mucosal-luminal interface proteomics reveals biomarkers of pediatric inflammatory bowel disease-associated colitis. (2018) Am J Gastroenterol. 113, 713-724 Pubmed Am J Gastroenterol

Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M and Figeys D. Proteomic and Metaproteomic Approaches to Understand Host-Microbe Interactions. (2018) Anal Chem. 90, 86-109 Pubmed Anal Chem

Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang CK, Mack D, Stintzi A and Figeys D. Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach. (2018) J Proteome Res. 17, 154-163 Pubmed J Proteome Res

Cheng K, Ning Z, Zhang X, Li L, Liao B, Mayne J, Stintzi A and Figeys D. MetaLab: an automated pipeline for metaproteomic data analysis. (2017) Microbiome. 5, 157 Pubmed Microbiome PMC Article

Zhang X, Chen W, Ning Z, Mayne J, Mack D, Stintzi A, Tian R and Figeys D. Deep Metaproteomics Approach for the Study of Human Microbiomes. (2017) Anal Chem. 89, 9407-9415 Pubmed Anal Chem

Starr AE, Deeke SA, Ning Z, Chiang CK, Zhang X, Mottawea W, Singleton R, Benchimol EI, Wen M, Mack DR, Stintzi A and Figeys D. Proteomic analysis of ascending colon biopsies from a paediatric inflammatory bowel disease inception cohort identifies protein biomarkers that differentiate Crohn's disease from UC. (2017) Gut. 66, 1573-1583 Pubmed Gut PMC Article

Zhang X, Ning Z, Mayne J, Moore JI, Li J, Butcher J, Deeke SA, Chen R, Chiang CK, Wen M, Mack D, Stintzi A and Figeys D. MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. (2016) Microbiome. 4, 31 Pubmed Microbiome PMC Article

Zhang X, Ning Z, Mayne J, Deeke SA, Li J, Starr AE, Chen R, Singleton R, Butcher J, Mack DR, Stintzi A and Figeys D. In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics. (2016) Anal Chem. 88, 6120-5 Pubmed Anal Chem

Ning Z, Zhang X, Mayne J and Figeys D. Peptide-Centric Approaches Provide an Alternative Perspective To Re-Examine Quantitative Proteomic Data. (2016) Anal Chem. 88, 1973-8 Pubmed Anal Chem

Mayne J, Ning Z, Zhang X, Starr AE, Chen R, Deeke S, Chiang CK, Xu B, Wen M, Cheng K, Seebun D, Star A, Moore JI and Figeys D. Bottom-Up Proteomics (2013-2015): Keeping up in the Era of Systems Biology. (2016) Anal Chem. 88, 95-121 Pubmed Anal Chem

Li L, Ryan J, Ning Z, Zhang X, Mayne J, Lavallée-Adam M, Stintzi A and Figeys D. A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches. (2020) Comput Struct Biotechnol J. 18, 3833-3842 Pubmed Comput Struct Biotechnol J PMC Article

Zhang X, Walker K, Mayne J, Li L, Ning Z, Stintzi A and Figeys D. Evaluating live microbiota biobanking using an microbiome assay and metaproteomics. Gut Microbes. 14, 2035658 Pubmed Gut Microbes PMC Article

Adler P, Chiang CK, Mayne J, Ning Z, Zhang X, Xu B, Cheng HM and Figeys D. Aging Disrupts the Circadian Patterns of Protein Expression in the Murine Hippocampus. (2019) Front Aging Neurosci. 11, 368 Pubmed Front Aging Neurosci PMC Article

Previous Publications:

Zhang X, Zheng J, Zhao L, Zhao Y and Ma S. [The role and research progress of IL-17 in the pathogenesis of osteoarthritis]. (2021) Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 37, 1138-1142 Pubmed Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi

Zhao L, Zhang X, Wang X, Guan X, Zhang W and Ma J. Recent advances in selective photothermal therapy of tumor. (2021) J Nanobiotechnology. 19, 335 Pubmed J Nanobiotechnology PMC Article

Wang J, Tang H, Wang X, Zhang X, Zhang C, Zhang M, Zhao Y, Zhao L and Shen J. The structural alteration of gut microbiota in low-birth-weight mice undergoing accelerated postnatal growth. (2016) Sci Rep. 6, 27780 Pubmed Sci Rep PMC Article

Zhang X, Zhao Y, Xu J, Xue Z, Zhang M, Pang X, Zhang X and Zhao L. Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats. (2015) Sci Rep. 5, 14405 Pubmed Sci Rep PMC Article

Xu J, Lian F, Zhao L, Zhao Y, Chen X, Zhang X, Guo Y, Zhang C, Zhou Q, Xue Z, Pang X, Zhao L and Tong X. Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula. (2015) ISME J. 9, 552-62 Pubmed ISME J PMC Article

Yin X, Peng J, Zhao L, Yu Y, Zhang X, Liu P, Feng Q, Hu Y and Pang X. Structural changes of gut microbiota in a rat non-alcoholic fatty liver disease model treated with a Chinese herbal formula. (2013) Syst Appl Microbiol. 36, 188-96 Pubmed Syst Appl Microbiol

Zhao L, Nicholson JK, Lu A, Wang Z, Tang H, Holmes E, Shen J, Zhang X, Li JV and Lindon JC. Targeting the human genome-microbiome axis for drug discovery: inspirations from global systems biology and traditional Chinese medicine. (2012) J Proteome Res. 11, 3509-19 Pubmed J Proteome Res

Zhang X, Zhao Y, Zhang M, Pang X, Xu J, Kang C, Li M, Zhang C, Zhang Z, Zhang Y, Li X, Ning G and Zhao L. Structural changes of gut microbiota during berberine-mediated prevention of obesity and insulin resistance in high-fat diet-fed rats. (2012) PLoS One. 7, e42529 Pubmed PLoS One PMC Article

Wang J, Wang Y, Zhang X, Liu J, Zhang Q, Zhao Y, Peng J, Feng Q, Dai J, Sun S, Zhao Y, Zhao L, Zhang Y, Hu Y and Zhang M. Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients. (2017) Front Microbiol. 8, 2222 Pubmed Front Microbiol PMC Article