Dr Xiaotao Jiang

Dr Xiaotao Jiang

Bachelor of Engineering (Bioinformatics)

Doctor of Philosophy (Water and Environmental Microbiology)

Medicine & Health
School of Clinical Medicine

My Current Research Interests:

1. Microbiome in health and diseases

2. Antimicrobial resistance 

3. Virome

4. Microbiome bioinformatics 

Dr. Jiang leads the bioinformatics unit at the MRC and has been involved in an extensive number of projects for the human microbiome and diseases including liver cancer, colon cancer, IBD, schizophrenia et. al. He is interested in developing bioinformatics algorithms and software to analyze next/third generation sequencing data for multi-omics data (metagenomics, metatranscriptomics, and metabolomics). Another interest of Dr Jiang is antimicrobial resistance. He is interested in developing methods to combat the ever-increasing issue of antimicrobial resistance from the medical applications. 

My Background:

Dr Jiang completed his PhD at The University of Hong Kong, Hong Kong. In his PhD study, he applied large-scale metagenomics sequencing to understand the activated sludge microbial ecology in a spatial and temporal dimension.  He developed ARGs-OAP to obtain the quantitative profiling of resistome for multiple shotgun metagenomics data, which is widely used in the AMR area.  

+61 02 9113 2582
  • Journal articles | 2023
    Liou JM; Jiang XT; Chen CC; Luo JC; Bair MJ; Chen PY; Chou CK; Fang YJ; Chen MJ; Chen CC; Lee JY; Yang TH; Yu CC; Kuo CC; Chiu MC; Chen CY; Shun CT; Hu WH; Tsai MH; Hsu YC; Tseng CH; Chang CY; Lin JT; El-Omar EM; Wu MS; Wu CY; Lee YC; Tseng PH; Wu JY; Tai CM; Lee CT; Wang WL, 2023, 'Second-line levofloxacin-based quadruple therapy versus bismuth-based quadruple therapy for Helicobacter pylori eradication and long-term changes to the gut microbiota and antibiotic resistome: a multicentre, open-label, randomised controlled trial', The Lancet Gastroenterology and Hepatology, vol. 8, pp. 228 - 241, http://dx.doi.org/10.1016/S2468-1253(22)00384-3
    Journal articles | 2022
    Susic DF; Wang L; Roberts LM; Bai M; Gia A; McGovern E; Jiang XT; Davis GK; El-Omar E; Henry A, 2022, 'The P4 Study: Postpartum Maternal and Infant Faecal Microbiome 6 Months After Hypertensive Versus Normotensive Pregnancy', Frontiers in Cellular and Infection Microbiology, vol. 12, pp. 646165, http://dx.doi.org/10.3389/fcimb.2022.646165
    Journal articles | 2022
    Zhang F; Gia A; Chen G; Gong L; Behary J; Hold GL; Zekry A; Tang X; Sun Y; El-Omar E; Jiang XT, 2022, 'Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients', Viruses, vol. 15, pp. 53 - 53, http://dx.doi.org/10.3390/v15010053
    Journal articles | 2021
    Behary J; Amorim N; Jiang XT; Raposo A; Gong L; McGovern E; Ibrahim R; Chu F; Stephens C; Jebeili H; Fragomeli V; Koay YC; Jackson M; O’Sullivan J; Weltman M; McCaughan G; El-Omar E; Zekry A, 2021, 'Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma', Nature Communications, vol. 12, pp. 187, http://dx.doi.org/10.1038/s41467-020-20422-7
    Journal articles | 2021
    Wang Y; Qin W; Jiang X; Ju F; Mao Y; Zhang A; Stahl DA; Zhang T, 2021, 'Seasonal prevalence of ammonia-oxidizing archaea in a full-scale municipal wastewater treatment plant treating saline wastewater revealed by a 6-year time-series analysis', Environmental Science and Technology, vol. 55, pp. 2662 - 2673, http://dx.doi.org/10.1021/acs.est.0c07703
    Journal articles | 2021
    Wang Y; Ye J; Ju F; Liu L; Boyd JA; Deng Y; Parks DH; Jiang X; Yin X; Woodcroft BJ; Tyson GW; Hugenholtz P; Polz MF; Zhang T, 2021, 'Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years', Microbiome, vol. 9, http://dx.doi.org/10.1186/s40168-021-01151-5
    Journal articles | 2019
    Liu J; Li B; Wang Y; Zhang G; Jiang X; Li X, 2019, 'Passage and community changes of filterable bacteria during microfiltration of a surface water supply', Environment International, vol. 131, pp. 104998 - 104998, http://dx.doi.org/10.1016/j.envint.2019.104998
    Journal articles | 2019
    Ng C; Tan B; Jiang XT; Gu X; Chen H; Schmitz BW; Haller L; Charles FR; Zhang T; Gin K, 2019, 'Metagenomic and resistome analysis of a full-scale municipal wastewater treatment plant in Singapore containing membrane bioreactors', Frontiers in Microbiology, vol. 10, pp. 172, http://dx.doi.org/10.3389/fmicb.2019.00172
    Journal articles | 2018
    Feng J; Li B; Jiang X; Yang Y; Wells GF; Zhang T; Li X, 2018, 'Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses', Environmental microbiology, vol. 20, pp. 355 - 368, http://dx.doi.org/10.1111/1462-2920.14009
    Journal articles | 2018
    Jiang X-T; Ye L; Ju F; Wang Y-L; Zhang T, 2018, 'Toward an Intensive Longitudinal Understanding of Activated Sludge Bacterial Assembly and Dynamics', Environmental Science & Technology, vol. 52, pp. 8224 - 8232
    Journal articles | 2018
    Jiang XT; Ye L; Ju F; Li B; Ma LP; Zhang T, 2018, 'Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants', Applied Microbiology and Biotechnology, vol. 102, pp. 9379 - 9388, http://dx.doi.org/10.1007/s00253-018-9287-8
    Journal articles | 2018
    Liu T; Zhang AN; Wang J; Liu S; Jiang X; Dang C; Ma T; Liu S; Chen Q; Xie S; others , 2018, 'Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River', Microbiome, vol. 6, pp. 16 - 16, http://dx.doi.org/10.1186/s40168-017-0388-x
    Journal articles | 2018
    Wang Y; Jiang X-T; Liu L; Li B; Zhang T, 2018, 'High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems', Environmental science & technology
    Journal articles | 2018
    Xiong W; Wang Y; Sun Y; Ma L; Zeng Q; Jiang X; Li A; Zeng Z; Zhang T, 2018, 'Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes', Microbiome, vol. 6, pp. 34 - 34, http://dx.doi.org/10.1186/s40168-018-0419-2
    Journal articles | 2018
    Yin X; Jiang XT; Chai B; Li L; Yang Y; Cole JR; Tiedje JM; Zhang T, 2018, 'ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes', Bioinformatics, vol. 34, pp. 2263 - 2270, http://dx.doi.org/10.1093/bioinformatics/bty053
    Journal articles | 2018
    Zhang G; Li B; Liu J; Luan M; Yue L; Jiang XT; Yu K; Guan Y, 2018, 'The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems', Microbiome, vol. 6, http://dx.doi.org/10.1186/s40168-018-0610-5
    Journal articles | 2017
    Li AD; Ma L; Jiang XT; Zhang T, 2017, 'Cultivation-dependent and high-throughput sequencing approaches studying the co-occurrence of antibiotic resistance genes in municipal sewage system', Applied Microbiology and Biotechnology, vol. 101, pp. 8197 - 8207, http://dx.doi.org/10.1007/s00253-017-8573-1
    Journal articles | 2017
    Ma L; Li B; Jiang X-T; Wang Y-L; Xia Y; Li A-D; Zhang T, 2017, 'Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey', Microbiome, vol. 5, pp. 154 - 154, http://dx.doi.org/10.1186/s40168-017-0369-0
    Journal articles | 2017
    Wang Y; Ma L; Mao Y; Jiang X; Xia Y; Yu K; Li B; Zhang T, 2017, 'Comammox in drinking water systems', Water Research, vol. 116, pp. 332 - 341, http://dx.doi.org/10.1016/j.watres.2017.03.042
    Journal articles | 2017
    Xia Y; Li AD; Deng Y; Jiang XT; Li LG; Zhang T, 2017, 'MinION Nanopore sequencing enables correlation between resistome phenotype and genotype of coliform bacteria in municipal sewage', Frontiers in Microbiology, vol. 8, http://dx.doi.org/10.3389/fmicb.2017.02105
    Journal articles | 2017
    Yuan K; Xiao S; Jiang X; Yang L; Chen B; Luan T; Lin L; Tam NFY, 2017, 'Effects of endocrine disrupting chemicals (EDCs) on bacterial communities in mangrove sediments', Marine Pollution Bulletin, vol. 122, pp. 122 - 128, http://dx.doi.org/10.1016/j.marpolbul.2017.06.035
    Journal articles | 2016
    Jiang XT; Guo F; Zhang T, 2016, 'Population dynamics of bulking and foaming bacteria in a full-scale wastewater treatment plant over five years', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep24180
    Journal articles | 2016
    Mao Y; Wang Z; Li L; Jiang X; Zhang X; Ren H; Zhang T, 2016, 'Exploring the shift in structure and function of microbial communities performing biological phosphorus removal', PLoS ONE, vol. 11, pp. e0161506, http://dx.doi.org/10.1371/journal.pone.0161506
    Journal articles | 2016
    Yang Y; Jiang X; Chai B; Ma L; Li B; Zhang A; Cole JR; Tiedje JM; Zhang T, 2016, 'ARGs-OAP: Online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database', Bioinformatics, vol. 32, pp. 2346 - 2351, http://dx.doi.org/10.1093/bioinformatics/btw136
    Journal articles | 2015
    He Y; Caporaso JG; Jiang X-T; Sheng H-F; Huse SM; Rideout JR; Edgar RC; Kopylova E; Walters WA; Knight R; Zhou H-W, 2015, 'Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity', MICROBIOME, vol. 3, http://dx.doi.org/10.1186/s40168-015-0081-x
    Journal articles | 2014
    Yang Y; Jiang XT; Zhang T, 2014, 'Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes', PLoS ONE, vol. 9, pp. e110947, http://dx.doi.org/10.1371/journal.pone.0110947
    Journal articles | 2013
    He Y; Zhou BJ; Deng GH; Jiang XT; Zhang H; Zhou HW, 2013, 'Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons', BMC Microbiology, vol. 13, http://dx.doi.org/10.1186/1471-2180-13-208
    Journal articles | 2013
    Jiang XT; Peng X; Deng GH; Sheng HF; Wang Y; Zhou HW; Tam NFY, 2013, 'Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland', Microbial Ecology, vol. 66, pp. 96 - 104, http://dx.doi.org/10.1007/s00248-013-0238-8
    Journal articles | 2012
    Jiang XT; Zhang H; Sheng HF; Wang Y; He Y; Zou F; Zhou HW, 2012, 'Two-stage clustering (TSC): A pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons', PLoS ONE, vol. 7, pp. e30230, http://dx.doi.org/10.1371/journal.pone.0030230
    Journal articles | 2011
    Zhou HW; Li DF; Tam NFY; Jiang XT; Zhang H; Sheng HF; Qin J; Liu X; Zou F, 2011, 'BIPES, a cost-effective high-throughput method for assessing microbial diversity', ISME Journal, vol. 5, pp. 741 - 749, http://dx.doi.org/10.1038/ismej.2010.160
    Journal articles | 2010
    Wu JY; Jiang XT; Jiang YX; Lu SY; Zou F; Zhou HW, 2010, 'Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method', BMC Microbiology, vol. 10, http://dx.doi.org/10.1186/1471-2180-10-255

Recruiting Honour students for HOAM project 2023


Defining the Australian Optimal Healthy Microbiome (HOAM) through Artificial Intelligence

We are seeking talented ILP/honour students to join our ICONIC microbiome project: The Healthy Optimal Australian Microbiome (HOAM) project in the Australian First dedicated Microbiome Research Centre (MRC). This project is supported by Medical Research Future Fund (MRFF).  This ambitious project aims to hunt the optimal healthy microbiome in the Australian population, which will be a crucial target to manipulate the microbiome to, especially for faecal microbiome transplant (FMT) to cure diseases.

The microbiome plays an important role in human health and has been implicated in the pathogenesis of many diseases. However, the definition of a “normal microbiome” remains elusive. Previous definitions have focussed mainly on microbial taxonomy with less rigour in defining optimal health. We seek to define the healthy microbiome by studying supremely healthy individuals recruited through a stringent matrix and benchmarked against obesity and dementia patients. Meanwhile, we have established a huge publicly available human shotgun metagenomic microbiome data set of over 10,000 samples around 50 Tbs genetic data. This big data will be integrated and compared with our HOAM dataset with an artificial intelligence algorithm to define a healthy microbiome. MRC has established powerful high-performance computing facilities and use national computing infrastructure (NCI) to support the project. 

The project is led by Prof. Emad EI-Omar and Dr Xiaotao Jiang. Prof. EI-Omar is a word class scientist in gastroenterology and microbiome, he is the director of MRC and Chief Editor of the Journal GUT (Impact Factor 19.89). Dr Xiaotao Jiang is the lead bioinformatician of MRC, he had over 10 years’ experience in microbiome bioinformatics and next-generation sequencing.

If you have interest in joining this exciting project, please contact either Dr Xiaotao Jiang (xiaotao.jiang@unsw.edu.au) or Prof. EI-Omar (e.el-omar@unsw.edu.au).  


Advisory topic board member for the journal Antibiotics 

Editor on board of Gut


Member of Australian bioinformatics and computational society (ABACBS)

My Research Supervision

Dr Jiang currently supervise honour students on topics of virome, healthy microbiome and disease.